- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 6a7cc3: Bring Galaxy, reports, and shed run scripts in syn...
by GitHub 12 Aug '17

12 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 6a7cc34e1b1ade9580e464570fc6b83a488e941f https://github.com/galaxyproject/galaxy/commit/6a7cc34e1b1ade9580e464570fc6… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-10 (Thu, 10 Aug 2017) Changed paths: M run.sh M run_reports.sh M run_tool_shed.sh A scripts/common_startup_functions.sh Log Message: ----------- Bring Galaxy, reports, and shed run scripts in sync. - They now uniformly handle server option processing. - Reports and Tool Shed now respect many new and important options such as --skip_venv. - Reports and Tool Shed now do extra checking around Python version that Galaxy does. In addition to improving the reports and tool shed startup scripts and reducing cognative load with respect to option handling, this is an important pre-condition to us being able us to switch on uwsgi by default for all three services simultaneously without a bunch of copy and pasting. Commit: 72e5a00ba0ad9c1a8e56ad9544bec23c843d900d https://github.com/galaxyproject/galaxy/commit/72e5a00ba0ad9c1a8e56ad9544be… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-10 (Thu, 10 Aug 2017) Changed paths: M run_reports.sh M run_tool_shed.sh M scripts/common_startup_functions.sh Log Message: ----------- Centralize launching server for reports and tool shed. Initial outline of allowing launch via uwsgi. Commit: 1bdb99bbd76d0827cd3a7e617d288564584863ea https://github.com/galaxyproject/galaxy/commit/1bdb99bbd76d0827cd3a7e617d28… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-10 (Thu, 10 Aug 2017) Changed paths: M lib/galaxy/dependencies/__init__.py M lib/galaxy/util/properties.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/webapps/tool_shed/buildapp.py M scripts/manage_tools.py Log Message: ----------- Update galaxy.util.properties to allow YAML. Commit: 8189a1f1e289e14d362fcb8871b9339c3355e8b2 https://github.com/galaxyproject/galaxy/commit/8189a1f1e289e14d362fcb8871b9… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-10 (Thu, 10 Aug 2017) Changed paths: A lib/galaxy/webapps/config_manage.py A scripts/config_sample_to_kwalify.py A test/unit/config/1607_root_filters/config/galaxy.ini A test/unit/config/1607_root_filters/config/tool_shed.ini A test/unit/config/1607_root_samples/config/galaxy.ini A test/unit/config/1607_root_samples/config/reports.ini A test/unit/config/1607_root_samples/config/tool_shed.ini A test/unit/config/test_config_manage.py Log Message: ----------- Scripts to manage configuration infrastructure. This has been rebased several times and includes a variety of fixes (some thanks to martenson). Commit: 7973a914e0beef9680475d54947bd953c0b062cd https://github.com/galaxyproject/galaxy/commit/7973a914e0beef9680475d54947b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-10 (Thu, 10 Aug 2017) Changed paths: A lib/galaxy/webapps/uwsgi_schema.yml Log Message: ----------- Add uwsgi_schema.yml. Commit: 90e899d68fbf21effad1cf309efbd786c54be556 https://github.com/galaxyproject/galaxy/commit/90e899d68fbf21effad1cf309efb… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-10 (Thu, 10 Aug 2017) Changed paths: R config/tool_shed.ini.sample A config/tool_shed.yml.sample M lib/galaxy/webapps/tool_shed/buildapp.py A lib/galaxy/webapps/tool_shed/config_schema.yml A lib/galaxy/webapps/tool_shed/uwsgi_schema.yml M run_tool_shed.sh Log Message: ----------- Update tool shed to use newer configuration schema. - Implement kwalify schema to validate/define the schema. - Replace ini configuration with YAML (completely backward compatible). - Rebuild a sample configuration from the schema (config/tool_shed.yml.sample). Commit: 102566dd5e1c5903726057f1077a1d7fc614b815 https://github.com/galaxyproject/galaxy/commit/102566dd5e1c5903726057f1077a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-10 (Thu, 10 Aug 2017) Changed paths: R config/reports.ini.sample A config/reports.yml.sample M lib/galaxy/webapps/reports/buildapp.py A lib/galaxy/webapps/reports/config_schema.yml A lib/galaxy/webapps/reports/uwsgi_schema.yml M run_reports.sh Log Message: ----------- Update Galaxy Reports to use newer configuration schema. - Implement kwalify schema to validate/define the schema. - Replace ini configuration with YAML (completely backward compatible). - Rebuild a sample configuration from the schema (config/reports.yml.sample). Commit: 50d426ed2b9ae2aff8b243143478ce84c7731816 https://github.com/galaxyproject/galaxy/commit/50d426ed2b9ae2aff8b243143478… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-10 (Thu, 10 Aug 2017) Changed paths: A doc/source/admin/reports.rst A doc/source/admin/reports_options.rst Log Message: ----------- Add reports documentation to ``doc/``. - Automatically generate RST docs from config schema. - Describe older functionality as well as new YAML-based configuration. - Replace https://wiki.galaxyproject.org/Admin/UsageReports. Commit: 4945f55e4fe28842b58c025b37c4d6c96a07028f https://github.com/galaxyproject/galaxy/commit/4945f55e4fe28842b58c025b37c4… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-10 (Thu, 10 Aug 2017) Changed paths: M Makefile Log Message: ----------- Makefile shortcuts for configuration script. Commit: ef46a60a829e3dae44d935f6f886feef39b873e3 https://github.com/galaxyproject/galaxy/commit/ef46a60a829e3dae44d935f6f886… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-10 (Thu, 10 Aug 2017) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt Log Message: ----------- Add required dependency on uwsgi. Required for the new out-of-the-box configuration of tool shed and reports. Commit: 8191fd492819214b12c0aa28b35e5b6c4ea7bfa1 https://github.com/galaxyproject/galaxy/commit/8191fd492819214b12c0aa28b35e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-10 (Thu, 10 Aug 2017) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt Log Message: ----------- Add pykwalify as dependency for the new config validation stuff. xref https://github.com/galaxyproject/starforge/pull/110 Commit: ffe295e96dbd82615c987a2b9ba9bd15ea253826 https://github.com/galaxyproject/galaxy/commit/ffe295e96dbd82615c987a2b9ba9… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-10 (Thu, 10 Aug 2017) Changed paths: M test/unit/config/test_config_manage.py Log Message: ----------- Fix Python 3 linting problem with test_config_manage.py. Commit: 1ce93ccfdf7b54ec1efcf08b04c9f28b67ab0615 https://github.com/galaxyproject/galaxy/commit/1ce93ccfdf7b54ec1efcf08b04c9… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-10 (Thu, 10 Aug 2017) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt Log Message: ----------- Pin version of uWSGI to freshly released 2.0.15 available on wheels.galaxyproject.org. Commit: 539a62f642ada1f2d832f1f88ab339cafe672c1f https://github.com/galaxyproject/galaxy/commit/539a62f642ada1f2d832f1f88ab3… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-10 (Thu, 10 Aug 2017) Changed paths: M lib/galaxy/model/orm/scripts.py M lib/galaxy/util/properties.py Log Message: ----------- Fix ORM scripts for #3179. Commit: 98ca8ce7a68d18533f3bf85097490c5b66e9f876 https://github.com/galaxyproject/galaxy/commit/98ca8ce7a68d18533f3bf8509749… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-10 (Thu, 10 Aug 2017) Changed paths: M lib/galaxy/web/framework/webapp.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Update config overhaul branch for introduction of galaxy.web.stack package. Commit: 331851b0495d429220450ceb3a540fbba900143a https://github.com/galaxyproject/galaxy/commit/331851b0495d429220450ceb3a54… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-08-12 (Sat, 12 Aug 2017) Changed paths: M Makefile R config/reports.ini.sample A config/reports.yml.sample R config/tool_shed.ini.sample A config/tool_shed.yml.sample A doc/source/admin/reports.rst A doc/source/admin/reports_options.rst M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/model/orm/scripts.py M lib/galaxy/util/properties.py M lib/galaxy/web/framework/webapp.py A lib/galaxy/webapps/config_manage.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/reports/buildapp.py A lib/galaxy/webapps/reports/config_schema.yml A lib/galaxy/webapps/reports/uwsgi_schema.yml M lib/galaxy/webapps/tool_shed/buildapp.py A lib/galaxy/webapps/tool_shed/config_schema.yml A lib/galaxy/webapps/tool_shed/uwsgi_schema.yml A lib/galaxy/webapps/uwsgi_schema.yml M run.sh M run_reports.sh M run_tool_shed.sh A scripts/common_startup_functions.sh A scripts/config_sample_to_kwalify.py M scripts/manage_tools.py A test/unit/config/1607_root_filters/config/galaxy.ini A test/unit/config/1607_root_filters/config/tool_shed.ini A test/unit/config/1607_root_samples/config/galaxy.ini A test/unit/config/1607_root_samples/config/reports.ini A test/unit/config/1607_root_samples/config/tool_shed.ini A test/unit/config/test_config_manage.py Log Message: ----------- Merge pull request #3179 from jmchilton/web_config_overhaul_0 Configuration & Server Overhaul - Tool Shed and Reports Compare: https://github.com/galaxyproject/galaxy/compare/c6e45e7b0720...331851b0495d

1 0

[galaxyproject/galaxy] e72f5e: deals with .xls older file extension
by GitHub 11 Aug '17

11 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e72f5e81a4baffcb4679d6e74837daedcfa65f67 https://github.com/galaxyproject/galaxy/commit/e72f5e81a4baffcb4679d6e74837… Author: Frederic Sapet <frederic.sapet(a)biogemma.com> Date: 2017-06-16 (Fri, 16 Jun 2017) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- deals with .xls older file extension Commit: 5fec6c87cba14dd7692d8239669a02d6b5586748 https://github.com/galaxyproject/galaxy/commit/5fec6c87cba14dd7692d8239669a… Author: Frederic Sapet <frederic.sapet(a)biogemma.com> Date: 2017-06-16 (Fri, 16 Jun 2017) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- indentation for Travis Commit: 9cd9c81279d1d7749af7d9c64f8329e8cfc7f6bf https://github.com/galaxyproject/galaxy/commit/9cd9c81279d1d7749af7d9c64f83… Author: Frederic Sapet <frederic.sapet(a)biogemma.com> Date: 2017-06-16 (Fri, 16 Jun 2017) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- deals with .xls older file extension Commit: 93dadd6db491700de46cafa4d52a0efe74cd6e94 https://github.com/galaxyproject/galaxy/commit/93dadd6db491700de46cafa4d52a… Author: Frederic Sapet <frederic.sapet(a)biogemma.com> Date: 2017-06-16 (Fri, 16 Jun 2017) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- use subprocess instead of os.popen Commit: 83b19889314a922ba3cf906f26fe7d3a34926533 https://github.com/galaxyproject/galaxy/commit/83b19889314a922ba3cf906f26fe… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-07-05 (Wed, 05 Jul 2017) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/sniff.py A lib/galaxy/datatypes/test/1.xls Log Message: ----------- Refine new Excel XLS datatype. - Call it excel.xls so we maintain backward compatiblity with older xls datatype. - Add an example file with a sniff test. - Correct variable name for Python styling. - Quote paths when using file command-line trick to sniff for the new type. - Switch file command-line flag to one that produces the Mimetype on both Linux and Mac OS X. Commit: 10285b8ecbbc6891a4954b5067198df2839a2957 https://github.com/galaxyproject/galaxy/commit/10285b8ecbbc6891a4954b506719… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-11 (Fri, 11 Aug 2017) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Tweak Excel format phrasing based on review from @nsoranzo. Commit: fbde34f8c8e823badd0f565bce4922512448b532 https://github.com/galaxyproject/galaxy/commit/fbde34f8c8e823badd0f565bce49… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-11 (Fri, 11 Aug 2017) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Add EDAM format for excel.xls datatype. Commit: c6e45e7b0720376886626393ae355e3398561035 https://github.com/galaxyproject/galaxy/commit/c6e45e7b0720376886626393ae35… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-08-11 (Fri, 11 Aug 2017) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/sniff.py A lib/galaxy/datatypes/test/1.xls Log Message: ----------- Merge pull request #4410 from jmchilton/excel97 Add Excel97 Datatype Compare: https://github.com/galaxyproject/galaxy/compare/cca00ea5d87f...c6e45e7b0720

1 0

[galaxyproject/galaxy] e49ba4: Generalize allow_library_path_paste to allow_path_...
by GitHub 11 Aug '17

11 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e49ba40d771dae0d7056ed089c99f3d53a81b933 https://github.com/galaxyproject/galaxy/commit/e49ba40d771dae0d7056ed089c99… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-10 (Thu, 10 Aug 2017) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/tools/parameters/grouping.py Log Message: ----------- Generalize allow_library_path_paste to allow_path_paste. Enable pasting paths in the history upload GUI & general purpose tools API for admin users if enabled. Commit: f97efa6f90f80ced8bd0c794841e450813238710 https://github.com/galaxyproject/galaxy/commit/f97efa6f90f80ced8bd0c794841e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-10 (Thu, 10 Aug 2017) Changed paths: M lib/galaxy/tools/parameters/grouping.py Log Message: ----------- Remove unused dataset_info in parameters.grouping. Commit: cca00ea5d87fb0baba3ceca715038158cf2ceba0 https://github.com/galaxyproject/galaxy/commit/cca00ea5d87fb0baba3ceca71503… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-08-11 (Fri, 11 Aug 2017) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/tools/parameters/grouping.py Log Message: ----------- Merge pull request #4404 from jmchilton/allow_path_paste Generalize allow_library_path_paste to allow_path_paste. Compare: https://github.com/galaxyproject/galaxy/compare/33c794d27327...cca00ea5d87f

1 0

[galaxyproject/galaxy] 37a6c4: Remove unused template
by GitHub 11 Aug '17

11 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 37a6c488b0cb99450e2781656eee2462bf539900 https://github.com/galaxyproject/galaxy/commit/37a6c488b0cb99450e2781656eee… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-07-29 (Sat, 29 Jul 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Remove unused template Commit: 4ccb3e3874e0548289d746fee03a96250df9f1e3 https://github.com/galaxyproject/galaxy/commit/4ccb3e3874e0548289d746fee03a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-07-29 (Sat, 29 Jul 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Return roles grid as dictionary Commit: 6c91bc287ef0846869f1604d2ebfd684fb550df4 https://github.com/galaxyproject/galaxy/commit/6c91bc287ef0846869f1604d2ebf… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-07-29 (Sat, 29 Jul 2017) Changed paths: M client/galaxy/scripts/apps/admin.js M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin.py M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map Log Message: ----------- Add client side routes Commit: b8396a961facd7dada8d8db837386b656855c3b1 https://github.com/galaxyproject/galaxy/commit/b8396a961facd7dada8d8db83738… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-07-30 (Sun, 30 Jul 2017) Changed paths: M client/galaxy/scripts/apps/panels/admin-panel.js M lib/galaxy/webapps/galaxy/controllers/admin.py M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map Log Message: ----------- Add admin role editing options Commit: 00432345ff20bbcf5023995b6cfb54937eb4be9e https://github.com/galaxyproject/galaxy/commit/00432345ff20bbcf5023995b6cfb… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-07-31 (Mon, 31 Jul 2017) Changed paths: M lib/tool_shed/util/admin_util.py M templates/admin/user/reset_password.mako M templates/admin/user/user.mako Log Message: ----------- Merge branch 'revise_page' into admin_grid_roles Commit: d7717cfa8b8562d82742ba285d54e7d7ab794d2d https://github.com/galaxyproject/galaxy/commit/d7717cfa8b8562d82742ba285d54… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-07-31 (Mon, 31 Jul 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Remove unused galaxy role grid operations Commit: 8ee4c29a0579b2a9156f0cd4a70139758ed58b60 https://github.com/galaxyproject/galaxy/commit/8ee4c29a0579b2a9156f0cd4a701… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-01 (Tue, 01 Aug 2017) Changed paths: M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/panels/admin-panel.js M client/galaxy/scripts/galaxy.js M client/galaxy/scripts/layout/router.js A client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/grid/grid-view.js M client/galaxy/scripts/nls/fr/locale.js M config/tool_shed.ini.sample M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/jobs/runners/cli.py M lib/galaxy/model/mapping.py M lib/galaxy/model/metadata.py M lib/galaxy/security/__init__.py M lib/galaxy/web/base/controller.py M lib/galaxy/webapps/galaxy/api/quotas.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/tool_shed/buildapp.py M lib/galaxy/workflow/modules.py M static/maps/galaxy.js.map M static/maps/layout/router.js.map A static/maps/mvc/dataset/dataset-edit-attributes.js.map M static/maps/mvc/dataset/dataset-li-edit.js.map M static/maps/mvc/grid/grid-view.js.map M static/maps/nls/fr/locale.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/galaxy.js M static/scripts/layout/router.js A static/scripts/mvc/dataset/dataset-edit-attributes.js M static/scripts/mvc/dataset/dataset-li-edit.js M static/scripts/mvc/grid/grid-view.js M static/scripts/nls/fr/locale.js R templates/webapps/galaxy/dataset/edit_attributes.mako Log Message: ----------- Merge branch 'revise_page' into admin_grid_roles Commit: f76f9515a3b243bfb510f89aaa50e95a4990465f https://github.com/galaxyproject/galaxy/commit/f76f9515a3b243bfb510f89aaa50… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-01 (Tue, 01 Aug 2017) Changed paths: M client/galaxy/scripts/apps/admin.js M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Parse url parameters for message handling Commit: e32661301cef0815fdd36743d1ab9901d2576ef2 https://github.com/galaxyproject/galaxy/commit/e32661301cef0815fdd36743d1ab… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-02 (Wed, 02 Aug 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/mvc/user/user-preferences.js R client/galaxy/scripts/mvc/workflow/workflow-configure-menu.js M client/galaxy/scripts/mvc/workflow/workflow.js M client/galaxy/style/less/base.less M config/plugins/webhooks/demo/search/static/script.js M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/buildapp.py M static/maps/mvc/user/user-preferences.js.map M static/maps/mvc/workflow/workflow.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/user/user-preferences.js M static/scripts/mvc/workflow/workflow.js M static/style/blue/base.css Log Message: ----------- Merge branch 'dev' into admin_grid_roles Commit: 77608ac4105ee90e3323d74e2273618fd2d06ca7 https://github.com/galaxyproject/galaxy/commit/77608ac4105ee90e3323d74e2273… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-04 (Fri, 04 Aug 2017) Changed paths: M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/form/form-view.js A client/galaxy/scripts/mvc/form/form-wrapper.js M client/galaxy/scripts/mvc/grid/grid-template.js M client/galaxy/scripts/mvc/user/user-preferences.js M client/galaxy/scripts/mvc/workflow/workflow-forms.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/scripts/utils/query-string-parsing.js M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/proteomics.py M lib/galaxy/jobs/actions/post.py M lib/galaxy/managers/tags.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/tool_shed/grids/admin_grids.py M lib/tool_shed/util/admin_util.py M static/maps/layout/menu.js.map M static/maps/mvc/form/form-view.js.map A static/maps/mvc/form/form-wrapper.js.map M static/maps/mvc/grid/grid-template.js.map M static/maps/mvc/user/user-preferences.js.map M static/maps/mvc/workflow/workflow-forms.js.map M static/maps/mvc/workflow/workflow-view.js.map M static/maps/utils/query-string-parsing.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/layout/menu.js M static/scripts/mvc/form/form-view.js A static/scripts/mvc/form/form-wrapper.js M static/scripts/mvc/grid/grid-template.js M static/scripts/mvc/user/user-preferences.js M static/scripts/mvc/workflow/workflow-forms.js M static/scripts/mvc/workflow/workflow-view.js M static/scripts/utils/query-string-parsing.js R templates/admin/dataset_security/group/grid.mako R templates/admin/dataset_security/role/grid.mako R templates/admin/quota/grid.mako R templates/admin/tool_version/grid.mako R templates/admin/user/grid.mako R templates/admin/user/reset_password.mako R templates/admin/user/user.mako A templates/webapps/tool_shed/admin/user/reset_password.mako A templates/webapps/tool_shed/admin/user/user.mako R templates/webapps/tool_shed/repository/grid.mako Log Message: ----------- Merge branch 'revise_grid_forms' into admin_grid_roles Commit: b46f4e4c84f042a3b668020d6767b6777e2babb4 https://github.com/galaxyproject/galaxy/commit/b46f4e4c84f042a3b668020d6767… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-04 (Fri, 04 Aug 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Remove unused routing message handler Commit: 44a339546b1849131b9c9f993aee332171217709 https://github.com/galaxyproject/galaxy/commit/44a339546b1849131b9c9f993aee… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-04 (Fri, 04 Aug 2017) Changed paths: M client/galaxy/scripts/apps/panels/admin-panel.js M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Fix menu link Commit: ffe3ac294d8a21a10546f45518e4d2c52e1bc966 https://github.com/galaxyproject/galaxy/commit/ffe3ac294d8a21a10546f45518e4… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-04 (Fri, 04 Aug 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Do not parse empty messages Commit: 246e94ae8470e1ef78f1b136bcdc117f45e036ef https://github.com/galaxyproject/galaxy/commit/246e94ae8470e1ef78f1b136bcdc… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-04 (Fri, 04 Aug 2017) Changed paths: M client/galaxy/scripts/apps/admin.js M lib/galaxy/webapps/galaxy/controllers/admin.py M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Build role renaming in client Commit: 20ce574e3304af6cb09d98b9d8e17a7ff7c3c628 https://github.com/galaxyproject/galaxy/commit/20ce574e3304af6cb09d98b9d8e1… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-04 (Fri, 04 Aug 2017) Changed paths: M client/galaxy/scripts/apps/admin.js M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Add role renaming feature to revised endpoint Commit: 99bf6809bebb621a33050164f2c7e2a2f203ae40 https://github.com/galaxyproject/galaxy/commit/99bf6809bebb621a33050164f2c7… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-04 (Fri, 04 Aug 2017) Changed paths: M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Repack scripts Commit: 5ab9ea4ffdb7c5359d32a0653f6ac59d9fc37d21 https://github.com/galaxyproject/galaxy/commit/5ab9ea4ffdb7c5359d32a0653f6a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-04 (Fri, 04 Aug 2017) Changed paths: M client/galaxy/scripts/mvc/form/form-wrapper.js M static/maps/mvc/form/form-wrapper.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/form/form-wrapper.js Log Message: ----------- Use primary button Commit: 4d542820e70d02c0809d3bd8482746b90e68642d https://github.com/galaxyproject/galaxy/commit/4d542820e70d02c0809d3bd84827… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-04 (Fri, 04 Aug 2017) Changed paths: M client/galaxy/scripts/mvc/form/form-wrapper.js M lib/galaxy/webapps/galaxy/api/users.py M static/maps/mvc/form/form-wrapper.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/form/form-wrapper.js Log Message: ----------- Remove unused messages, set default message status Commit: 502b2a068c06e190484fda2adcdc43ffef7d07e2 https://github.com/galaxyproject/galaxy/commit/502b2a068c06e190484fda2adcdc… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-04 (Fri, 04 Aug 2017) Changed paths: M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/mvc/form/form-wrapper.js M client/galaxy/scripts/mvc/user/user-preferences.js M static/maps/mvc/form/form-wrapper.js.map M static/maps/mvc/user/user-preferences.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/form/form-wrapper.js M static/scripts/mvc/user/user-preferences.js Log Message: ----------- Use redirect option for user preferences Commit: b908e98e37de20aff2b18acd6b93b79b9020f4a8 https://github.com/galaxyproject/galaxy/commit/b908e98e37de20aff2b18acd6b93… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-04 (Fri, 04 Aug 2017) Changed paths: M client/galaxy/scripts/mvc/form/form-repeat.js M client/galaxy/scripts/mvc/form/form-wrapper.js M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/scripts/mvc/ui/ui-buttons.js M client/galaxy/style/less/ui.less M static/maps/mvc/form/form-repeat.js.map M static/maps/mvc/form/form-wrapper.js.map M static/maps/mvc/tool/tool-form.js.map M static/maps/mvc/ui/ui-buttons.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/form/form-repeat.js M static/scripts/mvc/form/form-wrapper.js M static/scripts/mvc/tool/tool-form.js M static/scripts/mvc/ui/ui-buttons.js M static/style/blue/base.css Log Message: ----------- Fix button and operations floating handling Commit: bf6e2d26bd128e773ae3c604216e7b939abf8c01 https://github.com/galaxyproject/galaxy/commit/bf6e2d26bd128e773ae3c604216e… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-04 (Fri, 04 Aug 2017) Changed paths: M client/galaxy/scripts/mvc/user/user-custom-builds.js M static/maps/mvc/user/user-custom-builds.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/user/user-custom-builds.js Log Message: ----------- Fix floating for custom build form button Commit: afa6964994fb6aa6acad44d03f4123f2f7726839 https://github.com/galaxyproject/galaxy/commit/afa6964994fb6aa6acad44d03f41… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-04 (Fri, 04 Aug 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-list.js M client/galaxy/style/less/ui.less M static/maps/mvc/ui/ui-list.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/ui/ui-list.js M static/style/blue/base.css Log Message: ----------- Fix style for list parameter Commit: d11fc568a41a3dba540457f9d861182acfbae117 https://github.com/galaxyproject/galaxy/commit/d11fc568a41a3dba540457f9d861… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-04 (Fri, 04 Aug 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py M lib/tool_shed/grids/repository_grids.py R templates/admin/tool_shed_repository/grid.mako Log Message: ----------- Merge branch 'revise_grid_forms' into admin_grid_roles Commit: 9d8bdc6f304d676157f8c0e5a76f6c49dd9e5d4b https://github.com/galaxyproject/galaxy/commit/9d8bdc6f304d676157f8c0e5a76f… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-05 (Sat, 05 Aug 2017) Changed paths: M lib/galaxy/web/base/controller.py M static/maps/galaxy.js.map M static/scripts/galaxy.js Log Message: ----------- Repack scripts Commit: 1675b9cca2cc1c5aa8a4e495e23c0877a781cf39 https://github.com/galaxyproject/galaxy/commit/1675b9cca2cc1c5aa8a4e495e23c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-05 (Sat, 05 Aug 2017) Changed paths: M client/galaxy/scripts/galaxy.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/user/user-preferences.js M lib/galaxy/jobs/rule_helper.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/web/base/controller.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/user.py M static/maps/galaxy.js.map M static/maps/layout/menu.js.map M static/maps/mvc/user/user-preferences.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/galaxy.js M static/scripts/layout/menu.js M static/scripts/mvc/user/user-preferences.js M templates/galaxy_client_app.mako M templates/user/login.mako M templates/user/register.mako M templates/webapps/galaxy/history/display_structured.mako M templates/webapps/galaxy/workflow/build_from_current_history.mako M test/shed_functional/base/twilltestcase.py Log Message: ----------- Merge branch 'revise_grid_forms' into admin_grid_roles Commit: d698d32ceb043fdb9820b68615748ca13e0825c8 https://github.com/galaxyproject/galaxy/commit/d698d32ceb043fdb9820b6861574… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-07 (Mon, 07 Aug 2017) Changed paths: M client/galaxy/scripts/apps/admin.js M lib/galaxy/webapps/galaxy/controllers/admin.py M static/maps/mvc/user/user-preferences.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/user/user-preferences.js Log Message: ----------- Manage users and groups for role Commit: 9ee062bd4622481165d4cb1e783454a49fcdd704 https://github.com/galaxyproject/galaxy/commit/9ee062bd4622481165d4cb1e7834… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-07 (Mon, 07 Aug 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Show current name and description when renaming roles Commit: 183176a05c95e063a710ff469a368c463e18db2f https://github.com/galaxyproject/galaxy/commit/183176a05c95e063a710ff469a36… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-07 (Mon, 07 Aug 2017) Changed paths: M client/galaxy/scripts/apps/admin.js M lib/galaxy/webapps/galaxy/controllers/admin.py M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Add create role form Commit: 663c6c13975b01cf0472a083a68164d9bd010871 https://github.com/galaxyproject/galaxy/commit/663c6c13975b01cf0472a083a681… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-07 (Mon, 07 Aug 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py R templates/admin/dataset_security/role/role.mako R templates/admin/dataset_security/role/role_create.mako R templates/admin/dataset_security/role/role_rename.mako A templates/webapps/tool_shed/admin/dataset_security/role/role.mako A templates/webapps/tool_shed/admin/dataset_security/role/role_create.mako A templates/webapps/tool_shed/admin/dataset_security/role/role_rename.mako Log Message: ----------- Fix boolean title, and move unused role makos to toolshed Commit: e77fd47b034e6af5b19756bd778f5081332e7c85 https://github.com/galaxyproject/galaxy/commit/e77fd47b034e6af5b19756bd778f… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-07 (Mon, 07 Aug 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Fix boolean handling Commit: 419f3db64fb3614d5a70ed9a9eea8a260b6f5865 https://github.com/galaxyproject/galaxy/commit/419f3db64fb3614d5a70ed9a9eea… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-07 (Mon, 07 Aug 2017) Changed paths: M lib/tool_shed/util/admin_util.py Log Message: ----------- Remove unused information feature for toolshed Commit: 733e225ec96b058dd159dda4e18ba1f7572573fd https://github.com/galaxyproject/galaxy/commit/733e225ec96b058dd159dda4e18b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-07 (Mon, 07 Aug 2017) Changed paths: M client/galaxy/scripts/utils/query-string-parsing.js M static/maps/utils/query-string-parsing.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/utils/query-string-parsing.js Log Message: ----------- Fix message handling in user preference main view Commit: a5d7c0fa84d8fe24fc94ac814b9f7502283de7c2 https://github.com/galaxyproject/galaxy/commit/a5d7c0fa84d8fe24fc94ac814b9f… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-07 (Mon, 07 Aug 2017) Changed paths: M client/galaxy/scripts/mvc/form/form-wrapper.js M static/maps/mvc/form/form-wrapper.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/form/form-wrapper.js Log Message: ----------- Scroll to highlight message Commit: 4b2eca373e936308b0550b9fabfc6494228b837a https://github.com/galaxyproject/galaxy/commit/4b2eca373e936308b0550b9fabfc… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-07 (Mon, 07 Aug 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/users.py Log Message: ----------- Remove duplicate roles from selection list Commit: 5a8adbf8b77dc985353803a724fc4344dcbbdc79 https://github.com/galaxyproject/galaxy/commit/5a8adbf8b77dc985353803a724fc… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-07 (Mon, 07 Aug 2017) Changed paths: M doc/source/admin/special_topics/grt.rst M lib/galaxy/dataset_collections/matching.py M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/jobs/runners/util/cli/__init__.py M lib/galaxy/jobs/runners/util/cli/shell/local.py M lib/galaxy/jobs/runners/util/cli/shell/rsh.py M lib/galaxy/objectstore/s3_multipart_upload.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/execute.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/parser/yaml.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/webapps/galaxy/api/users.py M lib/galaxy/webapps/galaxy/controllers/async.py M lib/galaxy/webapps/galaxy/controllers/history.py R scripts/grt.py R scripts/grt.yml.sample A scripts/grt/export.py A scripts/grt/grt.yml.sample A scripts/grt/upload.py M test/api/test_tools.py A test/functional/tools/identifier_source.xml M test/functional/tools/samples_tool_conf.xml A test/unit/test_remote_shell.py M test/unit/tools/test_toolbox.py M test/unit/tools_support.py M tox.ini Log Message: ----------- Merge branch 'remove_duplicates' into admin_grid_roles Commit: a7c6c69cbf6a6eeffdf53815144e623576c47b13 https://github.com/galaxyproject/galaxy/commit/a7c6c69cbf6a6eeffdf53815144e… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-08 (Tue, 08 Aug 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Fix lint Commit: d3b8889c04ef22d740f8b668a8212c728ba5832c https://github.com/galaxyproject/galaxy/commit/d3b8889c04ef22d740f8b668a821… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-08 (Tue, 08 Aug 2017) Changed paths: M client/galaxy/scripts/apps/panels/admin-panel.js M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Fix second role link in admin panel Commit: c01023b5adc402a6a8662e9f319afcd9e4f5fc6e https://github.com/galaxyproject/galaxy/commit/c01023b5adc402a6a8662e9f319a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-09 (Wed, 09 Aug 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Fix indention Commit: d32a3a58a50bdbdbe6144a265ef3424a2f011ae2 https://github.com/galaxyproject/galaxy/commit/d32a3a58a50bdbdbe6144a265ef3… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-09 (Wed, 09 Aug 2017) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M config/datatypes_conf.xml.sample A config/user_preferences_extra_conf.yml.sample M lib/galaxy/config.py M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/molecules.py M lib/galaxy/datatypes/mothur.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/text.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/managers/workflows.py M lib/galaxy/tools/parser/interface.py M lib/galaxy/tools/parser/output_objects.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/web/base/controller.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/web/base/pluginframework.py M lib/galaxy/webapps/galaxy/api/users.py M lib/galaxy/workflow/extract.py M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/util/workflow_util.py M lib/tool_shed/utility_containers/utility_container_manager.py M templates/webapps/tool_shed/repository/common.mako M test/unit/tools/test_parsing.py Log Message: ----------- Merge branch 'revise_page' into admin_grid_roles Commit: 938bf525f46c8d3c7568d9b2a97edfa958ba900f https://github.com/galaxyproject/galaxy/commit/938bf525f46c8d3c7568d9b2a97e… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-10 (Thu, 10 Aug 2017) Changed paths: M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M lib/galaxy/managers/tags.py M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py A lib/galaxy/model/migrate/versions/0135_add_library_tags.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/web/base/controller.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py M lib/galaxy/webapps/galaxy/api/library_contents.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M static/maps/mvc/library/library-dataset-view.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/mvc/user/user-preferences.js.map M static/scripts/mvc/library/library-dataset-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/user/user-preferences.js Log Message: ----------- Merge branch 'revise_grid_forms' into admin_grid_roles Commit: be19b36ecaab43dd9cbf2fd5f80995e7ac9ff507 https://github.com/galaxyproject/galaxy/commit/be19b36ecaab43dd9cbf2fd5f809… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-10 (Thu, 10 Aug 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js A client/galaxy/scripts/mvc/dataset/dataset-error.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js A client/galaxy/scripts/mvc/job/job-params.js M client/galaxy/style/less/galaxy_bootstrap/overrides.less M config/datatypes_conf.xml.sample A config/error_report.yml.sample M config/tool_conf.xml.sample A doc/source/admin/special_topics/bug_reports.rst M doc/source/admin/special_topics/index.rst M lib/galaxy/app.py M lib/galaxy/config.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/jobs/__init__.py M lib/galaxy/tools/__init__.py A lib/galaxy/tools/error_reports/__init__.py A lib/galaxy/tools/error_reports/plugins/__init__.py A lib/galaxy/tools/error_reports/plugins/biostars.py A lib/galaxy/tools/error_reports/plugins/email.py A lib/galaxy/tools/error_reports/plugins/json.py A lib/galaxy/tools/error_reports/plugins/sentry.py M lib/galaxy/tools/errors.py A lib/galaxy/tools/sort_collection_list.xml M lib/galaxy/util/biostar.py M lib/galaxy/util/plugin_config.py M lib/galaxy/webapps/galaxy/api/jobs.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M scripts/grt/export.py M scripts/grt/upload.py A static/maps/mvc/dataset/dataset-error.js.map M static/maps/mvc/dataset/dataset-li-edit.js.map A static/maps/mvc/job/job-params.js.map M static/maps/mvc/user/user-preferences.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map A static/scripts/mvc/dataset/dataset-error.js M static/scripts/mvc/dataset/dataset-li-edit.js A static/scripts/mvc/job/job-params.js M static/scripts/mvc/user/user-preferences.js M static/style/blue/base.css M templates/show_params.mako R templates/webapps/galaxy/dataset/errors.mako A test-data/test.vcf.gz M test/functional/tools/sample_datatypes_conf.xml M test/functional/tools/samples_tool_conf.xml A test/functional/tools/vcf_bgzip.xml Log Message: ----------- Merge branch 'revise_grid_forms' into admin_grid_roles Commit: 33c794d273271b14732fb8037c2ea8105a3c688e https://github.com/galaxyproject/galaxy/commit/33c794d273271b14732fb8037c2e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-11 (Fri, 11 Aug 2017) Changed paths: M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/panels/admin-panel.js M client/galaxy/scripts/mvc/form/form-repeat.js M client/galaxy/scripts/mvc/form/form-wrapper.js M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/scripts/mvc/ui/ui-buttons.js M client/galaxy/scripts/mvc/ui/ui-list.js M client/galaxy/scripts/mvc/user/user-custom-builds.js M client/galaxy/scripts/mvc/user/user-preferences.js M client/galaxy/scripts/utils/query-string-parsing.js M client/galaxy/style/less/ui.less M lib/galaxy/webapps/galaxy/api/users.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/tool_shed/util/admin_util.py M static/maps/mvc/form/form-repeat.js.map M static/maps/mvc/form/form-wrapper.js.map M static/maps/mvc/tool/tool-form.js.map M static/maps/mvc/ui/ui-buttons.js.map M static/maps/mvc/ui/ui-list.js.map M static/maps/mvc/user/user-custom-builds.js.map M static/maps/mvc/user/user-preferences.js.map M static/maps/utils/query-string-parsing.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/form/form-repeat.js M static/scripts/mvc/form/form-wrapper.js M static/scripts/mvc/tool/tool-form.js M static/scripts/mvc/ui/ui-buttons.js M static/scripts/mvc/ui/ui-list.js M static/scripts/mvc/user/user-custom-builds.js M static/scripts/mvc/user/user-preferences.js M static/scripts/utils/query-string-parsing.js M static/style/blue/base.css R templates/admin/dataset_security/role/role.mako R templates/admin/dataset_security/role/role_create.mako R templates/admin/dataset_security/role/role_rename.mako A templates/webapps/tool_shed/admin/dataset_security/role/role.mako A templates/webapps/tool_shed/admin/dataset_security/role/role_create.mako A templates/webapps/tool_shed/admin/dataset_security/role/role_rename.mako Log Message: ----------- Merge pull request #4385 from guerler/admin_grid_roles Admin grid roles revision Compare: https://github.com/galaxyproject/galaxy/compare/600b0aad7ce1...33c794d27327

1 0

[galaxyproject/galaxy] a7885e: Generalize how user preferences build forms
by GitHub 11 Aug '17

11 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a7885e0b6e195ecc1beaab6f526ce52e927053c2 https://github.com/galaxyproject/galaxy/commit/a7885e0b6e195ecc1beaab6f526c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-03 (Thu, 03 Aug 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js A client/galaxy/scripts/mvc/form/form-wrapper.js M client/galaxy/scripts/mvc/user/user-preferences.js A static/maps/mvc/form/form-wrapper.js.map M static/maps/mvc/user/user-preferences.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map A static/scripts/mvc/form/form-wrapper.js M static/scripts/mvc/user/user-preferences.js Log Message: ----------- Generalize how user preferences build forms Commit: ddcace7527d6fc20ce93c983d795ff3b35117191 https://github.com/galaxyproject/galaxy/commit/ddcace7527d6fc20ce93c983d795… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-03 (Thu, 03 Aug 2017) Changed paths: M client/galaxy/scripts/mvc/form/form-wrapper.js M static/maps/mvc/form/form-wrapper.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/form/form-wrapper.js Log Message: ----------- Remove unused options parsing Commit: 6c11ffbe84f2e279607a5dd16f6d0532d26dc1f9 https://github.com/galaxyproject/galaxy/commit/6c11ffbe84f2e279607a5dd16f6d… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-03 (Thu, 03 Aug 2017) Changed paths: M client/galaxy/scripts/apps/admin.js M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin.py M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map Log Message: ----------- User generic form wrapper to reset password Commit: cd8314808e67dc8a880c0bb16a1faf4e5a571456 https://github.com/galaxyproject/galaxy/commit/cd8314808e67dc8a880c0bb16a1f… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-03 (Thu, 03 Aug 2017) Changed paths: M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/utils/query-string-parsing.js M lib/galaxy/webapps/galaxy/controllers/admin.py M static/maps/utils/query-string-parsing.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/utils/query-string-parsing.js Log Message: ----------- Allow array parsing through url Commit: 06b5be23ddec4298cd78503e6e07f2949d882a6e https://github.com/galaxyproject/galaxy/commit/06b5be23ddec4298cd78503e6e07… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-03 (Thu, 03 Aug 2017) Changed paths: M client/galaxy/scripts/apps/admin.js M lib/galaxy/webapps/galaxy/controllers/admin.py M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map Log Message: ----------- Specify password reset form Commit: e0ccec46b3f4f4d8f13091fa2f5dcafd987c7b51 https://github.com/galaxyproject/galaxy/commit/e0ccec46b3f4f4d8f13091fa2f5d… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-03 (Thu, 03 Aug 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Move help info Commit: c6dee98c55a46b23e9373ea53c4fa22e545978a3 https://github.com/galaxyproject/galaxy/commit/c6dee98c55a46b23e9373ea53c4f… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-04 (Fri, 04 Aug 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map Log Message: ----------- Fix input types, repack scripts Commit: 23b141a2ec3e5ff865a8ea0718d41b9845e79d64 https://github.com/galaxyproject/galaxy/commit/23b141a2ec3e5ff865a8ea0718d4… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-04 (Fri, 04 Aug 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Complete new controller endpoint to reset passwords Commit: 8312b07e60ee945fdde6ecc29eadcac9423ab3d5 https://github.com/galaxyproject/galaxy/commit/8312b07e60ee945fdde6ecc29ead… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-04 (Fri, 04 Aug 2017) Changed paths: M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/mvc/form/form-wrapper.js M client/galaxy/scripts/mvc/grid/grid-template.js M static/maps/mvc/form/form-wrapper.js.map M static/maps/mvc/grid/grid-template.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/form/form-wrapper.js M static/scripts/mvc/grid/grid-template.js Log Message: ----------- Allow form redirect to grid view Commit: 4e050282652ea3c3cbf20998653acb9a34a85415 https://github.com/galaxyproject/galaxy/commit/4e050282652ea3c3cbf20998653a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-04 (Fri, 04 Aug 2017) Changed paths: M client/galaxy/scripts/apps/admin.js M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Create dictionary for form definitions Commit: f50e0ba5bba5fe6605bcbcc446ddb10f58ae898b https://github.com/galaxyproject/galaxy/commit/f50e0ba5bba5fe6605bcbcc446dd… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-04 (Fri, 04 Aug 2017) Changed paths: M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/form/form-wrapper.js M lib/galaxy/webapps/galaxy/controllers/admin.py M static/maps/mvc/form/form-view.js.map M static/maps/mvc/form/form-wrapper.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/form/form-view.js M static/scripts/mvc/form/form-wrapper.js Log Message: ----------- Revise endpoint to manage user roles and groups, add initial message support to form wrapper Commit: 7e1c40799efa67f43fe13b589ef2432b05fdebc3 https://github.com/galaxyproject/galaxy/commit/7e1c40799efa67f43fe13b589ef2… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-04 (Fri, 04 Aug 2017) Changed paths: M client/galaxy/scripts/mvc/form/form-wrapper.js M lib/galaxy/webapps/galaxy/controllers/admin.py M static/maps/mvc/form/form-wrapper.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/form/form-wrapper.js Log Message: ----------- Use initial method parsing for reset password info Commit: 63ebee1a415a9433b01164ef72e90e08c177fc18 https://github.com/galaxyproject/galaxy/commit/63ebee1a415a9433b01164ef72e9… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-04 (Fri, 04 Aug 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Add put handling to revised manage_roles_and_groups_for_user controller endpoint Commit: e791ac29bb310cefcbcc8afd762c7c7ddec54586 https://github.com/galaxyproject/galaxy/commit/e791ac29bb310cefcbcc8afd762c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-04 (Fri, 04 Aug 2017) Changed paths: M lib/tool_shed/grids/admin_grids.py M lib/tool_shed/util/admin_util.py R templates/admin/user/grid.mako R templates/admin/user/reset_password.mako R templates/admin/user/user.mako A templates/webapps/tool_shed/admin/user/reset_password.mako A templates/webapps/tool_shed/admin/user/user.mako Log Message: ----------- Move user form grid makos to toolshed Commit: 3007122bd9c9e111ef8d0010707ddac51bff6387 https://github.com/galaxyproject/galaxy/commit/3007122bd9c9e111ef8d0010707d… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-04 (Fri, 04 Aug 2017) Changed paths: M templates/webapps/tool_shed/admin/user/reset_password.mako M templates/webapps/tool_shed/admin/user/user.mako Log Message: ----------- Remove custom case handling for galaxy app from makos, restoring previous state Commit: 146dd82f043c9adaa8f2891f03ab31f76b16af2e https://github.com/galaxyproject/galaxy/commit/146dd82f043c9adaa8f2891f03ab… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-04 (Fri, 04 Aug 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/tool_shed/grids/admin_grids.py R templates/admin/dataset_security/group/grid.mako R templates/admin/dataset_security/role/grid.mako R templates/admin/quota/grid.mako R templates/admin/tool_version/grid.mako R templates/webapps/tool_shed/repository/grid.mako Log Message: ----------- Remove unnecessary grid makos Commit: c2b98bce78366b4daf33b76c7a1fe2d465212274 https://github.com/galaxyproject/galaxy/commit/c2b98bce78366b4daf33b76c7a1f… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-04 (Fri, 04 Aug 2017) Changed paths: M lib/tool_shed/grids/repository_grids.py Log Message: ----------- Remove unused grid makos Commit: 010a7dfb9ce1e0002c2ea81d7ff88dbe3c1ecb38 https://github.com/galaxyproject/galaxy/commit/010a7dfb9ce1e0002c2ea81d7ff8… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-04 (Fri, 04 Aug 2017) Changed paths: M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py R templates/admin/tool_shed_repository/grid.mako Log Message: ----------- Remove unused toolshed grid mako Commit: 96cc67a2caf6470c235d871878a86e6ebaca3b1c https://github.com/galaxyproject/galaxy/commit/96cc67a2caf6470c235d871878a8… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-04 (Fri, 04 Aug 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Fix lint Commit: 9dc5ace31a5ec847e408baeaccb9dbd7433f02b7 https://github.com/galaxyproject/galaxy/commit/9dc5ace31a5ec847e408baeaccb9… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-04 (Fri, 04 Aug 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Remove lines Commit: d2d250b847f22934a2f1d3c1d2256b40c52abc55 https://github.com/galaxyproject/galaxy/commit/d2d250b847f22934a2f1d3c1d225… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-05 (Sat, 05 Aug 2017) Changed paths: M client/galaxy/scripts/galaxy.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/user/user-preferences.js M lib/galaxy/jobs/rule_helper.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/web/base/controller.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/user.py M static/maps/galaxy.js.map M static/maps/layout/menu.js.map M static/maps/mvc/user/user-preferences.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/galaxy.js M static/scripts/layout/menu.js M static/scripts/mvc/user/user-preferences.js M templates/galaxy_client_app.mako M templates/user/login.mako M templates/user/register.mako M templates/webapps/galaxy/history/display_structured.mako M templates/webapps/galaxy/workflow/build_from_current_history.mako M test/shed_functional/base/twilltestcase.py Log Message: ----------- Merge branch 'dev' into revise_grid_forms Commit: f531d2c0c9810b2d0ee8f0482cb12e163bbc0de2 https://github.com/galaxyproject/galaxy/commit/f531d2c0c9810b2d0ee8f0482cb1… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-05 (Sat, 05 Aug 2017) Changed paths: M lib/galaxy/web/base/controller.py M static/maps/galaxy.js.map M static/maps/layout/menu.js.map M static/maps/mvc/user/user-preferences.js.map M static/scripts/galaxy.js M static/scripts/layout/menu.js M static/scripts/mvc/user/user-preferences.js Log Message: ----------- Repack scripts Commit: c49e749534f76c8bb2d0ea8bb629a6ee236ff5cc https://github.com/galaxyproject/galaxy/commit/c49e749534f76c8bb2d0ea8bb629… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-07 (Mon, 07 Aug 2017) Changed paths: M lib/tool_shed/util/admin_util.py Log Message: ----------- Fix user info link for toolshed Commit: e477cce9b68d90a313d1534c3ad156f9eb8cc6ec https://github.com/galaxyproject/galaxy/commit/e477cce9b68d90a313d1534c3ad1… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-10 (Thu, 10 Aug 2017) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M config/datatypes_conf.xml.sample A config/user_preferences_extra_conf.yml.sample M doc/source/admin/special_topics/grt.rst M lib/galaxy/config.py M lib/galaxy/dataset_collections/matching.py M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/molecules.py M lib/galaxy/datatypes/mothur.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/text.py M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/runners/util/cli/__init__.py M lib/galaxy/jobs/runners/util/cli/shell/local.py M lib/galaxy/jobs/runners/util/cli/shell/rsh.py M lib/galaxy/managers/tags.py M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py A lib/galaxy/model/migrate/versions/0135_add_library_tags.py M lib/galaxy/objectstore/s3_multipart_upload.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/tools/execute.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/tools/parser/interface.py M lib/galaxy/tools/parser/output_objects.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/parser/yaml.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/web/base/controller.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/web/base/pluginframework.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py M lib/galaxy/webapps/galaxy/api/library_contents.py M lib/galaxy/webapps/galaxy/api/users.py M lib/galaxy/webapps/galaxy/controllers/async.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/workflow/extract.py M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/util/workflow_util.py M lib/tool_shed/utility_containers/utility_container_manager.py R scripts/grt.py R scripts/grt.yml.sample A scripts/grt/export.py A scripts/grt/grt.yml.sample A scripts/grt/upload.py M static/maps/mvc/library/library-dataset-view.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/mvc/library/library-dataset-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js M templates/webapps/tool_shed/repository/common.mako M test/api/test_tools.py A test/functional/tools/identifier_source.xml M test/functional/tools/samples_tool_conf.xml A test/unit/test_remote_shell.py M test/unit/tools/test_parsing.py M test/unit/tools/test_toolbox.py M test/unit/tools_support.py M tox.ini Log Message: ----------- Merge branch 'revise_page' into revise_grid_forms Commit: b8c05ede4dd188dce24c914912f8fa35963d9562 https://github.com/galaxyproject/galaxy/commit/b8c05ede4dd188dce24c914912f8… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-10 (Thu, 10 Aug 2017) Log Message: ----------- Merge branch 'dev' into revise_grid_forms Commit: 583765c7c087c77c6d1f2756e4233ce97a71240f https://github.com/galaxyproject/galaxy/commit/583765c7c087c77c6d1f2756e423… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-10 (Thu, 10 Aug 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js A client/galaxy/scripts/mvc/dataset/dataset-error.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js A client/galaxy/scripts/mvc/job/job-params.js M client/galaxy/style/less/galaxy_bootstrap/overrides.less M config/datatypes_conf.xml.sample A config/error_report.yml.sample M config/tool_conf.xml.sample A doc/source/admin/special_topics/bug_reports.rst M doc/source/admin/special_topics/index.rst M lib/galaxy/app.py M lib/galaxy/config.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/jobs/__init__.py M lib/galaxy/tools/__init__.py A lib/galaxy/tools/error_reports/__init__.py A lib/galaxy/tools/error_reports/plugins/__init__.py A lib/galaxy/tools/error_reports/plugins/biostars.py A lib/galaxy/tools/error_reports/plugins/email.py A lib/galaxy/tools/error_reports/plugins/json.py A lib/galaxy/tools/error_reports/plugins/sentry.py M lib/galaxy/tools/errors.py A lib/galaxy/tools/sort_collection_list.xml M lib/galaxy/util/biostar.py M lib/galaxy/util/plugin_config.py M lib/galaxy/webapps/galaxy/api/jobs.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M scripts/grt/export.py M scripts/grt/upload.py A static/maps/mvc/dataset/dataset-error.js.map M static/maps/mvc/dataset/dataset-li-edit.js.map A static/maps/mvc/job/job-params.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map A static/scripts/mvc/dataset/dataset-error.js M static/scripts/mvc/dataset/dataset-li-edit.js A static/scripts/mvc/job/job-params.js M static/style/blue/base.css M templates/show_params.mako R templates/webapps/galaxy/dataset/errors.mako A test-data/test.vcf.gz M test/functional/tools/sample_datatypes_conf.xml M test/functional/tools/samples_tool_conf.xml A test/functional/tools/vcf_bgzip.xml Log Message: ----------- Merge branch 'dev' into revise_grid_forms Commit: 600b0aad7ce10c1e427513684c4cd7423f5b52aa https://github.com/galaxyproject/galaxy/commit/600b0aad7ce10c1e427513684c4c… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-08-11 (Fri, 11 Aug 2017) Changed paths: M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/mvc/form/form-view.js A client/galaxy/scripts/mvc/form/form-wrapper.js M client/galaxy/scripts/mvc/grid/grid-template.js M client/galaxy/scripts/mvc/user/user-preferences.js M client/galaxy/scripts/utils/query-string-parsing.js M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py M lib/tool_shed/grids/admin_grids.py M lib/tool_shed/grids/repository_grids.py M lib/tool_shed/util/admin_util.py M static/maps/mvc/form/form-view.js.map A static/maps/mvc/form/form-wrapper.js.map M static/maps/mvc/grid/grid-template.js.map M static/maps/mvc/user/user-preferences.js.map M static/maps/utils/query-string-parsing.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/form/form-view.js A static/scripts/mvc/form/form-wrapper.js M static/scripts/mvc/grid/grid-template.js M static/scripts/mvc/user/user-preferences.js M static/scripts/utils/query-string-parsing.js R templates/admin/dataset_security/group/grid.mako R templates/admin/dataset_security/role/grid.mako R templates/admin/quota/grid.mako R templates/admin/tool_shed_repository/grid.mako R templates/admin/tool_version/grid.mako R templates/admin/user/grid.mako R templates/admin/user/reset_password.mako R templates/admin/user/user.mako A templates/webapps/tool_shed/admin/user/reset_password.mako A templates/webapps/tool_shed/admin/user/user.mako R templates/webapps/tool_shed/repository/grid.mako Log Message: ----------- Merge pull request #4377 from guerler/revise_grid_forms Remove makos of admin user grid forms Compare: https://github.com/galaxyproject/galaxy/compare/6353704e4b44...600b0aad7ce1

1 0

[galaxyproject/galaxy] aa1ce5: Updated missing parameters check for OpenID
by GitHub 10 Aug '17

10 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: aa1ce50689dd464c5c1e8b8b333397031914afb5 https://github.com/galaxyproject/galaxy/commit/aa1ce50689dd464c5c1e8b8b3333… Author: Vahid <VJalili(a)users.noreply.github.com> Date: 2017-05-05 (Fri, 05 May 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- Updated missing parameters check for OpenID When you have the OpenID URL, you don't need to recreate the provider. Only create the provider, if its not already created. Commit: dedc8eb1dc80804c7f43e08f8022f74edc2c91b3 https://github.com/galaxyproject/galaxy/commit/dedc8eb1dc80804c7f43e08f8022… Author: Vahid <VJalili(a)users.noreply.github.com> Date: 2017-05-12 (Fri, 12 May 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- Inform that the default provider is being used. Commit: a0e863f5706bfb7706e8dcb9e023a0f3c32a7629 https://github.com/galaxyproject/galaxy/commit/a0e863f5706bfb7706e8dcb9e023… Author: Vahid <VJalili(a)users.noreply.github.com> Date: 2017-05-12 (Fri, 12 May 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- Updated all `openid_url` and `openid_provider` checks Commit: a3c2ddff2b10a05eca6dfb460f8d539f2f595f19 https://github.com/galaxyproject/galaxy/commit/a3c2ddff2b10a05eca6dfb460f8d… Author: Vahid <VJalili(a)users.noreply.github.com> Date: 2017-05-12 (Fri, 12 May 2017) Changed paths: M openid/yahoo.xml Log Message: ----------- Corrected Yahoo OpenID endpoint At the time of making this change, Yahoo OpenID endpoint has issues--It's not accessible. This should be checked again later. Commit: 6353704e4b44e9eded6571b467f52a6dd288387d https://github.com/galaxyproject/galaxy/commit/6353704e4b44e9eded6571b467f5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-10 (Thu, 10 Aug 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py M openid/yahoo.xml Log Message: ----------- Merge pull request #4039 from VJalili/patch-11 Updated parameters check for OpenID Compare: https://github.com/galaxyproject/galaxy/compare/bcdf2c84f6df...6353704e4b44

1 0

[galaxyproject/galaxy] 63865e: Add VcfGz datatype
by GitHub 10 Aug '17

10 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 63865e11935724a02ae641857d802f8650a7f97d https://github.com/galaxyproject/galaxy/commit/63865e11935724a02ae641857d80… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-07-07 (Fri, 07 Jul 2017) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/tabular.py Log Message: ----------- Add VcfGz datatype This adds support for uploading VcfGz files in the upload box. When a user does this, the file will not be uncompressed. Also adds uncompressed preview. TODO: - Move Vcf class to BaseVcf - Vcf and VcfGz should both inherit from BaseVcf - Add a metadata element for VcfGz indexes (vzf.gz.tbi) - Create index (in set_meta method of VcfGz class) - Write test tools This is a kcikstart to @ffinfo GCC hack project. Commit: 83f1e82e84a79673b2913f9f4a6c63dc6d6526f4 https://github.com/galaxyproject/galaxy/commit/83f1e82e84a79673b2913f9f4a6c… Author: Peter van 't Hof <p.j.van_t_hof(a)lumc.nl> Date: 2017-07-07 (Fri, 07 Jul 2017) Changed paths: M lib/galaxy/datatypes/tabular.py Log Message: ----------- Added index job to vcf.gz files Commit: f4e02700f5c27dfffab0034f2201b208533e42ba https://github.com/galaxyproject/galaxy/commit/f4e02700f5c27dfffab0034f2201… Author: Peter van 't Hof <p.j.van_t_hof(a)lumc.nl> Date: 2017-07-07 (Fri, 07 Jul 2017) Changed paths: M lib/galaxy/datatypes/tabular.py Log Message: ----------- Fixed some spacings Commit: e9daa0d74464534a490129476f027455dbf26a69 https://github.com/galaxyproject/galaxy/commit/e9daa0d74464534a490129476f02… Author: Peter van 't Hof <p.j.van_t_hof(a)lumc.nl> Date: 2017-07-07 (Fri, 07 Jul 2017) Changed paths: M lib/galaxy/datatypes/tabular.py Log Message: ----------- Fixed import order Commit: b96b5076cec2624cc1700bfcec43fd7745d0c0e5 https://github.com/galaxyproject/galaxy/commit/b96b5076cec2624cc1700bfcec43… Author: Peter van 't Hof <p.j.van_t_hof(a)lumc.nl> Date: 2017-07-07 (Fri, 07 Jul 2017) Changed paths: M lib/galaxy/datatypes/tabular.py Log Message: ----------- Fixed import order (again ;) ) Commit: 986379fd0d65c0e5d2d6bdcf1428ba5182713ae7 https://github.com/galaxyproject/galaxy/commit/986379fd0d65c0e5d2d6bdcf1428… Author: Peter van 't Hof <p.j.van_t_hof(a)lumc.nl> Date: 2017-07-07 (Fri, 07 Jul 2017) Changed paths: M lib/galaxy/datatypes/tabular.py Log Message: ----------- Fixed import order (again ;) ) Commit: 9d98f10767d7c43e979720ba8a9badee86501c78 https://github.com/galaxyproject/galaxy/commit/9d98f10767d7c43e979720ba8a9b… Author: Peter van 't Hof <p.j.van_t_hof(a)lumc.nl> Date: 2017-07-07 (Fri, 07 Jul 2017) Changed paths: M lib/galaxy/datatypes/tabular.py M test/functional/tools/samples_tool_conf.xml A test/functional/tools/vcf_bgzip.xml Log Message: ----------- Adding test tool Commit: 99703469c0a30348683190a894a0fc682f92ff68 https://github.com/galaxyproject/galaxy/commit/99703469c0a30348683190a894a0… Author: pjvan_thof <pjrvanthof(a)gmail.com> Date: 2017-07-07 (Fri, 07 Jul 2017) Changed paths: A test-data/test.vcf.gz Log Message: ----------- Added test file Commit: e29611f52dba5e44924b39009ee28c933f4ba7fd https://github.com/galaxyproject/galaxy/commit/e29611f52dba5e44924b39009ee2… Author: Peter van 't Hof <p.j.van_t_hof(a)lumc.nl> Date: 2017-07-07 (Fri, 07 Jul 2017) Changed paths: M test/functional/tools/vcf_bgzip.xml Log Message: ----------- Fixing formats in test Commit: ed2e71a8383698543d97f339bd2b1175a5c07986 https://github.com/galaxyproject/galaxy/commit/ed2e71a8383698543d97f339bd2b… Author: Peter van 't Hof <p.j.van_t_hof(a)lumc.nl> Date: 2017-07-07 (Fri, 07 Jul 2017) Changed paths: M test/functional/tools/vcf_bgzip.xml Log Message: ----------- Fixing tool format Commit: 77b948678d69769c3d6c117a4dc718b3b3cb8388 https://github.com/galaxyproject/galaxy/commit/77b948678d69769c3d6c117a4dc7… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-07-07 (Fri, 07 Jul 2017) Changed paths: M test/functional/tools/sample_datatypes_conf.xml Log Message: ----------- Add vcf_bgzip and dependent datatypes to test/functional/tools/sample_datatypes_conf.xml Commit: 5cc71d2e3c009841c96657d2c359dbe5182548b8 https://github.com/galaxyproject/galaxy/commit/5cc71d2e3c009841c96657d2c359… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-07-07 (Fri, 07 Jul 2017) Changed paths: M lib/galaxy/datatypes/tabular.py M test/functional/tools/vcf_bgzip.xml Log Message: ----------- Simplify vcf_bgzip.xml test wrapper and fix index file access Commit: ed67b117517920affeb71982f08bc355ed0a6cda https://github.com/galaxyproject/galaxy/commit/ed67b117517920affeb71982f08b… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-08-07 (Mon, 07 Aug 2017) Changed paths: M lib/galaxy/datatypes/tabular.py Log Message: ----------- Use with statement in VcfGz class Commit: bcdf2c84f6df020e81c8868b10bcf337e2d72630 https://github.com/galaxyproject/galaxy/commit/bcdf2c84f6df020e81c8868b10bc… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-10 (Thu, 10 Aug 2017) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/tabular.py A test-data/test.vcf.gz M test/functional/tools/sample_datatypes_conf.xml M test/functional/tools/samples_tool_conf.xml A test/functional/tools/vcf_bgzip.xml Log Message: ----------- Merge pull request #4254 from ffinfo/vcf_gz_datatype Vcf gz datatype Compare: https://github.com/galaxyproject/galaxy/compare/e3de5e250d02...bcdf2c84f6df

1 0

[galaxyproject/galaxy] e0d8db: Created alphabetic and numerical sort tool for col...
by GitHub 10 Aug '17

10 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e0d8db05b8707b01a42a7be3e46df627bbdf0307 https://github.com/galaxyproject/galaxy/commit/e0d8db05b8707b01a42a7be3e46d… Author: Jorrit Boekel <jorrit.boekel(a)scilifelab.se> Date: 2017-07-21 (Fri, 21 Jul 2017) Changed paths: M config/tool_conf.xml.sample M lib/galaxy/tools/__init__.py A lib/galaxy/tools/sort_collection_list.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Created alphabetic and numerical sort tool for collection operations Commit: e3de5e250d02d105aff4265a0caf13553e3c3ade https://github.com/galaxyproject/galaxy/commit/e3de5e250d02d105aff4265a0caf… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-10 (Thu, 10 Aug 2017) Changed paths: M config/tool_conf.xml.sample M lib/galaxy/tools/__init__.py A lib/galaxy/tools/sort_collection_list.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #4329 from glormph/collection_list_sort Created alphabetic and numerical sort tool for collection operations Compare: https://github.com/galaxyproject/galaxy/compare/fcd06a96d613...e3de5e250d02

1 0

[galaxyproject/galaxy] bdbe36: fix pardir
by GitHub 10 Aug '17

10 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: bdbe3603059b84bb2a91646ebcad003477bb9590 https://github.com/galaxyproject/galaxy/commit/bdbe3603059b84bb2a91646ebcad… Author: E Rasche <hxr(a)hx42.org> Date: 2017-08-10 (Thu, 10 Aug 2017) Changed paths: M scripts/grt/export.py Log Message: ----------- fix pardir Commit: f4383bd983ee14d4e85ef610dba4b11266b196ed https://github.com/galaxyproject/galaxy/commit/f4383bd983ee14d4e85ef610dba4… Author: E Rasche <hxr(a)hx42.org> Date: 2017-08-10 (Thu, 10 Aug 2017) Changed paths: M scripts/grt/export.py Log Message: ----------- Fun things you find in production Commit: c5b36128644310e1ac52647df53f226c1457aaeb https://github.com/galaxyproject/galaxy/commit/c5b36128644310e1ac52647df53f… Author: E Rasche <hxr(a)hx42.org> Date: 2017-08-10 (Thu, 10 Aug 2017) Changed paths: M scripts/grt/upload.py Log Message: ----------- cleanup url in case Commit: 847df13fc0ea349ab2103099b696715a6d66b38f https://github.com/galaxyproject/galaxy/commit/847df13fc0ea349ab2103099b696… Author: E Rasche <hxr(a)hx42.org> Date: 2017-08-10 (Thu, 10 Aug 2017) Changed paths: M scripts/grt/upload.py Log Message: ----------- this should not have been missed Commit: 496169719465e18c899b991152a9e327d83e2446 https://github.com/galaxyproject/galaxy/commit/496169719465e18c899b991152a9… Author: E Rasche <hxr(a)hx42.org> Date: 2017-08-10 (Thu, 10 Aug 2017) Changed paths: M scripts/grt/upload.py Log Message: ----------- fix extension Commit: a177ccd0268805e0079f39d5d141ae4da39c0a00 https://github.com/galaxyproject/galaxy/commit/a177ccd0268805e0079f39d5d141… Author: E Rasche <hxr(a)hx42.org> Date: 2017-08-10 (Thu, 10 Aug 2017) Changed paths: M scripts/grt/upload.py Log Message: ----------- not needed Commit: fcd06a96d61342564febfaf652198bd009c9c76f https://github.com/galaxyproject/galaxy/commit/fcd06a96d61342564febfaf65219… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-10 (Thu, 10 Aug 2017) Changed paths: M scripts/grt/export.py M scripts/grt/upload.py Log Message: ----------- Merge pull request #4408 from erasche/grt-pardir Small GRT bugfixes Compare: https://github.com/galaxyproject/galaxy/compare/6d7d4e9e8e55...fcd06a96d613

1 0

[galaxyproject/galaxy] 70a64b: Refactor bug reporting into plugins
by GitHub 10 Aug '17

10 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 70a64b304eb2b5c9642581061f345e669251eac6 https://github.com/galaxyproject/galaxy/commit/70a64b304eb2b5c9642581061f34… Author: E Rasche <hxr(a)hx42.org> Date: 2017-08-10 (Thu, 10 Aug 2017) Changed paths: A config/error_report.xml.sample M lib/galaxy/app.py M lib/galaxy/config.py M lib/galaxy/jobs/__init__.py A lib/galaxy/tools/error_reports/__init__.py A lib/galaxy/tools/error_reports/sinks/__init__.py A lib/galaxy/tools/error_reports/sinks/email.py A lib/galaxy/tools/error_reports/sinks/json.py A lib/galaxy/tools/error_reports/sinks/sentry.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/webapps/galaxy/controllers/dataset.py A templates/messages.mako Log Message: ----------- Refactor bug reporting into plugins Commit: 9dd27dcc3de5eff03c4a37c34fc810d3f295c85c https://github.com/galaxyproject/galaxy/commit/9dd27dcc3de5eff03c4a37c34fc8… Author: E Rasche <hxr(a)hx42.org> Date: 2017-08-10 (Thu, 10 Aug 2017) Changed paths: M lib/galaxy/tools/error_reports/__init__.py M lib/galaxy/tools/error_reports/sinks/__init__.py M lib/galaxy/webapps/galaxy/controllers/dataset.py Log Message: ----------- flake8 Commit: 181a72a6f383aa54c4a053cedba05e345eda2584 https://github.com/galaxyproject/galaxy/commit/181a72a6f383aa54c4a053cedba0… Author: E Rasche <hxr(a)hx42.org> Date: 2017-08-10 (Thu, 10 Aug 2017) Changed paths: M lib/galaxy/tools/error_reports/sinks/email.py M lib/galaxy/tools/error_reports/sinks/json.py M lib/galaxy/tools/error_reports/sinks/sentry.py Log Message: ----------- flake8 import Commit: 437ab325da8b49b9f0e9b796f8515899aa10d035 https://github.com/galaxyproject/galaxy/commit/437ab325da8b49b9f0e9b796f851… Author: E Rasche <hxr(a)hx42.org> Date: 2017-08-10 (Thu, 10 Aug 2017) Changed paths: A doc/source/admin/special_topics/bug_reports.rst M doc/source/admin/special_topics/index.rst Log Message: ----------- document Commit: 46b621708aa4b9973c3e6bf6b02417dc3931523c https://github.com/galaxyproject/galaxy/commit/46b621708aa4b9973c3e6bf6b024… Author: E Rasche <hxr(a)hx42.org> Date: 2017-08-10 (Thu, 10 Aug 2017) Changed paths: M doc/source/admin/special_topics/bug_reports.rst M lib/galaxy/tools/error_reports/sinks/sentry.py Log Message: ----------- Allow sentry to be verbose Commit: d7e400c96ddf51caca3df26e8dc8a75089be2b06 https://github.com/galaxyproject/galaxy/commit/d7e400c96ddf51caca3df26e8dc8… Author: E Rasche <hxr(a)hx42.org> Date: 2017-08-10 (Thu, 10 Aug 2017) Changed paths: R config/error_report.xml.sample A config/error_report.yml.sample M lib/galaxy/config.py Log Message: ----------- Per @jmchilton comment, rewrite as yml Commit: f4a823c27a9b533994c593670cf5a13740e5bf7a https://github.com/galaxyproject/galaxy/commit/f4a823c27a9b533994c593670cf5… Author: E Rasche <hxr(a)hx42.org> Date: 2017-08-10 (Thu, 10 Aug 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js Log Message: ----------- add bug reporter Commit: ed7551e09679b940bd084fd5e5ce5fcf97320ffa https://github.com/galaxyproject/galaxy/commit/ed7551e09679b940bd084fd5e5ce… Author: E Rasche <hxr(a)hx42.org> Date: 2017-08-10 (Thu, 10 Aug 2017) Changed paths: A client/galaxy/scripts/mvc/dataset/dataset-error.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js A client/galaxy/scripts/mvc/job/job-params.js Log Message: ----------- redirect to new url Commit: 2f8347d5bc4bdf52a7d2b10d3e69b55290d104ca https://github.com/galaxyproject/galaxy/commit/2f8347d5bc4bdf52a7d2b10d3e69… Author: E Rasche <hxr(a)hx42.org> Date: 2017-08-10 (Thu, 10 Aug 2017) Changed paths: M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- add clientside route Commit: ef6b8cbeea5a0578683df8f013a0739a1e022fe0 https://github.com/galaxyproject/galaxy/commit/ef6b8cbeea5a0578683df8f013a0… Author: E Rasche <hxr(a)hx42.org> Date: 2017-08-10 (Thu, 10 Aug 2017) Changed paths: M client/galaxy/style/less/galaxy_bootstrap/overrides.less M templates/show_params.mako Log Message: ----------- move css rule to a more generic location Commit: 98ac18661865e958249f9a21bc847ba558b00893 https://github.com/galaxyproject/galaxy/commit/98ac18661865e958249f9a21bc84… Author: E Rasche <hxr(a)hx42.org> Date: 2017-08-10 (Thu, 10 Aug 2017) Changed paths: M lib/galaxy/tools/error_reports/sinks/email.py M lib/galaxy/tools/error_reports/sinks/json.py M lib/galaxy/tools/error_reports/sinks/sentry.py Log Message: ----------- change report code Commit: 6f8f38170c976b2152ef2e21fc46a47922da4b56 https://github.com/galaxyproject/galaxy/commit/6f8f38170c976b2152ef2e21fc46… Author: E Rasche <hxr(a)hx42.org> Date: 2017-08-10 (Thu, 10 Aug 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/jobs.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/dataset.py Log Message: ----------- refactor into an API Commit: 838b23358e6d00ce2d65f6a5fde6a413505eaf10 https://github.com/galaxyproject/galaxy/commit/838b23358e6d00ce2d65f6a5fde6… Author: E Rasche <hxr(a)hx42.org> Date: 2017-08-10 (Thu, 10 Aug 2017) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-error.js Log Message: ----------- Handle error report submission Commit: 64174113bfd8e18b2e87581137a134f8f4520bd7 https://github.com/galaxyproject/galaxy/commit/64174113bfd8e18b2e87581137a1… Author: E Rasche <hxr(a)hx42.org> Date: 2017-08-10 (Thu, 10 Aug 2017) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-error.js Log Message: ----------- refactor a bit Commit: 73369a2e8dd098d59083c61f67ec140a7c3cd102 https://github.com/galaxyproject/galaxy/commit/73369a2e8dd098d59083c61f67ec… Author: E Rasche <hxr(a)hx42.org> Date: 2017-08-10 (Thu, 10 Aug 2017) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-error.js Log Message: ----------- Add extra parameter to allow multiple messages Commit: cdb82dd8e64b83e14244b3b46163be1715afcfe2 https://github.com/galaxyproject/galaxy/commit/cdb82dd8e64b83e14244b3b46163… Author: E Rasche <hxr(a)hx42.org> Date: 2017-08-10 (Thu, 10 Aug 2017) Changed paths: M lib/galaxy/tools/error_reports/__init__.py M lib/galaxy/webapps/galaxy/api/jobs.py Log Message: ----------- Change invocation to pass user information Commit: 5980bd91bb0f916b576b27386d2b052609610d57 https://github.com/galaxyproject/galaxy/commit/5980bd91bb0f916b576b27386d2b… Author: E Rasche <hxr(a)hx42.org> Date: 2017-08-10 (Thu, 10 Aug 2017) Changed paths: M lib/galaxy/tools/errors.py Log Message: ----------- Link in expected places Commit: fd6c247398133d6f8df26b447328ec64801fcd11 https://github.com/galaxyproject/galaxy/commit/fd6c247398133d6f8df26b447328… Author: E Rasche <hxr(a)hx42.org> Date: 2017-08-10 (Thu, 10 Aug 2017) Changed paths: A lib/galaxy/tools/error_reports/sinks/biostars.py M lib/galaxy/util/biostar.py Log Message: ----------- Switch biostars to using HTML submission Commit: fb78a2118d0e45a11378bbc5e0daf0e351c8b763 https://github.com/galaxyproject/galaxy/commit/fb78a2118d0e45a11378bbc5e0da… Author: E Rasche <hxr(a)hx42.org> Date: 2017-08-10 (Thu, 10 Aug 2017) Changed paths: M static/maps/mvc/dataset/dataset-li-edit.js.map M static/scripts/mvc/dataset/dataset-li-edit.js M static/style/blue/base.css Log Message: ----------- merge Commit: e8a5b48da9ce98c72ac92171be56435ca2b9565f https://github.com/galaxyproject/galaxy/commit/e8a5b48da9ce98c72ac92171be56… Author: E Rasche <hxr(a)hx42.org> Date: 2017-08-10 (Thu, 10 Aug 2017) Changed paths: R templates/webapps/galaxy/dataset/errors.mako Log Message: ----------- Now unused Commit: 550cb7dfae8706e06a2b7638b078c9b9b134281d https://github.com/galaxyproject/galaxy/commit/550cb7dfae8706e06a2b7638b078… Author: E Rasche <hxr(a)hx42.org> Date: 2017-08-10 (Thu, 10 Aug 2017) Changed paths: M lib/galaxy/config.py M lib/galaxy/tools/error_reports/__init__.py A lib/galaxy/tools/error_reports/plugins/__init__.py A lib/galaxy/tools/error_reports/plugins/biostars.py A lib/galaxy/tools/error_reports/plugins/email.py A lib/galaxy/tools/error_reports/plugins/json.py A lib/galaxy/tools/error_reports/plugins/sentry.py R lib/galaxy/tools/error_reports/sinks/__init__.py R lib/galaxy/tools/error_reports/sinks/biostars.py R lib/galaxy/tools/error_reports/sinks/email.py R lib/galaxy/tools/error_reports/sinks/json.py R lib/galaxy/tools/error_reports/sinks/sentry.py Log Message: ----------- Requested renames, sink + yml Commit: fcd94f0483c119a4db0e84e469af3aade0f2847c https://github.com/galaxyproject/galaxy/commit/fcd94f0483c119a4db0e84e469af… Author: E Rasche <hxr(a)hx42.org> Date: 2017-08-10 (Thu, 10 Aug 2017) Changed paths: M config/error_report.yml.sample M lib/galaxy/app.py M lib/galaxy/jobs/__init__.py M lib/galaxy/tools/error_reports/__init__.py M lib/galaxy/webapps/galaxy/api/jobs.py Log Message: ----------- more renames Commit: 7c1c60d82643b100a55edefb6f88d13671defafa https://github.com/galaxyproject/galaxy/commit/7c1c60d82643b100a55edefb6f88… Author: E Rasche <hxr(a)hx42.org> Date: 2017-08-10 (Thu, 10 Aug 2017) Changed paths: A static/maps/mvc/dataset/dataset-error.js.map A static/maps/mvc/job/job-params.js.map A static/scripts/mvc/dataset/dataset-error.js A static/scripts/mvc/job/job-params.js Log Message: ----------- forgot static files Commit: 61a5b7c9e139cfa73fefa048f6ec34a7511b741c https://github.com/galaxyproject/galaxy/commit/61a5b7c9e139cfa73fefa048f6ec… Author: E Rasche <hxr(a)hx42.org> Date: 2017-08-10 (Thu, 10 Aug 2017) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M static/maps/mvc/dataset/dataset-li-edit.js.map M static/scripts/mvc/dataset/dataset-li-edit.js Log Message: ----------- another merge Commit: a6aedc695336b122c5e552ced771a97b5f62ee52 https://github.com/galaxyproject/galaxy/commit/a6aedc695336b122c5e552ced771… Author: E Rasche <hxr(a)hx42.org> Date: 2017-08-10 (Thu, 10 Aug 2017) Changed paths: M lib/galaxy/tools/error_reports/plugins/biostars.py Log Message: ----------- address flaking Commit: 1e9c31241c419cb53306232856ed7c368d8c6e92 https://github.com/galaxyproject/galaxy/commit/1e9c31241c419cb53306232856ed… Author: E Rasche <hxr(a)hx42.org> Date: 2017-08-10 (Thu, 10 Aug 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/jobs.py Log Message: ----------- remove comment Commit: 538ef006f36b3e525bb87d18944d596afb5f1639 https://github.com/galaxyproject/galaxy/commit/538ef006f36b3e525bb87d18944d… Author: E Rasche <hxr(a)hx42.org> Date: 2017-08-10 (Thu, 10 Aug 2017) Changed paths: M lib/galaxy/util/plugin_config.py Log Message: ----------- Also load yaml sample files. cc @jmchilton, is this ok? Commit: 3e8919c41643352feb6df50d04a71f2291024ef7 https://github.com/galaxyproject/galaxy/commit/3e8919c41643352feb6df50d04a7… Author: E Rasche <hxr(a)hx42.org> Date: 2017-08-10 (Thu, 10 Aug 2017) Changed paths: M config/error_report.yml.sample Log Message: ----------- correct name to type Commit: 5563ecc3ffa7d0565be42eea99276d64ec5232dd https://github.com/galaxyproject/galaxy/commit/5563ecc3ffa7d0565be42eea9927… Author: E Rasche <hxr(a)hx42.org> Date: 2017-08-10 (Thu, 10 Aug 2017) Changed paths: M lib/galaxy/tools/error_reports/plugins/biostars.py Log Message: ----------- fix import order Commit: 00ee109ed4538b6a032489a07807deb7e13c9882 https://github.com/galaxyproject/galaxy/commit/00ee109ed4538b6a032489a07807… Author: E Rasche <hxr(a)hx42.org> Date: 2017-08-10 (Thu, 10 Aug 2017) Changed paths: M lib/galaxy/tools/error_reports/plugins/email.py Log Message: ----------- fix css class Commit: 4c36b5a7a189f9586c061460bfdec7a84b6774c4 https://github.com/galaxyproject/galaxy/commit/4c36b5a7a189f9586c061460bfde… Author: E Rasche <hxr(a)hx42.org> Date: 2017-08-10 (Thu, 10 Aug 2017) Changed paths: M lib/galaxy/tools/error_reports/plugins/sentry.py Log Message: ----------- not a useful test in this location Commit: a2b02065ebbfa9759aad5e56db0c251f7ad514bc https://github.com/galaxyproject/galaxy/commit/a2b02065ebbfa9759aad5e56db0c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-10 (Thu, 10 Aug 2017) Changed paths: M lib/galaxy/web/framework/webapp.py R templates/messages.mako Log Message: ----------- Remove unneeded messages.mako. Commit: 41461235b2429ef84c50336021d9921ca6ef8a4a https://github.com/galaxyproject/galaxy/commit/41461235b2429ef84c50336021d9… Author: E Rasche <hxr(a)hx42.org> Date: 2017-08-10 (Thu, 10 Aug 2017) Changed paths: M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map Log Message: ----------- rebuild client Commit: 6d7d4e9e8e55cfcaa504f43e6288c1d39c0ed932 https://github.com/galaxyproject/galaxy/commit/6d7d4e9e8e55cfcaa504f43e6288… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-10 (Thu, 10 Aug 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js A client/galaxy/scripts/mvc/dataset/dataset-error.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js A client/galaxy/scripts/mvc/job/job-params.js M client/galaxy/style/less/galaxy_bootstrap/overrides.less A config/error_report.yml.sample A doc/source/admin/special_topics/bug_reports.rst M doc/source/admin/special_topics/index.rst M lib/galaxy/app.py M lib/galaxy/config.py M lib/galaxy/jobs/__init__.py A lib/galaxy/tools/error_reports/__init__.py A lib/galaxy/tools/error_reports/plugins/__init__.py A lib/galaxy/tools/error_reports/plugins/biostars.py A lib/galaxy/tools/error_reports/plugins/email.py A lib/galaxy/tools/error_reports/plugins/json.py A lib/galaxy/tools/error_reports/plugins/sentry.py M lib/galaxy/tools/errors.py M lib/galaxy/util/biostar.py M lib/galaxy/util/plugin_config.py M lib/galaxy/webapps/galaxy/api/jobs.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/dataset.py A static/maps/mvc/dataset/dataset-error.js.map M static/maps/mvc/dataset/dataset-li-edit.js.map A static/maps/mvc/job/job-params.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map A static/scripts/mvc/dataset/dataset-error.js M static/scripts/mvc/dataset/dataset-li-edit.js A static/scripts/mvc/job/job-params.js M static/style/blue/base.css M templates/show_params.mako R templates/webapps/galaxy/dataset/errors.mako Log Message: ----------- Merge pull request #4305 from erasche/bug-report-actions Refactor bug reporting into plugins / Remove bug report mako Compare: https://github.com/galaxyproject/galaxy/compare/5e43fcef3c94...6d7d4e9e8e55

1 0

[galaxyproject/galaxy] 3164fc: Allow app specific client side routing
by GitHub 10 Aug '17

10 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 3164fc88d0861f5ea1853803741cdc008e4f9459 https://github.com/galaxyproject/galaxy/commit/3164fc88d0861f5ea1853803741c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-07-19 (Wed, 19 Jul 2017) Changed paths: M lib/galaxy/web/base/controller.py M lib/galaxy/web/framework/base.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/root.py Log Message: ----------- Allow app specific client side routing Commit: e5e390d829e373301ab169a4ecb1a01c4fb6548d https://github.com/galaxyproject/galaxy/commit/e5e390d829e373301ab169a4ecb1… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-07-19 (Wed, 19 Jul 2017) Changed paths: M client/galaxy/scripts/apps/admin.js M lib/galaxy/webapps/galaxy/buildapp.py M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map Log Message: ----------- Create admin specific client router Commit: 0679534a1ff6ade2e3c9341f5a6e95fb59509248 https://github.com/galaxyproject/galaxy/commit/0679534a1ff6ade2e3c9341f5a6e… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-07-19 (Wed, 19 Jul 2017) Changed paths: M client/galaxy/scripts/apps/admin.js M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map Log Message: ----------- Load grid client Commit: 2671f2ae01a53d67c9f38f0cc77c12926b78055b https://github.com/galaxyproject/galaxy/commit/2671f2ae01a53d67c9f38f0cc77c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-07-19 (Wed, 19 Jul 2017) Changed paths: M client/galaxy/scripts/apps/admin.js A client/galaxy/scripts/layout/router.js A static/maps/layout/router.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map A static/scripts/layout/router.js Log Message: ----------- Add shared base router Commit: f74947b816843da19a80060e78996c1e53a9de83 https://github.com/galaxyproject/galaxy/commit/f74947b816843da19a80060e7899… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-07-19 (Wed, 19 Jul 2017) Changed paths: M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/layout/page.js M static/maps/layout/page.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/layout/page.js Log Message: ----------- Used shared base router for admin and analysis app Repack scripts Commit: 770deb58f08bfe2c5c7e885bffe5dd73da12fa8c https://github.com/galaxyproject/galaxy/commit/770deb58f08bfe2c5c7e885bffe5… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-07-19 (Wed, 19 Jul 2017) Changed paths: M client/galaxy/scripts/apps/admin.js M lib/galaxy/web/base/controllers/admin.py M lib/galaxy/webapps/galaxy/buildapp.py M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Use transformed user grid list endpoint Commit: c95ea0956f632d3c874b5c5035ec12fa66c89af0 https://github.com/galaxyproject/galaxy/commit/c95ea0956f632d3c874b5c5035ec… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-07-19 (Wed, 19 Jul 2017) Changed paths: M client/galaxy/scripts/apps/panels/admin-panel.js M lib/galaxy/web/base/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/admin.py M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Move user list endpoint to admin controller Commit: dba9c5cbf3aeacd65f41e2e7a6e5be55f9787379 https://github.com/galaxyproject/galaxy/commit/dba9c5cbf3aeacd65f41e2e7a6e5… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-07-19 (Wed, 19 Jul 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Fix base operations Commit: 8dd816d6db39bb6da9b7f82339df001af6610ef3 https://github.com/galaxyproject/galaxy/commit/8dd816d6db39bb6da9b7f82339df… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-07-19 (Wed, 19 Jul 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Remove out commented legacy operation Commit: 95cf5f7e07c1af2cdb3d08a99af22261291807e8 https://github.com/galaxyproject/galaxy/commit/95cf5f7e07c1af2cdb3d08a99af2… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-07-19 (Wed, 19 Jul 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Reset passwords individually Commit: 9b7a7a2398b185217cc06b526083c7512019074d https://github.com/galaxyproject/galaxy/commit/9b7a7a2398b185217cc06b526083… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-07-19 (Wed, 19 Jul 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Remove unused roles operation Commit: 7f4d199256628fa6f8c4b24c051670d819781206 https://github.com/galaxyproject/galaxy/commit/7f4d199256628fa6f8c4b24c0516… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-07-20 (Thu, 20 Jul 2017) Changed paths: M lib/galaxy/web/base/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/tool_shed/controllers/admin.py Log Message: ----------- Separate toolshed and galaxy, index and center endpoints Commit: 0a7202d68014ceadb408e47b455dfe7e6a348f86 https://github.com/galaxyproject/galaxy/commit/0a7202d68014ceadb408e47b455d… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-07-20 (Thu, 20 Jul 2017) Changed paths: M lib/galaxy/web/base/controllers/admin.py M lib/galaxy/webapps/tool_shed/controllers/admin.py Log Message: ----------- Restore mako based users endpoint for toolshed Commit: c075eae1d5b8425d62c3a4ea47a52c0f44ef4d6a https://github.com/galaxyproject/galaxy/commit/c075eae1d5b8425d62c3a4ea47a5… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-07-20 (Thu, 20 Jul 2017) Changed paths: M lib/galaxy/web/base/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/tool_shed/controllers/admin.py Log Message: ----------- Move tool version and role grid Commit: dca5e70c02cbbc3e443fab13586ced4296baea3c https://github.com/galaxyproject/galaxy/commit/dca5e70c02cbbc3e443fab13586c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-07-20 (Thu, 20 Jul 2017) Changed paths: M lib/galaxy/webapps/tool_shed/controllers/admin.py Log Message: ----------- Replicate legacy admin handler in toolshed before modification Commit: ce2938b6204685862c26fd8a3bc61cb6c4664d37 https://github.com/galaxyproject/galaxy/commit/ce2938b6204685862c26fd8a3bc6… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-07-20 (Thu, 20 Jul 2017) Changed paths: M lib/galaxy/webapps/tool_shed/controllers/admin.py Log Message: ----------- Remove functions not used in toolshed admin, package and reload tools Commit: b504095183be4d3b0b3abea792fc45d12c79de46 https://github.com/galaxyproject/galaxy/commit/b504095183be4d3b0b3abea792fc… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-07-20 (Thu, 20 Jul 2017) Changed paths: M lib/galaxy/webapps/tool_shed/controllers/admin.py Log Message: ----------- Combine both toolshed controllers into one Commit: e967a3321b7209cd10c0079e109bd4c7ed2508a4 https://github.com/galaxyproject/galaxy/commit/e967a3321b7209cd10c0079e109b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-07-24 (Mon, 24 Jul 2017) Changed paths: R lib/galaxy/web/base/controllers/__init__.py R lib/galaxy/web/base/controllers/admin.py M lib/galaxy/webapps/galaxy/api/quotas.py M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/tool_shed/controllers/admin.py A lib/tool_shed/util/admin_util.py Log Message: ----------- Merge branch 'separate_admin_controllers' into revise_page Commit: b6379a9ede442c0e76d50bcea51c91cc8ec22b53 https://github.com/galaxyproject/galaxy/commit/b6379a9ede442c0e76d50bcea51c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-07-24 (Mon, 24 Jul 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Remove legacy user controller endpoint Commit: 3decf1bed960e9daee09adffa993ab4fb46f6d09 https://github.com/galaxyproject/galaxy/commit/3decf1bed960e9daee09adffa993… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-07-24 (Mon, 24 Jul 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Restore multiple password option Commit: b9beb4723b16e270b16597e89039a3880041dc38 https://github.com/galaxyproject/galaxy/commit/b9beb4723b16e270b16597e89039… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-07-24 (Mon, 24 Jul 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Move user identification to shared method Commit: 50948f23695fd1cc9e95c2f95296103212ff3ae1 https://github.com/galaxyproject/galaxy/commit/50948f23695fd1cc9e95c2f95296… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-07-25 (Tue, 25 Jul 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Align admin user grid operations and messages Commit: f33c06dd8d8328dd1abdf846d9ba11037c1fb8ec https://github.com/galaxyproject/galaxy/commit/f33c06dd8d8328dd1abdf846d9ba… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-07-25 (Tue, 25 Jul 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Fix message and user information link Commit: 3829d3dea5b9128b5f7b4e1b5b4d4c6cff10f40a https://github.com/galaxyproject/galaxy/commit/3829d3dea5b9128b5f7b4e1b5b4d… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-07-25 (Tue, 25 Jul 2017) Changed paths: M client/galaxy/scripts/mvc/grid/grid-view.js M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/webapps/galaxy/controllers/admin.py M static/maps/mvc/grid/grid-view.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/grid/grid-view.js Log Message: ----------- Add support for redirecting multiple select operations to the client instead of redirecting through controller Commit: 415939709448ffe9fdec44e749f022eaea9ddcec https://github.com/galaxyproject/galaxy/commit/415939709448ffe9fdec44e749f0… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-07-26 (Wed, 26 Jul 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Keep error messages on form page, remove duplicate center function Commit: 17eff91b2335428d8a5a4b2c86545acae2a96498 https://github.com/galaxyproject/galaxy/commit/17eff91b2335428d8a5a4b2c8654… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-07-26 (Wed, 26 Jul 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/tool_shed/util/admin_util.py Log Message: ----------- Fix toolshed center endpoint Commit: 149de8b44f621aac8274770f813e2b471e025ed5 https://github.com/galaxyproject/galaxy/commit/149de8b44f621aac8274770f813e… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-07-26 (Wed, 26 Jul 2017) Changed paths: M client/galaxy/scripts/mvc/grid/grid-view.js M static/maps/mvc/grid/grid-view.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/grid/grid-view.js Log Message: ----------- Fix request submission Commit: a8720aaf8cecb3182c676a74ef16107e8ecbd047 https://github.com/galaxyproject/galaxy/commit/a8720aaf8cecb3182c676a74ef16… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-07-26 (Wed, 26 Jul 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Make disk size calculation operation async Commit: f449f7e4b7309b7b230187fcf0fdd374c76cb72c https://github.com/galaxyproject/galaxy/commit/f449f7e4b7309b7b230187fcf0fd… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-07-26 (Wed, 26 Jul 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Remove unused dependency Commit: fa9ac881e0b600b73912bf29eac06e3a3dabb609 https://github.com/galaxyproject/galaxy/commit/fa9ac881e0b600b73912bf29eac0… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-07-28 (Fri, 28 Jul 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Remove duplicate callers Commit: d46adeff19d9b36326f70ed15a647676d7d812fe https://github.com/galaxyproject/galaxy/commit/d46adeff19d9b36326f70ed15a64… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-07-28 (Fri, 28 Jul 2017) Changed paths: M lib/galaxy/web/framework/helpers/grids.py Log Message: ----------- Fix href parsing for multiselect operation with redirect Commit: ba0cb1d6058acc4347f751979c950795cb4e1c3b https://github.com/galaxyproject/galaxy/commit/ba0cb1d6058acc4347f751979c95… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-07-28 (Fri, 28 Jul 2017) Changed paths: M client/galaxy/scripts/layout/page.js M static/maps/layout/page.js.map M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/page.js Log Message: ----------- Only initialize router if passed Commit: 876b1ca9040b0d1fa586654d5443331f45e3d845 https://github.com/galaxyproject/galaxy/commit/876b1ca9040b0d1fa586654d5443… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-07-31 (Mon, 31 Jul 2017) Changed paths: M templates/admin/user/user.mako Log Message: ----------- Add masthead header to manage user page Commit: 38125518aff32b6589ea52396f9340ab5db94c32 https://github.com/galaxyproject/galaxy/commit/38125518aff32b6589ea52396f93… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-07-31 (Mon, 31 Jul 2017) Changed paths: M lib/tool_shed/util/admin_util.py Log Message: ----------- Fix user grid controller for toolshed Commit: 308a4adaf5f4034943a7cf4cb2f245f5763b7c0b https://github.com/galaxyproject/galaxy/commit/308a4adaf5f4034943a7cf4cb2f2… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-07-31 (Mon, 31 Jul 2017) Changed paths: M templates/admin/user/user.mako Log Message: ----------- Fix js insertion in user roles mako Commit: 9fdfb41852db80eaaafde4e69e0f3d25b6bb1fbd https://github.com/galaxyproject/galaxy/commit/9fdfb41852db80eaaafde4e69e0f… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-07-31 (Mon, 31 Jul 2017) Changed paths: M templates/admin/user/reset_password.mako Log Message: ----------- Add panels to reset_password mako Commit: 13e09b58550b7e805240e618f98991bb3bebe053 https://github.com/galaxyproject/galaxy/commit/13e09b58550b7e805240e618f989… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-07-31 (Mon, 31 Jul 2017) Changed paths: M templates/admin/user/reset_password.mako M templates/admin/user/user.mako Log Message: ----------- Add messages to form makos Commit: b44e780867999464a1c1cb6675bb622c50848347 https://github.com/galaxyproject/galaxy/commit/b44e780867999464a1c1cb6675bb… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-07-31 (Mon, 31 Jul 2017) Changed paths: M templates/admin/user/reset_password.mako M templates/admin/user/user.mako Log Message: ----------- Enable overflow for form makos Commit: 41a2904128db4f642834754931305791a38db0c3 https://github.com/galaxyproject/galaxy/commit/41a2904128db4f64283475493130… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-01 (Tue, 01 Aug 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js A client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/nls/fr/locale.js M config/tool_shed.ini.sample M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/jobs/runners/cli.py M lib/galaxy/model/mapping.py M lib/galaxy/model/metadata.py M lib/galaxy/security/__init__.py M lib/galaxy/webapps/galaxy/api/quotas.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/tool_shed/buildapp.py M lib/galaxy/workflow/modules.py A static/maps/mvc/dataset/dataset-edit-attributes.js.map M static/maps/mvc/dataset/dataset-li-edit.js.map M static/maps/nls/fr/locale.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map A static/scripts/mvc/dataset/dataset-edit-attributes.js M static/scripts/mvc/dataset/dataset-li-edit.js M static/scripts/nls/fr/locale.js R templates/webapps/galaxy/dataset/edit_attributes.mako Log Message: ----------- Merge branch 'dev' into revise_page Commit: b3e095d66c499a31f3b0a9b0e25690e70f653bec https://github.com/galaxyproject/galaxy/commit/b3e095d66c499a31f3b0a9b0e256… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-01 (Tue, 01 Aug 2017) Changed paths: M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/galaxy.js M lib/galaxy/web/base/controller.py M lib/galaxy/webapps/galaxy/controllers/root.py M static/maps/galaxy.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/galaxy.js Log Message: ----------- Parse url parameters for all client apps Commit: 1f27ad541d7d3dd542152d70ca2d0e207904286b https://github.com/galaxyproject/galaxy/commit/1f27ad541d7d3dd542152d70ca2d… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-01 (Tue, 01 Aug 2017) Changed paths: M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/mvc/grid/grid-view.js M lib/galaxy/webapps/galaxy/controllers/admin.py M static/maps/mvc/grid/grid-view.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/grid/grid-view.js Log Message: ----------- Fix url parameter forwarding to grid view Commit: 068ff8c55d1b7b0c8c22fe2beebd583fa52c4634 https://github.com/galaxyproject/galaxy/commit/068ff8c55d1b7b0c8c22fe2beebd… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-01 (Tue, 01 Aug 2017) Changed paths: M client/galaxy/scripts/apps/panels/admin-panel.js M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Use router to load grid, avoids page refresh Commit: e952a45af9271ce72f676a9df2f799fd5d910031 https://github.com/galaxyproject/galaxy/commit/e952a45af9271ce72f676a9df2f7… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-01 (Tue, 01 Aug 2017) Changed paths: M client/galaxy/scripts/layout/router.js M static/maps/layout/router.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/router.js Log Message: ----------- Reset url parameters when pushing new states Commit: f800b38dbd6957b4b2d21342c5a53aaef72fa23b https://github.com/galaxyproject/galaxy/commit/f800b38dbd6957b4b2d21342c5a5… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-02 (Wed, 02 Aug 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/mvc/user/user-preferences.js R client/galaxy/scripts/mvc/workflow/workflow-configure-menu.js M client/galaxy/scripts/mvc/workflow/workflow.js M client/galaxy/style/less/base.less M config/plugins/webhooks/demo/search/static/script.js M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/buildapp.py M static/maps/mvc/user/user-preferences.js.map M static/maps/mvc/workflow/workflow.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/user/user-preferences.js M static/scripts/mvc/workflow/workflow.js M static/style/blue/base.css Log Message: ----------- Merge branch 'dev' into revise_page Commit: 11244ac2ee3d6c3acae5c44ac1e74d3f61da2767 https://github.com/galaxyproject/galaxy/commit/11244ac2ee3d6c3acae5c44ac1e7… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-02 (Wed, 02 Aug 2017) Changed paths: M client/galaxy/scripts/mvc/grid/grid-template.js M static/maps/mvc/grid/grid-template.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/grid/grid-template.js Log Message: ----------- Escape grid messages Commit: 2626eec1ab893371ea9e2d9ea723bbd1edf9c86a https://github.com/galaxyproject/galaxy/commit/2626eec1ab893371ea9e2d9ea723… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-03 (Thu, 03 Aug 2017) Changed paths: M client/galaxy/scripts/layout/menu.js M static/maps/layout/menu.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/menu.js Log Message: ----------- Use regular anchors for masthead routes Commit: 88b8016b4638e1da23826b9241df1da617ea6245 https://github.com/galaxyproject/galaxy/commit/88b8016b4638e1da23826b9241df… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-03 (Thu, 03 Aug 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-forms.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/proteomics.py M lib/galaxy/jobs/actions/post.py M lib/galaxy/managers/tags.py M static/maps/mvc/workflow/workflow-forms.js.map M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/mvc/workflow/workflow-forms.js M static/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Merge branch 'dev' into revise_page Commit: 8f056c2bbc78040c790255c874b6c321c4ba5b97 https://github.com/galaxyproject/galaxy/commit/8f056c2bbc78040c790255c874b6… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-09 (Wed, 09 Aug 2017) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M client/galaxy/scripts/galaxy.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/user/user-preferences.js M config/datatypes_conf.xml.sample A config/user_preferences_extra_conf.yml.sample M doc/source/admin/special_topics/grt.rst M lib/galaxy/config.py M lib/galaxy/dataset_collections/matching.py M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/molecules.py M lib/galaxy/datatypes/mothur.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/text.py M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/rule_helper.py M lib/galaxy/jobs/runners/util/cli/__init__.py M lib/galaxy/jobs/runners/util/cli/shell/local.py M lib/galaxy/jobs/runners/util/cli/shell/rsh.py M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/objectstore/s3_multipart_upload.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/execute.py M lib/galaxy/tools/parser/interface.py M lib/galaxy/tools/parser/output_objects.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/parser/yaml.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/web/base/controller.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/web/base/pluginframework.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/webapps/galaxy/api/users.py M lib/galaxy/webapps/galaxy/controllers/async.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/workflow/extract.py M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/util/workflow_util.py M lib/tool_shed/utility_containers/utility_container_manager.py R scripts/grt.py R scripts/grt.yml.sample A scripts/grt/export.py A scripts/grt/grt.yml.sample A scripts/grt/upload.py M static/maps/galaxy.js.map M static/maps/layout/menu.js.map M static/maps/mvc/user/user-preferences.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/galaxy.js M static/scripts/layout/menu.js M static/scripts/mvc/user/user-preferences.js M templates/galaxy_client_app.mako M templates/user/login.mako M templates/user/register.mako M templates/webapps/galaxy/history/display_structured.mako M templates/webapps/galaxy/workflow/build_from_current_history.mako M templates/webapps/tool_shed/repository/common.mako M test/api/test_tools.py A test/functional/tools/identifier_source.xml M test/functional/tools/samples_tool_conf.xml M test/shed_functional/base/twilltestcase.py A test/unit/test_remote_shell.py M test/unit/tools/test_parsing.py M test/unit/tools/test_toolbox.py M test/unit/tools_support.py M tox.ini Log Message: ----------- Merge branch 'dev' into revise_page Commit: cfa3220d9f2d257b94795b6f63592459d3011f30 https://github.com/galaxyproject/galaxy/commit/cfa3220d9f2d257b94795b6f6359… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-09 (Wed, 09 Aug 2017) Changed paths: M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M lib/galaxy/managers/tags.py M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py A lib/galaxy/model/migrate/versions/0135_add_library_tags.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/web/base/controller.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py M lib/galaxy/webapps/galaxy/api/library_contents.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M static/maps/mvc/library/library-dataset-view.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/mvc/library/library-dataset-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- Merge branch 'dev' into revise_page Commit: 5e43fcef3c94e9b3f6d700fc5258067d0547e30d https://github.com/galaxyproject/galaxy/commit/5e43fcef3c94e9b3f6d700fc5258… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-10 (Thu, 10 Aug 2017) Changed paths: M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/panels/admin-panel.js M client/galaxy/scripts/galaxy.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/page.js A client/galaxy/scripts/layout/router.js M client/galaxy/scripts/mvc/grid/grid-template.js M client/galaxy/scripts/mvc/grid/grid-view.js M lib/galaxy/web/base/controller.py M lib/galaxy/web/framework/base.py M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/root.py M static/maps/galaxy.js.map M static/maps/layout/menu.js.map M static/maps/layout/page.js.map A static/maps/layout/router.js.map M static/maps/mvc/grid/grid-template.js.map M static/maps/mvc/grid/grid-view.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/galaxy.js M static/scripts/layout/menu.js M static/scripts/layout/page.js A static/scripts/layout/router.js M static/scripts/mvc/grid/grid-template.js M static/scripts/mvc/grid/grid-view.js M templates/admin/user/reset_password.mako M templates/admin/user/user.mako Log Message: ----------- Merge pull request #4341 from guerler/revise_page Admin user grid conversion Compare: https://github.com/galaxyproject/galaxy/compare/429771820200...5e43fcef3c94

1 0

[galaxyproject/galaxy] 64a1e5: Adds tags to library dataset items, and allows use...
by GitHub 09 Aug '17

09 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 64a1e514587ea4d2d9fa870ebb9230212dbec244 https://github.com/galaxyproject/galaxy/commit/64a1e514587ea4d2d9fa870ebb92… Author: Brad Langhorst <langhorst(a)neb.com> Date: 2017-07-05 (Wed, 05 Jul 2017) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M lib/galaxy/managers/tags.py M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py A lib/galaxy/model/migrate/versions/0135_add_library_tags.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- Adds tags to library dataset items, and allows users to specify that tags should be generated from filenames Commit: dcdbfd64d1e94c200c023e1d3b51a8a96c60ca1a https://github.com/galaxyproject/galaxy/commit/dcdbfd64d1e94c200c023e1d3b51… Author: Brad Langhorst <langhorst(a)neb.com> Date: 2017-07-05 (Wed, 05 Jul 2017) Changed paths: M lib/galaxy/web/base/controller.py Log Message: ----------- According to John, this is not actually deprecated Commit: ce7e10cf07ca0061a168bd637cd8ca5a0b88bec5 https://github.com/galaxyproject/galaxy/commit/ce7e10cf07ca0061a168bd637cd8… Author: Brad Langhorst <langhorst(a)neb.com> Date: 2017-07-05 (Wed, 05 Jul 2017) Changed paths: M client/galaxy/scripts/mvc/library/library-dataset-view.js M lib/galaxy/webapps/galaxy/api/lda_datasets.py Log Message: ----------- shows tags in library views Commit: 14a0de0c21e40a88ab9b917db28c5a6365ebc7c9 https://github.com/galaxyproject/galaxy/commit/14a0de0c21e40a88ab9b917db28c… Author: Brad Langhorst <langhorst(a)neb.com> Date: 2017-07-05 (Wed, 05 Jul 2017) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- copies tags on library items to history (and to copies of library items, though I don’t think anything called this) Commit: 72e9e69467125afd9cff9e086c3b153c1f20a289 https://github.com/galaxyproject/galaxy/commit/72e9e69467125afd9cff9e086c3b… Author: Brad Langhorst <langhorst(a)neb.com> Date: 2017-07-05 (Wed, 05 Jul 2017) Changed paths: M lib/galaxy/model/migrate/versions/0135_add_library_tags.py Log Message: ----------- Removes unused import Commit: 3b0c25f73b542022c706787b4cb910a6365c1c75 https://github.com/galaxyproject/galaxy/commit/3b0c25f73b542022c706787b4cb9… Author: Brad Langhorst <langhorst(a)neb.com> Date: 2017-07-05 (Wed, 05 Jul 2017) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Fixes style violation # comment not #comment Commit: efd6d053bcae0c9eeede93dc17e0069302646967 https://github.com/galaxyproject/galaxy/commit/efd6d053bcae0c9eeede93dc17e0… Author: Brad Langhorst <langhorst(a)neb.com> Date: 2017-07-05 (Wed, 05 Jul 2017) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py Log Message: ----------- fixes import order to comply with flake8 Commit: 5add359cde29a9e6ccc7b94b6b9420522e6d5fea https://github.com/galaxyproject/galaxy/commit/5add359cde29a9e6ccc7b94b6b94… Author: Brad Langhorst <langhorst(a)neb.com> Date: 2017-07-05 (Wed, 05 Jul 2017) Changed paths: M lib/galaxy/tools/parameters/grouping.py Log Message: ----------- need to construct this field to avoid a conditional check failure Commit: 33900e5bc913b494611373a9bd926643e760be95 https://github.com/galaxyproject/galaxy/commit/33900e5bc913b494611373a9bd92… Author: Brad Langhorst <langhorst(a)neb.com> Date: 2017-07-05 (Wed, 05 Jul 2017) Changed paths: M lib/galaxy/tools/actions/upload_common.py Log Message: ----------- Rather than trying to find every path into this Function, assume no tagging if dataset does not Have a tag_using_filenames property Commit: dd2224e92ddab51deaf646b04a23ec3112815733 https://github.com/galaxyproject/galaxy/commit/dd2224e92ddab51deaf646b04a23… Author: Brad Langhorst <langhorst(a)neb.com> Date: 2017-07-05 (Wed, 05 Jul 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/library_contents.py Log Message: ----------- updates doc to include tag_using_filenames Commit: 73012c942e77d5fe7993ddbd67559c51c2832813 https://github.com/galaxyproject/galaxy/commit/73012c942e77d5fe7993ddbd6755… Author: Brad Langhorst <langhorst(a)neb.com> Date: 2017-07-05 (Wed, 05 Jul 2017) Changed paths: M lib/galaxy/tools/parameters/grouping.py Log Message: ----------- Allow passing in tag_using_filenames via grouping Commit: cb7b34f320a82cb8e4efe96e72f4165f72e1930c https://github.com/galaxyproject/galaxy/commit/cb7b34f320a82cb8e4efe96e72f4… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-07-06 (Thu, 06 Jul 2017) Changed paths: M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py Log Message: ----------- Swap two more spots initializing TagManagers to new session instead of app Commit: 7b423e19c92868a6a3e7abee2a4ad6e92a03aad8 https://github.com/galaxyproject/galaxy/commit/7b423e19c92868a6a3e7abee2a4a… Author: Brad Langhorst <langhorst(a)neb.com> Date: 2017-08-07 (Mon, 07 Aug 2017) Changed paths: M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py Log Message: ----------- Merge pull request #1 from dannon/library_tags Swap two more spots initializing TagManagers to new session Commit: 06c70d34e2c218b826d813d3dd4e52d077ab94d4 https://github.com/galaxyproject/galaxy/commit/06c70d34e2c218b826d813d3dd4e… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-08-09 (Wed, 09 Aug 2017) Changed paths: M static/maps/mvc/library/library-dataset-view.js.map M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/library/library-dataset-view.js Log Message: ----------- make client Commit: cff21d350dc71b1e7b088985eeeb3f27b0fec1d0 https://github.com/galaxyproject/galaxy/commit/cff21d350dc71b1e7b088985eeeb… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-08-09 (Wed, 09 Aug 2017) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/galaxy.js M client/galaxy/scripts/galaxy.pages.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/scratchbook.js M client/galaxy/scripts/mvc/dataset/data.js A client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/grid/grid-model.js A client/galaxy/scripts/mvc/grid/grid-shared.js M client/galaxy/scripts/mvc/grid/grid-view.js R client/galaxy/scripts/mvc/page/page-list.js M client/galaxy/scripts/mvc/user/user-preferences.js R client/galaxy/scripts/mvc/workflow/workflow-configure-menu.js M client/galaxy/scripts/mvc/workflow/workflow-forms.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/scripts/mvc/workflow/workflow.js M client/galaxy/scripts/nls/fr/locale.js M client/galaxy/scripts/nls/ja/locale.js M client/galaxy/scripts/nls/locale.js M client/galaxy/scripts/viz/circster.js M client/galaxy/scripts/viz/phyloviz.js M client/galaxy/scripts/viz/trackster.js M client/galaxy/scripts/viz/trackster/tracks.js M client/galaxy/scripts/viz/visualization.js M client/galaxy/style/less/base.less M client/galaxy/style/less/galaxy_bootstrap/overrides.less A client/package-lock.json M config/datatypes_conf.xml.sample M config/galaxy.ini.sample M config/plugins/visualizations/charts/static/repository/build/biojs_phylocanvas.js M config/plugins/visualizations/charts/static/repository/build/biojs_phylocanvas.js.map M config/plugins/visualizations/charts/static/repository/build/registry.js M config/plugins/visualizations/charts/static/repository/build/registry.js.map M config/plugins/visualizations/charts/static/repository/visualizations/biojs/phylocanvas/config.js M config/plugins/visualizations/charts/static/repository/visualizations/biojs/phylocanvas/wrapper.js A config/plugins/visualizations/unipept/README.md A config/plugins/visualizations/unipept/config/unipept.xml A config/plugins/visualizations/unipept/static/style.css A config/plugins/visualizations/unipept/static/tooltip.css A config/plugins/visualizations/unipept/static/unipept-visualizations.es5.js A config/plugins/visualizations/unipept/static/unipept-visualizations.es5.js.map A config/plugins/visualizations/unipept/static/unipept_viz.js A config/plugins/visualizations/unipept/templates/glyphicons-86-repeat.png A config/plugins/visualizations/unipept/templates/unipept.mako M config/plugins/webhooks/demo/search/static/script.js M config/tool_conf.xml.main M config/tool_shed.ini.sample A config/user_preferences_extra_conf.yml.sample M doc/source/admin/special_topics/grt.rst M lib/galaxy/config.py M lib/galaxy/dataset_collections/matching.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/molecules.py M lib/galaxy/datatypes/mothur.py M lib/galaxy/datatypes/proteomics.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/text.py M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conditional-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/jobs/actions/post.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/rule_helper.py M lib/galaxy/jobs/runners/cli.py M lib/galaxy/jobs/runners/util/cli/__init__.py M lib/galaxy/jobs/runners/util/cli/shell/local.py M lib/galaxy/jobs/runners/util/cli/shell/rsh.py M lib/galaxy/managers/collections.py M lib/galaxy/managers/tags.py M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py M lib/galaxy/model/metadata.py M lib/galaxy/objectstore/__init__.py A lib/galaxy/objectstore/pithos.py M lib/galaxy/objectstore/s3_multipart_upload.py M lib/galaxy/security/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/data/__init__.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/execute.py M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/parser/interface.py M lib/galaxy/tools/parser/output_objects.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/parser/yaml.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/web/base/controller.py R lib/galaxy/web/base/controllers/__init__.py R lib/galaxy/web/base/controllers/admin.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/web/base/pluginframework.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/webapps/galaxy/api/quotas.py M lib/galaxy/webapps/galaxy/api/users.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/async.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/page.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/galaxy/webapps/tool_shed/buildapp.py M lib/galaxy/webapps/tool_shed/controllers/admin.py M lib/galaxy/workflow/extract.py M lib/galaxy/workflow/modules.py M lib/tool_shed/metadata/metadata_generator.py A lib/tool_shed/util/admin_util.py M lib/tool_shed/util/workflow_util.py M lib/tool_shed/utility_containers/utility_container_manager.py R scripts/grt.py R scripts/grt.yml.sample A scripts/grt/export.py A scripts/grt/grt.yml.sample A scripts/grt/upload.py M scripts/runtime_stats.py M static/maps/galaxy.js.map M static/maps/galaxy.pages.js.map M static/maps/layout/menu.js.map M static/maps/layout/scratchbook.js.map M static/maps/mvc/dataset/data.js.map A static/maps/mvc/dataset/dataset-edit-attributes.js.map M static/maps/mvc/dataset/dataset-li-edit.js.map M static/maps/mvc/grid/grid-model.js.map A static/maps/mvc/grid/grid-shared.js.map M static/maps/mvc/grid/grid-view.js.map R static/maps/mvc/page/page-list.js.map M static/maps/mvc/user/user-preferences.js.map M static/maps/mvc/workflow/workflow-forms.js.map M static/maps/mvc/workflow/workflow-view.js.map M static/maps/mvc/workflow/workflow.js.map M static/maps/nls/fr/locale.js.map M static/maps/nls/ja/locale.js.map M static/maps/nls/locale.js.map M static/maps/viz/circster.js.map M static/maps/viz/phyloviz.js.map M static/maps/viz/trackster.js.map M static/maps/viz/trackster/tracks.js.map M static/maps/viz/visualization.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/galaxy.js M static/scripts/galaxy.pages.js M static/scripts/layout/menu.js M static/scripts/layout/scratchbook.js M static/scripts/mvc/dataset/data.js A static/scripts/mvc/dataset/dataset-edit-attributes.js M static/scripts/mvc/dataset/dataset-li-edit.js A static/scripts/mvc/grid/grid-shared.js M static/scripts/mvc/grid/grid-view.js R static/scripts/mvc/page/page-list.js M static/scripts/mvc/user/user-preferences.js M static/scripts/mvc/workflow/workflow-forms.js M static/scripts/mvc/workflow/workflow-view.js M static/scripts/mvc/workflow/workflow.js M static/scripts/nls/fr/locale.js M static/scripts/nls/ja/locale.js M static/scripts/nls/locale.js M static/scripts/viz/circster.js M static/scripts/viz/phyloviz.js M static/scripts/viz/trackster.js M static/scripts/viz/trackster/tracks.js M static/scripts/viz/visualization.js M static/style/blue/base.css M templates/galaxy_client_app.mako M templates/user/login.mako M templates/user/register.mako R templates/webapps/galaxy/dataset/edit_attributes.mako M templates/webapps/galaxy/history/display_structured.mako R templates/webapps/galaxy/history/list_published.mako M templates/webapps/galaxy/page/editor.mako R templates/webapps/galaxy/page/select_items_grid.mako M templates/webapps/galaxy/requests/common/common.mako R templates/webapps/galaxy/tracks/add_to_viz.mako R templates/webapps/galaxy/tracks/add_tracks.mako R templates/webapps/galaxy/tracks/history_datasets_select_grid.mako R templates/webapps/galaxy/tracks/history_select_grid.mako R templates/webapps/galaxy/tracks/library_datasets_select_grid.mako R templates/webapps/galaxy/visualization/list.mako M templates/webapps/galaxy/workflow/build_from_current_history.mako M templates/webapps/tool_shed/repository/common.mako M test/api/test_tools.py A test/functional/tools/identifier_source.xml M test/functional/tools/samples_tool_conf.xml M test/shed_functional/base/twilltestcase.py A test/unit/test_remote_shell.py M test/unit/tools/test_parsing.py M test/unit/tools/test_toolbox.py M test/unit/tools_support.py M tox.ini Log Message: ----------- Merge branch 'dev' into library_tags Commit: fd0ce1284a9663fab95558fd38ad9477c98d8311 https://github.com/galaxyproject/galaxy/commit/fd0ce1284a9663fab95558fd38ad… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-08-09 (Wed, 09 Aug 2017) Changed paths: M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map Log Message: ----------- make client again... Commit: d52ac533daa8bcfef209f66f8c4e3020d93c09df https://github.com/galaxyproject/galaxy/commit/d52ac533daa8bcfef209f66f8c4e… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-08-09 (Wed, 09 Aug 2017) Changed paths: M lib/galaxy/model/migrate/versions/0135_add_library_tags.py Log Message: ----------- fix indentation Commit: 429771820200acd1a0d0b12c85a39ab7fe530195 https://github.com/galaxyproject/galaxy/commit/429771820200acd1a0d0b12c85a3… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-08-09 (Wed, 09 Aug 2017) Changed paths: M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M lib/galaxy/managers/tags.py M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py A lib/galaxy/model/migrate/versions/0135_add_library_tags.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/web/base/controller.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py M lib/galaxy/webapps/galaxy/api/library_contents.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M static/maps/mvc/library/library-dataset-view.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/library/library-dataset-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- Merge pull request #4262 from bwlang/library_tags Library tags Compare: https://github.com/galaxyproject/galaxy/compare/2e53858a2973...429771820200

1 0

[galaxyproject/galaxy] 7ca5cd: Fix import order and Python3 compatibility for lib...
by GitHub 09 Aug '17

09 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 7ca5cd6585ef8a69f07cfa8362287a800b48281a https://github.com/galaxyproject/galaxy/commit/7ca5cd6585ef8a69f07cfa836228… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-08-09 (Wed, 09 Aug 2017) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M lib/galaxy/web/base/controller.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/web/base/pluginframework.py Log Message: ----------- Fix import order and Python3 compatibility for lib/galaxy/web/base/ Commit: 2e53858a2973aa6d4f95c3e8401d9709809d1da3 https://github.com/galaxyproject/galaxy/commit/2e53858a2973aa6d4f95c3e8401d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-09 (Wed, 09 Aug 2017) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M lib/galaxy/web/base/controller.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/web/base/pluginframework.py Log Message: ----------- Merge pull request #4403 from nsoranzo/flake8-import-order Fix import order and Python3 compatibility for lib/galaxy/web/base/ Compare: https://github.com/galaxyproject/galaxy/compare/c7d7b6c4695b...2e53858a2973

1 0

[galaxyproject/galaxy] 11365e: Bugfix: __str__ method on tool parsers would throw...
by GitHub 09 Aug '17

09 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 11365e9620a5198ca88a35f5a10902744d94a7a3 https://github.com/galaxyproject/galaxy/commit/11365e9620a5198ca88a35f5a109… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-08 (Tue, 08 Aug 2017) Changed paths: M lib/galaxy/tools/parser/interface.py M test/unit/tools/test_parsing.py Log Message: ----------- Bugfix: __str__ method on tool parsers would throw an Exception. Commit: c7d7b6c4695b300739b572b9a94e0de312a0f6ef https://github.com/galaxyproject/galaxy/commit/c7d7b6c4695b300739b572b9a94e… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-08-09 (Wed, 09 Aug 2017) Changed paths: M lib/galaxy/tools/parser/interface.py M test/unit/tools/test_parsing.py Log Message: ----------- Merge pull request #4395 from jmchilton/parser_to_str_fix Bugfix: __str__ method on tool parsers would throw an Exception. Compare: https://github.com/galaxyproject/galaxy/compare/a001145278fb...c7d7b6c4695b

1 0

[galaxyproject/galaxy] aa29b3: Fix job splitting so it happens before dependency ...
by GitHub 09 Aug '17

09 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: aa29b3a1a18d9ee528bd33e58eb2cd8ff180f544 https://github.com/galaxyproject/galaxy/commit/aa29b3a1a18d9ee528bd33e58eb2… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-07 (Mon, 07 Aug 2017) Changed paths: M lib/galaxy/jobs/command_factory.py Log Message: ----------- Fix job splitting so it happens before dependency resolution? Commit: 061eb256409938179d29163ffb522abdc8d9796e https://github.com/galaxyproject/galaxy/commit/061eb256409938179d29163ffb52… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-07 (Mon, 07 Aug 2017) Changed paths: M lib/galaxy/jobs/command_factory.py Log Message: ----------- Add comment about fix for #4381. Commit: c03b29f4855dcce9677e2fe16779d2eb64b1646d https://github.com/galaxyproject/galaxy/commit/c03b29f4855dcce9677e2fe16779… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-08 (Tue, 08 Aug 2017) Changed paths: M lib/galaxy/jobs/command_factory.py Log Message: ----------- Revise comment thanks to note from @mvdbeek. Commit: a001145278fb0642325214123da0c5cec6fc6704 https://github.com/galaxyproject/galaxy/commit/a001145278fb0642325214123da0… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2017-08-09 (Wed, 09 Aug 2017) Changed paths: M lib/galaxy/jobs/command_factory.py Log Message: ----------- Merge pull request #4383 from jmchilton/split_conda Bugfix: Ensure task splitting handles before job resolution. Compare: https://github.com/galaxyproject/galaxy/compare/bc23c26cf421...a001145278fb

1 0

[galaxyproject/galaxy] a06069: Get tools with tool_version in more places
by GitHub 09 Aug '17

09 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a060690c3afa8f296404eb52e4986202d1d985ca https://github.com/galaxyproject/galaxy/commit/a060690c3afa8f296404eb52e498… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-08-08 (Tue, 08 Aug 2017) Changed paths: M lib/galaxy/managers/workflows.py M lib/galaxy/web/base/controller.py M lib/galaxy/workflow/extract.py M lib/tool_shed/util/workflow_util.py Log Message: ----------- Get tools with tool_version in more places Commit: bc23c26cf4210b46f4d17369902fdaec48a16e98 https://github.com/galaxyproject/galaxy/commit/bc23c26cf4210b46f4d17369902f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-08 (Tue, 08 Aug 2017) Changed paths: M lib/galaxy/managers/workflows.py M lib/galaxy/web/base/controller.py M lib/galaxy/workflow/extract.py M lib/tool_shed/util/workflow_util.py Log Message: ----------- Merge pull request #4391 from mvdbeek/more_version_fixes Get tools with tool_version in more places Compare: https://github.com/galaxyproject/galaxy/compare/cf34d8b75958...bc23c26cf421

1 0

[galaxyproject/galaxy] f8648b: Add deeptools datatypes to Galaxy
by GitHub 09 Aug '17

09 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f8648b658629d1313029bb1ad707023c44b626df https://github.com/galaxyproject/galaxy/commit/f8648b658629d1313029bb1ad707… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-08-08 (Tue, 08 Aug 2017) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Add deeptools datatypes to Galaxy Commit: cf34d8b75958db007dcaa5368557dda6850d6e95 https://github.com/galaxyproject/galaxy/commit/cf34d8b75958db007dcaa5368557… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-08 (Tue, 08 Aug 2017) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Merge pull request #4392 from bgruening/deeptools_datatypes Add deepTools datatypes to Galaxy Compare: https://github.com/galaxyproject/galaxy/compare/ff197fe915a6...cf34d8b75958

1 0

[galaxyproject/galaxy] 20f902: Show minimum required galaxy version in tool shed ...
by GitHub 08 Aug '17

08 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 20f90254bfae5e2e0579a69fa37b0c45e874d9ce https://github.com/galaxyproject/galaxy/commit/20f90254bfae5e2e0579a69fa37b… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-08-08 (Tue, 08 Aug 2017) Changed paths: M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/utility_containers/utility_container_manager.py M templates/webapps/tool_shed/repository/common.mako Log Message: ----------- Show minimum required galaxy version in tool shed and galaxy installation process Commit: a77c4587fb9eadfc62da6b8b430154ad18ce1136 https://github.com/galaxyproject/galaxy/commit/a77c4587fb9eadfc62da6b8b4301… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-08-08 (Tue, 08 Aug 2017) Changed paths: M lib/tool_shed/utility_containers/utility_container_manager.py Log Message: ----------- Shorten 'Minimum required Galaxy version' to 'Minimum Galaxy Version' Commit: ff197fe915a67c1ad2ba10ed9a6d433a55b45ee1 https://github.com/galaxyproject/galaxy/commit/ff197fe915a67c1ad2ba10ed9a6d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-08 (Tue, 08 Aug 2017) Changed paths: M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/utility_containers/utility_container_manager.py M templates/webapps/tool_shed/repository/common.mako Log Message: ----------- Merge pull request #4386 from mvdbeek/display_minimum_required_galaxy_version Show minimum required galaxy version in tool shed and galaxy installation process Compare: https://github.com/galaxyproject/galaxy/compare/0da4768c3535...ff197fe915a6

1 0

[galaxyproject/galaxy] fe2d60: Replace list with generator when iterating headers
by GitHub 08 Aug '17

08 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: fe2d607675acf5e18994957fb8ff4422079987ea https://github.com/galaxyproject/galaxy/commit/fe2d607675acf5e18994957fb8ff… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-08-08 (Tue, 08 Aug 2017) Changed paths: M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/molecules.py M lib/galaxy/datatypes/mothur.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/text.py Log Message: ----------- Replace list with generator when iterating headers This should be more memory-friendly. @blankenberg suggested doing this in #4319. Commit: e6c238e234ae4d16d1fd1118c1b7e585ba541645 https://github.com/galaxyproject/galaxy/commit/e6c238e234ae4d16d1fd1118c1b7… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-08-08 (Tue, 08 Aug 2017) Changed paths: M lib/galaxy/datatypes/interval.py Log Message: ----------- Move iter_headers into try clause (thx @nsoranzo) Commit: 43702ccacdbfe925d921dac413c02bb7f65b9c4f https://github.com/galaxyproject/galaxy/commit/43702ccacdbfe925d921dac413c0… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-08-08 (Tue, 08 Aug 2017) Changed paths: M lib/galaxy/datatypes/mothur.py Log Message: ----------- Process the first line when setting metdata for mother.otu files Commit: 0da4768c3535d13c0a141cc30f39e8b86b0c98d1 https://github.com/galaxyproject/galaxy/commit/0da4768c3535d13c0a141cc30f39… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-08 (Tue, 08 Aug 2017) Changed paths: M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/molecules.py M lib/galaxy/datatypes/mothur.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/text.py Log Message: ----------- Merge pull request #4388 from mvdbeek/iter_headers Replace list with generator when iterating headers Compare: https://github.com/galaxyproject/galaxy/compare/196a2bbcf50c...0da4768c3535

1 0

[galaxyproject/galaxy] 24dfba: add new API endpoint which reads a new config file...
by GitHub 08 Aug '17

08 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 24dfbafe4381406f2028af9076f37d30241536f1 https://github.com/galaxyproject/galaxy/commit/24dfbafe4381406f2028af9076f3… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2016-08-05 (Fri, 05 Aug 2016) Changed paths: M lib/galaxy/config.py M lib/galaxy/webapps/galaxy/api/user_preferences.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- add new API endpoint which reads a new config file for new user-preferences Commit: 7426693830e90501225aa0af2e150880c0fa0a67 https://github.com/galaxyproject/galaxy/commit/7426693830e90501225aa0af2e15… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2016-08-05 (Fri, 05 Aug 2016) Changed paths: A config/user_preferences_extra_conf.xml.sample Log Message: ----------- add new config file Commit: 910044e77370bfa4d6a6637d665624949dee7e38 https://github.com/galaxyproject/galaxy/commit/910044e77370bfa4d6a6637d6656… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2016-08-06 (Sat, 06 Aug 2016) Changed paths: A client/galaxy/scripts/mvc/user/extra-information.js M client/galaxy/scripts/mvc/user/user-preferences.js M client/galaxy/style/less/base.less M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/style/blue/base.css Log Message: ----------- Adding extra information page for the User Preferences Commit: d2caf4ce33b8f33806c3915adde87fb0f7b1b711 https://github.com/galaxyproject/galaxy/commit/d2caf4ce33b8f33806c3915adde8… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2016-08-06 (Sat, 06 Aug 2016) Changed paths: M client/galaxy/scripts/mvc/user/user-preferences.js Log Message: ----------- change comment Commit: 8a52c3ae89aaf17b28b2e98afc18543c33fce1ec https://github.com/galaxyproject/galaxy/commit/8a52c3ae89aaf17b28b2e98afc18… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2016-08-06 (Sat, 06 Aug 2016) Changed paths: M client/galaxy/scripts/mvc/user/extra-information.js M config/user_preferences_extra_conf.xml.sample M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Updates Commit: 93d97d83239dcaa71c48d556a75d600efeadba55 https://github.com/galaxyproject/galaxy/commit/93d97d83239dcaa71c48d556a75d… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2016-08-06 (Sat, 06 Aug 2016) Changed paths: M client/galaxy/scripts/mvc/user/extra-information.js M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- add save button and boilerplate Commit: 4268d61b6f32e1910a8a9f063ca801ee84bfb46b https://github.com/galaxyproject/galaxy/commit/4268d61b6f32e1910a8a9f063ca8… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2016-08-11 (Thu, 11 Aug 2016) Changed paths: M client/galaxy/scripts/mvc/user/extra-information.js M config/user_preferences_extra_conf.xml.sample M lib/galaxy/webapps/galaxy/api/user_preferences.py M lib/galaxy/webapps/galaxy/buildapp.py M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map Log Message: ----------- Adding save feature for extra user preferences Commit: 320f17be6ab29e668ec6f278b88c92dca2baf14c https://github.com/galaxyproject/galaxy/commit/320f17be6ab29e668ec6f278b88c… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2016-08-12 (Fri, 12 Aug 2016) Changed paths: M client/galaxy/scripts/mvc/user/extra-information.js M lib/galaxy/webapps/galaxy/api/user_preferences.py M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Adding serialization-deserialization to save dynamic user preferences Commit: ff9f39aa4181323aca1844953c633c9909215662 https://github.com/galaxyproject/galaxy/commit/ff9f39aa4181323aca1844953c63… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2016-08-12 (Fri, 12 Aug 2016) Changed paths: M client/galaxy/scripts/mvc/user/extra-information.js M lib/galaxy/webapps/galaxy/api/user_preferences.py Log Message: ----------- fix if we don't have a prefilled user objecte Commit: 85fde4c16d9fb5ca60a93c05c9c4248c463c5273 https://github.com/galaxyproject/galaxy/commit/85fde4c16d9fb5ca60a93c05c9c4… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2016-08-12 (Fri, 12 Aug 2016) Changed paths: M client/galaxy/scripts/mvc/user/extra-information.js M lib/galaxy/webapps/galaxy/api/user_preferences.py M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- fixing bugs related to empty data or config Commit: 4b53ae0b54790664732700b2b1dd1d45934afc92 https://github.com/galaxyproject/galaxy/commit/4b53ae0b54790664732700b2b1dd… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2016-08-12 (Fri, 12 Aug 2016) Changed paths: M client/galaxy/scripts/mvc/user/extra-information.js M config/user_preferences_extra_conf.xml.sample M lib/galaxy/webapps/galaxy/api/user_preferences.py M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- removing name from the plugin config Commit: b3d7a027243dd1143d98b341f06cc03494412e40 https://github.com/galaxyproject/galaxy/commit/b3d7a027243dd1143d98b341f06c… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2016-08-12 (Fri, 12 Aug 2016) Changed paths: M client/galaxy/scripts/mvc/user/manage-user-information.js M lib/galaxy/webapps/galaxy/api/user_preferences.py Log Message: ----------- bugfix in the json implementation Commit: aaa641b49cc229ea6a654fc8e22c071d7fb78240 https://github.com/galaxyproject/galaxy/commit/aaa641b49cc229ea6a654fc8e22c… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2016-08-13 (Sat, 13 Aug 2016) Changed paths: M client/galaxy/scripts/mvc/user/extra-information.js M lib/galaxy/webapps/galaxy/api/user_preferences.py M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- adding a stable jQuery selector Commit: 81b8f60b00e143e06dadf5f645cdf3ceccb312df https://github.com/galaxyproject/galaxy/commit/81b8f60b00e143e06dadf5f645cd… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2016-11-10 (Thu, 10 Nov 2016) Changed paths: M .ci/first_startup.sh M .ci/flake8_blacklist.txt A .ci/flake8_docstrings_include_list.txt A .ci/flake8_lint_include_list.txt M .ci/flake8_wrapper.sh A .ci/flake8_wrapper_docstrings.sh A .ci/flake8_wrapper_imports.sh M .ci/py3_sources.txt A .ci/validate_test_tools.sh M .gitignore M .travis.yml M CONTRIBUTORS.md M LICENSE.txt M Makefile M client/bower.json M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/history-panel.js A client/galaxy/scripts/layout/generic-nav-view.js M client/galaxy/scripts/layout/masthead.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/layout/panel.js M client/galaxy/scripts/layout/scratchbook.js A client/galaxy/scripts/libs/bbi/bigwig.js A client/galaxy/scripts/libs/bbi/jquery-ajax-native.js A client/galaxy/scripts/libs/bbi/jszlib.js A client/galaxy/scripts/libs/bbi/spans.js A client/galaxy/scripts/libs/jquery.complexify.js M client/galaxy/scripts/libs/jquery/jquery.js M client/galaxy/scripts/libs/raven.js M client/galaxy/scripts/mvc/annotation.js M client/galaxy/scripts/mvc/base-mvc.js A client/galaxy/scripts/mvc/base/controlled-fetch-collection.js M client/galaxy/scripts/mvc/collection/collection-li-edit.js M client/galaxy/scripts/mvc/collection/collection-li.js M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/collection/collection-view.js M client/galaxy/scripts/mvc/dataset/data.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/dataset/dataset-model.js M client/galaxy/scripts/mvc/form/form-data.js M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-repeat.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/history/copy-dialog.js M client/galaxy/scripts/mvc/history/hda-li-edit.js M client/galaxy/scripts/mvc/history/hda-li.js M client/galaxy/scripts/mvc/history/hda-model.js M client/galaxy/scripts/mvc/history/hdca-li.js M client/galaxy/scripts/mvc/history/hdca-model.js M client/galaxy/scripts/mvc/history/history-content-model.js M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/history/history-model.js A client/galaxy/scripts/mvc/history/history-preferences.js M client/galaxy/scripts/mvc/history/history-structure-view.js M client/galaxy/scripts/mvc/history/history-view-annotated.js M client/galaxy/scripts/mvc/history/history-view-edit-current.js M client/galaxy/scripts/mvc/history/history-view-edit.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/history/multi-panel.js M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-folderrow-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/list/list-item.js M client/galaxy/scripts/mvc/list/list-view.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/tool/tool-form-workflow.js M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/scripts/mvc/tool/tools.js M client/galaxy/scripts/mvc/ui/error-modal.js M client/galaxy/scripts/mvc/ui/ui-buttons.js M client/galaxy/scripts/mvc/ui/ui-color-picker.js M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/mvc/ui/ui-modal.js M client/galaxy/scripts/mvc/ui/ui-portlet.js M client/galaxy/scripts/mvc/ui/ui-select-content.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/scripts/mvc/ui/ui-tabs.js A client/galaxy/scripts/mvc/ui/ui-thumbnails.js M client/galaxy/scripts/mvc/upload/composite/composite-row.js M client/galaxy/scripts/mvc/upload/composite/composite-view.js M client/galaxy/scripts/mvc/upload/default/default-row.js M client/galaxy/scripts/mvc/upload/default/default-view.js M client/galaxy/scripts/mvc/upload/upload-button.js M client/galaxy/scripts/mvc/upload/upload-ftp.js M client/galaxy/scripts/mvc/upload/upload-model.js M client/galaxy/scripts/mvc/upload/upload-settings.js M client/galaxy/scripts/mvc/upload/upload-view.js R client/galaxy/scripts/mvc/user/change-password.js R client/galaxy/scripts/mvc/user/manage-user-information.js M client/galaxy/scripts/mvc/user/user-preferences.js A client/galaxy/scripts/mvc/webhooks.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/scripts/ui/search-input.js M client/galaxy/scripts/utils/ajax-queue.js M client/galaxy/scripts/utils/utils.js A client/galaxy/scripts/viz/bbi-data-manager.js M client/galaxy/scripts/viz/trackster/painters.js M client/galaxy/scripts/viz/trackster/tracks.js M client/galaxy/style/less/base.less A client/galaxy/style/less/collection.less R client/galaxy/style/less/collections.less A client/galaxy/style/less/dataset.less A client/galaxy/style/less/flex.less M client/galaxy/style/less/history.less M client/galaxy/style/less/library.less M client/galaxy/style/less/list-item.less M client/galaxy/style/less/ui.less A client/galaxy/style/less/ui/error-modal.less M client/galaxy/style/less/ui/search-input.less M client/galaxy/style/less/upload.less M client/galaxy/style/source_material/circle.py M client/grunt-tasks/install-libs.js M client/webpack.config.js M config/datatypes_conf.xml.sample M config/galaxy.ini.sample M config/job_conf.xml.sample_advanced M config/object_store_conf.xml.sample A config/plugins/interactive_environments/neo/config/allowed_images.yml.sample A config/plugins/interactive_environments/neo/config/neo.ini.sample A config/plugins/interactive_environments/neo/config/neo.xml A config/plugins/interactive_environments/neo/static/js/neo.js A config/plugins/interactive_environments/neo/templates/neo.mako M config/plugins/tours/core.galaxy_ui.yaml M config/plugins/tours/core.history.yaml M config/plugins/tours/core.scratchbook.yaml R config/plugins/visualizations/charts/Gruntfile.js M config/plugins/visualizations/charts/config/charts.xml M config/plugins/visualizations/charts/package.json R config/plugins/visualizations/charts/sample.txt R config/plugins/visualizations/charts/static/app.css R config/plugins/visualizations/charts/static/app.js R config/plugins/visualizations/charts/static/charts/forms/default.js R config/plugins/visualizations/charts/static/charts/jqplot/bar/config.js R config/plugins/visualizations/charts/static/charts/jqplot/bar/logo.png R config/plugins/visualizations/charts/static/charts/jqplot/bar/wrapper.js R config/plugins/visualizations/charts/static/charts/jqplot/boxplot/config.js R config/plugins/visualizations/charts/static/charts/jqplot/boxplot/logo.png R config/plugins/visualizations/charts/static/charts/jqplot/boxplot/wrapper.js R config/plugins/visualizations/charts/static/charts/jqplot/common/config.js R config/plugins/visualizations/charts/static/charts/jqplot/common/plot-config.js R config/plugins/visualizations/charts/static/charts/jqplot/common/wrapper.js R config/plugins/visualizations/charts/static/charts/jqplot/histogram_discrete/config.js R config/plugins/visualizations/charts/static/charts/jqplot/histogram_discrete/logo.png R config/plugins/visualizations/charts/static/charts/jqplot/histogram_discrete/wrapper.js R config/plugins/visualizations/charts/static/charts/jqplot/line/config.js R config/plugins/visualizations/charts/static/charts/jqplot/line/logo.png R config/plugins/visualizations/charts/static/charts/jqplot/line/wrapper.js R config/plugins/visualizations/charts/static/charts/jqplot/scatter/config.js R config/plugins/visualizations/charts/static/charts/jqplot/scatter/logo.png R config/plugins/visualizations/charts/static/charts/jqplot/scatter/wrapper.js R config/plugins/visualizations/charts/static/charts/nvd3/bar/config.js R config/plugins/visualizations/charts/static/charts/nvd3/bar/logo.png R config/plugins/visualizations/charts/static/charts/nvd3/bar/wrapper.js R config/plugins/visualizations/charts/static/charts/nvd3/bar_horizontal/config.js R config/plugins/visualizations/charts/static/charts/nvd3/bar_horizontal/logo.png R config/plugins/visualizations/charts/static/charts/nvd3/bar_horizontal/wrapper.js R config/plugins/visualizations/charts/static/charts/nvd3/bar_horizontal_stacked/config.js R config/plugins/visualizations/charts/static/charts/nvd3/bar_horizontal_stacked/logo.png R config/plugins/visualizations/charts/static/charts/nvd3/bar_horizontal_stacked/wrapper.js R config/plugins/visualizations/charts/static/charts/nvd3/bar_stacked/config.js R config/plugins/visualizations/charts/static/charts/nvd3/bar_stacked/logo.png R config/plugins/visualizations/charts/static/charts/nvd3/bar_stacked/wrapper.js R config/plugins/visualizations/charts/static/charts/nvd3/common/config.js R config/plugins/visualizations/charts/static/charts/nvd3/common/wrapper.js R config/plugins/visualizations/charts/static/charts/nvd3/histogram/config.js R config/plugins/visualizations/charts/static/charts/nvd3/histogram/logo.png R config/plugins/visualizations/charts/static/charts/nvd3/histogram/wrapper.js R config/plugins/visualizations/charts/static/charts/nvd3/histogram_discrete/config.js R config/plugins/visualizations/charts/static/charts/nvd3/histogram_discrete/logo.png R config/plugins/visualizations/charts/static/charts/nvd3/histogram_discrete/wrapper.js R config/plugins/visualizations/charts/static/charts/nvd3/line/config.js R config/plugins/visualizations/charts/static/charts/nvd3/line/logo.png R config/plugins/visualizations/charts/static/charts/nvd3/line/wrapper.js R config/plugins/visualizations/charts/static/charts/nvd3/line_focus/config.js R config/plugins/visualizations/charts/static/charts/nvd3/line_focus/logo.png R config/plugins/visualizations/charts/static/charts/nvd3/line_focus/wrapper.js R config/plugins/visualizations/charts/static/charts/nvd3/pie/config.js R config/plugins/visualizations/charts/static/charts/nvd3/pie/logo.png R config/plugins/visualizations/charts/static/charts/nvd3/pie/wrapper.js R config/plugins/visualizations/charts/static/charts/nvd3/scatter/config.js R config/plugins/visualizations/charts/static/charts/nvd3/scatter/logo.png R config/plugins/visualizations/charts/static/charts/nvd3/scatter/wrapper.js R config/plugins/visualizations/charts/static/charts/nvd3/stackedarea/config.js R config/plugins/visualizations/charts/static/charts/nvd3/stackedarea/logo.png R config/plugins/visualizations/charts/static/charts/nvd3/stackedarea/wrapper.js R config/plugins/visualizations/charts/static/charts/nvd3/stackedarea_full/config.js R config/plugins/visualizations/charts/static/charts/nvd3/stackedarea_full/logo.png R config/plugins/visualizations/charts/static/charts/nvd3/stackedarea_full/wrapper.js R config/plugins/visualizations/charts/static/charts/nvd3/stackedarea_stream/config.js R config/plugins/visualizations/charts/static/charts/nvd3/stackedarea_stream/logo.png R config/plugins/visualizations/charts/static/charts/nvd3/stackedarea_stream/wrapper.js R config/plugins/visualizations/charts/static/charts/others/heatmap/config.js R config/plugins/visualizations/charts/static/charts/others/heatmap/heatmap-parameters.js R config/plugins/visualizations/charts/static/charts/others/heatmap/heatmap-plugin.js R config/plugins/visualizations/charts/static/charts/others/heatmap/logo.png R config/plugins/visualizations/charts/static/charts/others/heatmap/wrapper.js R config/plugins/visualizations/charts/static/charts/others/heatmap_cluster/config.js R config/plugins/visualizations/charts/static/charts/others/heatmap_cluster/logo.png R config/plugins/visualizations/charts/static/charts/others/heatmap_cluster/wrapper.js R config/plugins/visualizations/charts/static/charts/tools.js R config/plugins/visualizations/charts/static/charts/types.js A config/plugins/visualizations/charts/static/client/app.css A config/plugins/visualizations/charts/static/client/app.js A config/plugins/visualizations/charts/static/client/components/model.js A config/plugins/visualizations/charts/static/client/components/screenshot.js A config/plugins/visualizations/charts/static/client/views/description.js A config/plugins/visualizations/charts/static/client/views/editor.js A config/plugins/visualizations/charts/static/client/views/groups.js A config/plugins/visualizations/charts/static/client/views/settings.js A config/plugins/visualizations/charts/static/client/views/viewer.js A config/plugins/visualizations/charts/static/client/views/viewport.js R config/plugins/visualizations/charts/static/library/datasets.js R config/plugins/visualizations/charts/static/library/jobs.js R config/plugins/visualizations/charts/static/library/screenshot.js R config/plugins/visualizations/charts/static/library/storage.js R config/plugins/visualizations/charts/static/models/chart.js R config/plugins/visualizations/charts/static/models/config.js R config/plugins/visualizations/charts/static/plugins/canvg/canvg.js R config/plugins/visualizations/charts/static/plugins/canvg/rgbcolor.js R config/plugins/visualizations/charts/static/plugins/crossfilter/crossfilter.js R config/plugins/visualizations/charts/static/plugins/jqplot/jquery.jqplot.css R config/plugins/visualizations/charts/static/plugins/jqplot/jquery.jqplot.js R config/plugins/visualizations/charts/static/plugins/jqplot/jquery.jqplot.plugins.js R config/plugins/visualizations/charts/static/plugins/jqplot/plugins/jqplot.barRenderer.min.js R config/plugins/visualizations/charts/static/plugins/jqplot/plugins/jqplot.blockRenderer.min.js R config/plugins/visualizations/charts/static/plugins/jqplot/plugins/jqplot.boxplotRenderer.min.js R config/plugins/visualizations/charts/static/plugins/jqplot/plugins/jqplot.canvasAxisLabelRenderer.min.js R config/plugins/visualizations/charts/static/plugins/jqplot/plugins/jqplot.canvasAxisTickRenderer.min.js R config/plugins/visualizations/charts/static/plugins/jqplot/plugins/jqplot.canvasOverlay.min.js R config/plugins/visualizations/charts/static/plugins/jqplot/plugins/jqplot.canvasTextRenderer.min.js R config/plugins/visualizations/charts/static/plugins/jqplot/plugins/jqplot.categoryAxisRenderer.min.js R config/plugins/visualizations/charts/static/plugins/jqplot/plugins/jqplot.cursor.min.js R config/plugins/visualizations/charts/static/plugins/jqplot/plugins/jqplot.enhancedLegendRenderer.min.js R config/plugins/visualizations/charts/static/plugins/jqplot/plugins/jqplot.highlighter.min.js R config/plugins/visualizations/charts/static/plugins/jqplot/plugins/jqplot.ohlcRenderer.min.js R config/plugins/visualizations/charts/static/plugins/nvd3/nv.d3.css R config/plugins/visualizations/charts/static/plugins/nvd3/nv.d3.js A config/plugins/visualizations/charts/static/repository/build/benfred_venn.js A config/plugins/visualizations/charts/static/repository/build/benfred_venn.js.map A config/plugins/visualizations/charts/static/repository/build/biojs_drawrnajs.js A config/plugins/visualizations/charts/static/repository/build/biojs_drawrnajs.js.map A config/plugins/visualizations/charts/static/repository/build/biojs_msa.js A config/plugins/visualizations/charts/static/repository/build/biojs_msa.js.map A config/plugins/visualizations/charts/static/repository/build/cytoscape_basic.js A config/plugins/visualizations/charts/static/repository/build/cytoscape_basic.js.map A config/plugins/visualizations/charts/static/repository/build/jqplot_bar.js A config/plugins/visualizations/charts/static/repository/build/jqplot_bar.js.map A config/plugins/visualizations/charts/static/repository/build/jqplot_boxplot.js A config/plugins/visualizations/charts/static/repository/build/jqplot_boxplot.js.map A config/plugins/visualizations/charts/static/repository/build/jqplot_histogram_discrete.js A config/plugins/visualizations/charts/static/repository/build/jqplot_histogram_discrete.js.map A config/plugins/visualizations/charts/static/repository/build/jqplot_line.js A config/plugins/visualizations/charts/static/repository/build/jqplot_line.js.map A config/plugins/visualizations/charts/static/repository/build/jqplot_scatter.js A config/plugins/visualizations/charts/static/repository/build/jqplot_scatter.js.map A config/plugins/visualizations/charts/static/repository/build/nvd3_bar.js A config/plugins/visualizations/charts/static/repository/build/nvd3_bar.js.map A config/plugins/visualizations/charts/static/repository/build/nvd3_bar_horizontal.js A config/plugins/visualizations/charts/static/repository/build/nvd3_bar_horizontal.js.map A config/plugins/visualizations/charts/static/repository/build/nvd3_bar_horizontal_stacked.js A config/plugins/visualizations/charts/static/repository/build/nvd3_bar_horizontal_stacked.js.map A config/plugins/visualizations/charts/static/repository/build/nvd3_bar_stacked.js A config/plugins/visualizations/charts/static/repository/build/nvd3_bar_stacked.js.map A config/plugins/visualizations/charts/static/repository/build/nvd3_histogram.js A config/plugins/visualizations/charts/static/repository/build/nvd3_histogram.js.map A config/plugins/visualizations/charts/static/repository/build/nvd3_histogram_discrete.js A config/plugins/visualizations/charts/static/repository/build/nvd3_histogram_discrete.js.map A config/plugins/visualizations/charts/static/repository/build/nvd3_line.js A config/plugins/visualizations/charts/static/repository/build/nvd3_line.js.map A config/plugins/visualizations/charts/static/repository/build/nvd3_line_focus.js A config/plugins/visualizations/charts/static/repository/build/nvd3_line_focus.js.map A config/plugins/visualizations/charts/static/repository/build/nvd3_pie.js A config/plugins/visualizations/charts/static/repository/build/nvd3_pie.js.map A config/plugins/visualizations/charts/static/repository/build/nvd3_scatter.js A config/plugins/visualizations/charts/static/repository/build/nvd3_scatter.js.map A config/plugins/visualizations/charts/static/repository/build/nvd3_stackedarea.js A config/plugins/visualizations/charts/static/repository/build/nvd3_stackedarea.js.map A config/plugins/visualizations/charts/static/repository/build/nvd3_stackedarea_full.js A config/plugins/visualizations/charts/static/repository/build/nvd3_stackedarea_full.js.map A config/plugins/visualizations/charts/static/repository/build/nvd3_stackedarea_stream.js A config/plugins/visualizations/charts/static/repository/build/nvd3_stackedarea_stream.js.map A config/plugins/visualizations/charts/static/repository/build/others_example.js A config/plugins/visualizations/charts/static/repository/build/others_example.js.map A config/plugins/visualizations/charts/static/repository/build/others_heatmap.js A config/plugins/visualizations/charts/static/repository/build/others_heatmap.js.map A config/plugins/visualizations/charts/static/repository/build/others_heatmap_cluster.js A config/plugins/visualizations/charts/static/repository/build/others_heatmap_cluster.js.map A config/plugins/visualizations/charts/static/repository/build/pv_viewer.js A config/plugins/visualizations/charts/static/repository/build/pv_viewer.js.map A config/plugins/visualizations/charts/static/repository/build/registry.js A config/plugins/visualizations/charts/static/repository/build/registry.js.map A config/plugins/visualizations/charts/static/repository/build/registry.tmp.js A config/plugins/visualizations/charts/static/repository/plugins/benfred/venn.css A config/plugins/visualizations/charts/static/repository/plugins/benfred/venn.js A config/plugins/visualizations/charts/static/repository/plugins/biojs/biojs.msa.js A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/drawrna.js A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/layouts/layout.js A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/layouts/naview/base.js A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/layouts/naview/connection.js A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/layouts/naview/getnaview.js A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/layouts/naview/loop.js A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/layouts/naview/naview.js A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/layouts/naview/radloop.js A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/layouts/naview/region.js A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/layouts/radiate/getradiate.js A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/models/link.js A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/models/linkcol.js A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/models/ncanno.js A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/models/residue.js A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/models/residuecol.js A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/models/structure.js A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/utils/.Rhistory A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/utils/lasso.js A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/utils/parsedbr.js A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/utils/spectrum.js A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/utils/style.js A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/views/annoview.js A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/views/optspanel.js A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/views/seqpanel.js A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/views/vispanel.js A config/plugins/visualizations/charts/static/repository/plugins/cytoscape/cytoscape.js A config/plugins/visualizations/charts/static/repository/plugins/jqplot/jquery.jqplot.css A config/plugins/visualizations/charts/static/repository/plugins/jqplot/jquery.jqplot.js A config/plugins/visualizations/charts/static/repository/plugins/jqplot/jquery.jqplot.plugins.js A config/plugins/visualizations/charts/static/repository/plugins/nvd3/nv.d3.css A config/plugins/visualizations/charts/static/repository/plugins/nvd3/nv.d3.js A config/plugins/visualizations/charts/static/repository/plugins/pv/viewer.js A config/plugins/visualizations/charts/static/repository/registry.json A config/plugins/visualizations/charts/static/repository/utilities/jobs.js A config/plugins/visualizations/charts/static/repository/utilities/utils.js A config/plugins/visualizations/charts/static/repository/visualizations/benfred/venn/config.js A config/plugins/visualizations/charts/static/repository/visualizations/benfred/venn/logo.png A config/plugins/visualizations/charts/static/repository/visualizations/benfred/venn/wrapper.js A config/plugins/visualizations/charts/static/repository/visualizations/biojs/drawrnajs/config.js A config/plugins/visualizations/charts/static/repository/visualizations/biojs/drawrnajs/logo.png A config/plugins/visualizations/charts/static/repository/visualizations/biojs/drawrnajs/wrapper.js A config/plugins/visualizations/charts/static/repository/visualizations/biojs/msa/config.js A config/plugins/visualizations/charts/static/repository/visualizations/biojs/msa/logo.png A config/plugins/visualizations/charts/static/repository/visualizations/biojs/msa/wrapper.js A config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/basic/config.js A config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/basic/logo.png A config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/basic/wrapper.js A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/bar/config.js A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/bar/logo.png A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/bar/wrapper.js A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/boxplot/config.js A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/boxplot/logo.png A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/boxplot/wrapper.js A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/common/config.js A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/common/plot-config.js A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/common/wrapper.js A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/histogram_discrete/config.js A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/histogram_discrete/logo.png A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/histogram_discrete/wrapper.js A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/line/config.js A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/line/logo.png A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/line/wrapper.js A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/scatter/config.js A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/scatter/logo.png A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/scatter/wrapper.js A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar/config.js A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar/logo.png A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar/wrapper.js A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar_horizontal/config.js A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar_horizontal/logo.png A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar_horizontal/wrapper.js A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar_horizontal_stacked/config.js A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar_horizontal_stacked/logo.png A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar_horizontal_stacked/wrapper.js A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar_stacked/config.js A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar_stacked/logo.png A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar_stacked/wrapper.js A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/common/config.js A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/common/wrapper.js A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/histogram/config.js A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/histogram/logo.png A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/histogram/wrapper.js A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/histogram_discrete/config.js A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/histogram_discrete/logo.png A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/histogram_discrete/wrapper.js A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/line/config.js A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/line/logo.png A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/line/wrapper.js A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/line_focus/config.js A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/line_focus/logo.png A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/line_focus/wrapper.js A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/pie/config.js A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/pie/logo.png A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/pie/wrapper.js A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/scatter/config.js A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/scatter/logo.png A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/scatter/wrapper.js A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/stackedarea/config.js A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/stackedarea/logo.png A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/stackedarea/wrapper.js A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/stackedarea_full/config.js A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/stackedarea_full/logo.png A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/stackedarea_full/wrapper.js A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/stackedarea_stream/config.js A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/stackedarea_stream/logo.png A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/stackedarea_stream/wrapper.js A config/plugins/visualizations/charts/static/repository/visualizations/others/example/config.js A config/plugins/visualizations/charts/static/repository/visualizations/others/example/logo.png A config/plugins/visualizations/charts/static/repository/visualizations/others/example/wrapper.js A config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap/config.js A config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap/heatmap-parameters.js A config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap/heatmap-plugin.js A config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap/logo.png A config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap/wrapper.js A config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap_cluster/config.js A config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap_cluster/logo.png A config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap_cluster/wrapper.js A config/plugins/visualizations/charts/static/repository/visualizations/pv/viewer/config.js A config/plugins/visualizations/charts/static/repository/visualizations/pv/viewer/logo.png A config/plugins/visualizations/charts/static/repository/visualizations/pv/viewer/wrapper.js A config/plugins/visualizations/charts/static/repository/visualizations/utilities/tabular-datasets.js A config/plugins/visualizations/charts/static/repository/visualizations/utilities/tabular-form.js A config/plugins/visualizations/charts/static/repository/visualizations/utilities/tabular-utilities.js R config/plugins/visualizations/charts/static/views/editor.js R config/plugins/visualizations/charts/static/views/groups.js R config/plugins/visualizations/charts/static/views/settings.js R config/plugins/visualizations/charts/static/views/types.js R config/plugins/visualizations/charts/static/views/viewer.js R config/plugins/visualizations/charts/static/views/viewport.js M config/plugins/visualizations/charts/templates/charts.mako A config/plugins/visualizations/charts/webpack.config.js A config/plugins/webhooks/demo/history_test1/config/history_test1.yml A config/plugins/webhooks/demo/history_test2/config/history_test2.yml A config/plugins/webhooks/demo/masthead_test/config/masthead_test.yml A config/plugins/webhooks/demo/phdcomics/config/phdcomics.yaml A config/plugins/webhooks/demo/phdcomics/helper/__init__.py A config/plugins/webhooks/demo/phdcomics/static/script.js A config/plugins/webhooks/demo/phdcomics/static/styles.css A config/plugins/webhooks/demo/trans_object/config/trans_object.yaml A config/plugins/webhooks/demo/trans_object/helper/__init__.py A config/plugins/webhooks/demo/xkcd/config/xkcd.yml A config/plugins/webhooks/demo/xkcd/static/script.js A config/plugins/webhooks/demo/xkcd/static/styles.css M config/reports.ini.sample M config/tool_conf.xml.sample M config/tool_data_table_conf.xml.sample M config/tool_shed.ini.sample M doc/Makefile A doc/parse_gx_xsd.py M doc/patch.py A doc/schema_template.md A doc/source/admin/chat-0.png A doc/source/admin/chat-1.png A doc/source/admin/chat-2.png A doc/source/admin/chat-3.png A doc/source/admin/chat-4.png A doc/source/admin/chat.rst A doc/source/admin/communication_server.png A doc/source/admin/communication_server_rooms.png A doc/source/admin/conda_faq.rst M doc/source/admin/dependency_resolvers.rst A doc/source/admin/images_webhooks/history-menu.png A doc/source/admin/images_webhooks/masthead.png A doc/source/admin/images_webhooks/masthead_trans_object.png A doc/source/admin/images_webhooks/tool.png A doc/source/admin/images_webhooks/workflow.png M doc/source/admin/index.rst M doc/source/admin/interactive_environments.rst R doc/source/admin/interactive_environments_success.png A doc/source/admin/mulled_containers.rst A doc/source/admin/webhooks.rst M doc/source/api/guidelines.rst M doc/source/conf.py A doc/source/dev/build_a_job_runner.rst M doc/source/dev/index.rst A doc/source/dev/inherit.png A doc/source/dev/interactive_environments_success.png A doc/source/dev/queue.png A doc/source/dev/queue_b.png A doc/source/dev/runner_diag.png M doc/source/index.rst M doc/source/lib/galaxy.datatypes.converters.rst M doc/source/lib/galaxy.jobs.rst M doc/source/lib/galaxy.objectstore.rst M doc/source/lib/galaxy.rst M doc/source/lib/galaxy.tools.linters.rst M doc/source/lib/galaxy.tools.parameters.rst R doc/source/lib/galaxy.util.backports.importlib.rst M doc/source/lib/galaxy.util.backports.rst M doc/source/lib/galaxy.util.rst M doc/source/project/issues.rst M doc/source/releases/16.04.rst M doc/source/releases/16.04_announce.rst A doc/source/releases/16.07.rst M doc/source/releases/16.07_announce.rst A doc/source/releases/16.10_announce.rst M doc/source/releases/index.rst A doc/source/slideshow/architecture/galaxy_architecture.md A doc/source/slideshow/architecture/images/backbone-model-view.svg A doc/source/slideshow/architecture/images/cluster_support.svg A doc/source/slideshow/architecture/images/data_managers.svg A doc/source/slideshow/architecture/images/docker-chart.png A doc/source/slideshow/architecture/images/family/team.png A doc/source/slideshow/architecture/images/galaxy_schema.png A doc/source/slideshow/architecture/images/hda.svg A doc/source/slideshow/architecture/images/hda_dataset.plantuml.svg A doc/source/slideshow/architecture/images/hda_dataset.plantuml.txt A doc/source/slideshow/architecture/images/hda_hdca.plantuml.svg A doc/source/slideshow/architecture/images/hda_hdca.plantuml.txt A doc/source/slideshow/architecture/images/jsload.png A doc/source/slideshow/architecture/images/libraries.svg A doc/source/slideshow/architecture/images/library_permissions.svg A doc/source/slideshow/architecture/images/objectstore.plantuml.svg A doc/source/slideshow/architecture/images/objectstore.plantuml.txt A doc/source/slideshow/architecture/images/objectstore_diagram.svg A doc/source/slideshow/architecture/images/plantuml_options.txt A doc/source/slideshow/architecture/images/sequence.json A doc/source/slideshow/architecture/images/server_client.plantuml.svg A doc/source/slideshow/architecture/images/server_client.plantuml.txt A doc/source/slideshow/architecture/images/server_client_old.plantuml.svg A doc/source/slideshow/architecture/images/server_client_old.plantuml.txt A doc/source/slideshow/architecture/images/sqla_arch_small.png A doc/source/slideshow/architecture/images/usegalaxy_webservers.svg A doc/source/slideshow/architecture/images/usegalaxyorg.svg A doc/source/slideshow/architecture/images/webapp.plantuml.svg A doc/source/slideshow/architecture/images/webapp.plantuml.txt A doc/source/slideshow/architecture/images/what-is-webpack.svg A doc/source/slideshow/architecture/images/workflow_definition.svg A doc/source/slideshow/architecture/images/workflow_run.svg A doc/source/slideshow/architecture/images/wsgi_app.svg A doc/source/slideshow/architecture/images/wsgi_request.svg A doc/source/slideshow/architecture/remark-latest.min.js A doc/source/slideshow/architecture/style.css M lib/galaxy/app.py M lib/galaxy/auth/__init__.py M lib/galaxy/auth/providers/alwaysreject.py M lib/galaxy/auth/providers/ldap_ad.py M lib/galaxy/auth/providers/localdb.py M lib/galaxy/auth/providers/pam_auth.py M lib/galaxy/config.py M lib/galaxy/dataset_collections/subcollections.py M lib/galaxy/datatypes/assembly.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/checkers.py M lib/galaxy/datatypes/constructive_solid_geometry.py M lib/galaxy/datatypes/converters/bam_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/interval_to_tabix_converter.py A lib/galaxy/datatypes/converters/tabular_to_dbnsfp.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/dataproviders/__init__.py M lib/galaxy/datatypes/dataproviders/base.py M lib/galaxy/datatypes/dataproviders/column.py M lib/galaxy/datatypes/dataproviders/dataset.py M lib/galaxy/datatypes/dataproviders/decorators.py M lib/galaxy/datatypes/dataproviders/line.py M lib/galaxy/datatypes/images.py M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/metadata.py M lib/galaxy/datatypes/msa.py A lib/galaxy/datatypes/neo4j.py M lib/galaxy/datatypes/ngsindex.py M lib/galaxy/datatypes/proteomics.py M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/set_metadata_tool.xml M lib/galaxy/datatypes/tabular.py A lib/galaxy/datatypes/test/test.CEL M lib/galaxy/datatypes/tracks.py M lib/galaxy/datatypes/triples.py R lib/galaxy/datatypes/util/image_util.py M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conda-environment.txt M lib/galaxy/dependencies/conditional-requirements.txt M lib/galaxy/dependencies/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt M lib/galaxy/exceptions/__init__.py M lib/galaxy/exceptions/error_codes.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/actions/post.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/deferred/data_transfer.py M lib/galaxy/jobs/deferred/manual_data_transfer.py M lib/galaxy/jobs/deferred/pacific_biosciences_smrt_portal.py M lib/galaxy/jobs/metrics/__init__.py M lib/galaxy/jobs/metrics/collectl/__init__.py M lib/galaxy/jobs/metrics/collectl/cli.py M lib/galaxy/jobs/metrics/collectl/processes.py M lib/galaxy/jobs/metrics/collectl/subsystems.py M lib/galaxy/jobs/metrics/formatting.py M lib/galaxy/jobs/metrics/instrumenters/__init__.py M lib/galaxy/jobs/metrics/instrumenters/collectl.py M lib/galaxy/jobs/metrics/instrumenters/core.py M lib/galaxy/jobs/metrics/instrumenters/cpuinfo.py M lib/galaxy/jobs/metrics/instrumenters/env.py M lib/galaxy/jobs/metrics/instrumenters/meminfo.py M lib/galaxy/jobs/metrics/instrumenters/uname.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/cli.py M lib/galaxy/jobs/runners/condor.py M lib/galaxy/jobs/runners/drmaa.py A lib/galaxy/jobs/runners/godocker.py M lib/galaxy/jobs/runners/kubernetes.py M lib/galaxy/jobs/runners/local.py M lib/galaxy/jobs/runners/pbs.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/jobs/runners/slurm.py M lib/galaxy/jobs/runners/state_handlers/resubmit.py M lib/galaxy/jobs/runners/tasks.py M lib/galaxy/jobs/runners/util/__init__.py M lib/galaxy/jobs/runners/util/drmaa/__init__.py M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh M lib/galaxy/jobs/runners/util/job_script/__init__.py M lib/galaxy/managers/__init__.py M lib/galaxy/managers/annotatable.py M lib/galaxy/managers/base.py M lib/galaxy/managers/collections_util.py M lib/galaxy/managers/configuration.py M lib/galaxy/managers/datasets.py M lib/galaxy/managers/hdas.py M lib/galaxy/managers/hdcas.py M lib/galaxy/managers/histories.py M lib/galaxy/managers/history_contents.py M lib/galaxy/managers/libraries.py M lib/galaxy/managers/rbac_secured.py M lib/galaxy/managers/roles.py M lib/galaxy/managers/users.py M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/model/item_attrs.py M lib/galaxy/model/mapping.py M lib/galaxy/model/metadata.py M lib/galaxy/model/migrate/check.py A lib/galaxy/model/migrate/versions/0133_add_dependency_column_to_job.py M lib/galaxy/model/orm/now.py M lib/galaxy/model/tool_shed_install/__init__.py M lib/galaxy/objectstore/__init__.py A lib/galaxy/objectstore/azure_blob.py M lib/galaxy/objectstore/rods.py M lib/galaxy/objectstore/s3.py M lib/galaxy/queue_worker.py M lib/galaxy/queues.py M lib/galaxy/security/validate_user_input.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/cwl/__init__.py M lib/galaxy/tools/cwl/cwltool_deps.py M lib/galaxy/tools/cwl/parser.py M lib/galaxy/tools/cwl/representation.py M lib/galaxy/tools/cwl/runtime_actions.py M lib/galaxy/tools/cwl/schema.py M lib/galaxy/tools/data/__init__.py M lib/galaxy/tools/data_manager/manager.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/brew_exts.py M lib/galaxy/tools/deps/commands.py A lib/galaxy/tools/deps/conda_compat.py M lib/galaxy/tools/deps/conda_util.py A lib/galaxy/tools/deps/container_resolvers/__init__.py A lib/galaxy/tools/deps/container_resolvers/explicit.py A lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/deps/docker_util.py M lib/galaxy/tools/deps/dockerfiles.py A lib/galaxy/tools/deps/installable.py A lib/galaxy/tools/deps/mulled/__init__.py A lib/galaxy/tools/deps/mulled/_cli.py A lib/galaxy/tools/deps/mulled/invfile.lua A lib/galaxy/tools/deps/mulled/mulled_build.py A lib/galaxy/tools/deps/mulled/mulled_build_channel.py A lib/galaxy/tools/deps/mulled/mulled_build_files.py A lib/galaxy/tools/deps/mulled/mulled_build_tool.py A lib/galaxy/tools/deps/mulled/mulled_search.py A lib/galaxy/tools/deps/mulled/util.py M lib/galaxy/tools/deps/requirements.py M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/deps/resolvers/brewed_tool_shed_packages.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/deps/resolvers/galaxy_packages.py M lib/galaxy/tools/deps/resolvers/homebrew.py M lib/galaxy/tools/deps/resolvers/modules.py M lib/galaxy/tools/deps/resolvers/resolver_mixins.py M lib/galaxy/tools/deps/resolvers/tool_shed_packages.py M lib/galaxy/tools/deps/resolvers/unlinked_tool_shed_packages.py M lib/galaxy/tools/deps/views.py M lib/galaxy/tools/exception_handling.py M lib/galaxy/tools/execute.py M lib/galaxy/tools/filter_failed_collection.xml M lib/galaxy/tools/imp_exp/export_history.py M lib/galaxy/tools/loader.py M lib/galaxy/tools/loader_directory.py A lib/galaxy/tools/merge_collection.xml M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/dataset_matcher.py M lib/galaxy/tools/parameters/dynamic_options.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/tools/parameters/meta.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/parameters/validation.py M lib/galaxy/tools/parameters/wrapped.py M lib/galaxy/tools/parameters/wrapped_json.py M lib/galaxy/tools/parser/__init__.py M lib/galaxy/tools/parser/cwl.py M lib/galaxy/tools/parser/factory.py M lib/galaxy/tools/parser/output_actions.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/parser/yaml.py M lib/galaxy/tools/toolbox/__init__.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/cache.py M lib/galaxy/tools/toolbox/filters/__init__.py M lib/galaxy/tools/toolbox/lineages/__init__.py M lib/galaxy/tools/toolbox/lineages/factory.py M lib/galaxy/tools/toolbox/lineages/tool_shed.py M lib/galaxy/tools/toolbox/panel.py M lib/galaxy/tools/toolbox/parser.py M lib/galaxy/tools/toolbox/tags.py M lib/galaxy/tools/toolbox/watcher.py M lib/galaxy/tools/verify/asserts/xml.py M lib/galaxy/tools/verify/test_data.py M lib/galaxy/tools/wrappers.py A lib/galaxy/tools/xsd/LICENSE A lib/galaxy/tools/xsd/README.md A lib/galaxy/tools/xsd/galaxy.jxb A lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/util/__init__.py M lib/galaxy/util/biostar.py M lib/galaxy/util/checkers.py A lib/galaxy/util/filelock.py M lib/galaxy/util/hash_util.py M lib/galaxy/util/heartbeat.py A lib/galaxy/util/image_util.py M lib/galaxy/util/json.py M lib/galaxy/util/lazy_process.py M lib/galaxy/util/none_like.py M lib/galaxy/util/object_wrapper.py M lib/galaxy/util/pastescript/loadwsgi.py M lib/galaxy/util/pastescript/serve.py M lib/galaxy/util/permutations.py A lib/galaxy/util/postfork.py M lib/galaxy/util/properties.py M lib/galaxy/util/sanitize_html.py M lib/galaxy/util/simplegraph.py M lib/galaxy/util/sockets.py M lib/galaxy/util/sqlite.py M lib/galaxy/util/streamball.py M lib/galaxy/util/submodules.py M lib/galaxy/util/template.py M lib/galaxy/util/topsort.py M lib/galaxy/util/validation.py M lib/galaxy/util/xml_macros.py M lib/galaxy/version.py M lib/galaxy/web/__init__.py M lib/galaxy/web/base/controller.py M lib/galaxy/web/buildapp.py M lib/galaxy/web/form_builder.py M lib/galaxy/web/framework/__init__.py M lib/galaxy/web/framework/base.py M lib/galaxy/web/framework/decorators.py M lib/galaxy/web/framework/helpers/__init__.py A lib/galaxy/web/framework/middleware/batch.py M lib/galaxy/web/framework/middleware/error.py M lib/galaxy/web/framework/middleware/remoteuser.py M lib/galaxy/web/framework/middleware/sentry.py M lib/galaxy/web/framework/middleware/static.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/web/proxy/__init__.py R lib/galaxy/web/proxy/filelock.py M lib/galaxy/web/proxy/js/lib/main.js M lib/galaxy/web/proxy/js/lib/proxy.js M lib/galaxy/web/proxy/js/package.json M lib/galaxy/webapps/galaxy/api/configuration.py M lib/galaxy/webapps/galaxy/api/datasets.py M lib/galaxy/webapps/galaxy/api/genomes.py M lib/galaxy/webapps/galaxy/api/history_contents.py M lib/galaxy/webapps/galaxy/api/jobs.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py M lib/galaxy/webapps/galaxy/api/tool_dependencies.py M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/api/tours.py R lib/galaxy/webapps/galaxy/api/user_preferences.py M lib/galaxy/webapps/galaxy/api/users.py A lib/galaxy/webapps/galaxy/api/webhooks.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/forms.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/webapps/galaxy/controllers/mobile.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/webapps/galaxy/controllers/userskeys.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/reports/__init__.py M lib/galaxy/webapps/reports/buildapp.py A lib/galaxy/webapps/reports/controllers/history.py A lib/galaxy/webapps/reports/controllers/tools.py M lib/galaxy/webapps/reports/controllers/users.py M lib/galaxy/webapps/tool_shed/__init__.py M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/app.py M lib/galaxy/webapps/tool_shed/buildapp.py M lib/galaxy/webapps/tool_shed/config.py M lib/galaxy/webapps/tool_shed/controllers/hg.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/webapps/tool_shed/controllers/user.py R lib/galaxy/webapps/tool_shed/framework/middleware/hg.py M lib/galaxy/webapps/tool_shed/model/__init__.py A lib/galaxy/webhooks/__init__.py M lib/galaxy/workflow/extract.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run.py M lib/galaxy/workflow/run_request.py M lib/galaxy/workflow/schedulers/core.py M lib/galaxy_ext/metadata/set_metadata.py M lib/tool_shed/capsule/capsule_manager.py M lib/tool_shed/dependencies/repository/relation_builder.py M lib/tool_shed/galaxy_install/datatypes/custom_datatype_manager.py M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/galaxy_install/installed_repository_manager.py M lib/tool_shed/galaxy_install/migrate/common.py M lib/tool_shed/galaxy_install/migrate/versions/0001_tools.py M lib/tool_shed/galaxy_install/migrate/versions/0002_tools.py M lib/tool_shed/galaxy_install/migrate/versions/0003_tools.py M lib/tool_shed/galaxy_install/migrate/versions/0004_tools.py M lib/tool_shed/galaxy_install/migrate/versions/0005_tools.py M lib/tool_shed/galaxy_install/migrate/versions/0006_tools.py M lib/tool_shed/galaxy_install/migrate/versions/0007_tools.py M lib/tool_shed/galaxy_install/migrate/versions/0008_tools.py M lib/tool_shed/galaxy_install/migrate/versions/0009_tools.py M lib/tool_shed/galaxy_install/migrate/versions/0010_tools.py M lib/tool_shed/galaxy_install/migrate/versions/0011_tools.py M lib/tool_shed/galaxy_install/migrate/versions/0012_tools.py M lib/tool_shed/galaxy_install/repair_repository_manager.py M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/install_environment.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py M lib/tool_shed/galaxy_install/tool_migration_manager.py M lib/tool_shed/galaxy_install/tools/data_manager.py M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py M lib/tool_shed/galaxy_install/update_repository_manager.py M lib/tool_shed/grids/admin_grids.py M lib/tool_shed/grids/repository_grids.py M lib/tool_shed/grids/repository_review_grids.py M lib/tool_shed/managers/repositories.py M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/metadata/repository_metadata_manager.py M lib/tool_shed/repository_types/registry.py M lib/tool_shed/tool_shed_registry.py M lib/tool_shed/tools/data_table_manager.py M lib/tool_shed/tools/tool_version_manager.py M lib/tool_shed/util/hg_util.py M lib/tool_shed/util/metadata_util.py M lib/tool_shed/util/readme_util.py M lib/tool_shed/util/repository_content_util.py M lib/tool_shed/util/repository_util.py M lib/tool_shed/util/shed_util_common.py M lib/tool_shed/util/tool_util.py M lib/tool_shed/util/web_util.py M lib/tool_shed/util/workflow_util.py M lib/tool_shed/utility_containers/utility_container_manager.py M run.sh M run_tests.sh M run_tool_shed.sh M scripts/bootstrap_history.py R scripts/bootstrap_history_announce_template.rst M scripts/common_startup.sh A scripts/communication/communication_server.py A scripts/communication/template/communication.css A scripts/communication/template/communication.html A scripts/communication/template/communication.js M scripts/db_shell.py M scripts/galaxy-main M scripts/nosetests.py A scripts/slideshow/__init__.py A scripts/slideshow/build_slideshow.py A scripts/slideshow/example.md A scripts/slideshow/slideshow_template.html A scripts/slideshow/style.sample.css M scripts/tool_shed/api/common.py M scripts/tool_shed/build_ts_whoosh_index.py A scripts/validate_tools.sh M setup.cfg A static/maps/layout/generic-nav-view.js.map M static/maps/layout/menu.js.map M static/maps/layout/page.js.map M static/maps/layout/panel.js.map M static/maps/layout/scratchbook.js.map A static/maps/libs/bbi/bigwig.js.map A static/maps/libs/bbi/jquery-ajax-native.js.map A static/maps/libs/bbi/jszlib.js.map A static/maps/libs/bbi/spans.js.map A static/maps/libs/jquery.complexify.js.map M static/maps/libs/jquery/jquery.js.map M static/maps/libs/raven.js.map M static/maps/mvc/annotation.js.map M static/maps/mvc/base-mvc.js.map A static/maps/mvc/base/controlled-fetch-collection.js.map M static/maps/mvc/collection/collection-li-edit.js.map M static/maps/mvc/collection/collection-li.js.map M static/maps/mvc/collection/collection-model.js.map M static/maps/mvc/collection/collection-view.js.map M static/maps/mvc/dataset/data.js.map M static/maps/mvc/dataset/dataset-li-edit.js.map M static/maps/mvc/dataset/dataset-li.js.map M static/maps/mvc/dataset/dataset-model.js.map M static/maps/mvc/form/form-data.js.map M static/maps/mvc/form/form-input.js.map M static/maps/mvc/form/form-parameters.js.map M static/maps/mvc/form/form-repeat.js.map M static/maps/mvc/form/form-section.js.map M static/maps/mvc/form/form-view.js.map M static/maps/mvc/history/copy-dialog.js.map M static/maps/mvc/history/hda-li-edit.js.map M static/maps/mvc/history/hda-li.js.map M static/maps/mvc/history/hda-model.js.map M static/maps/mvc/history/hdca-li.js.map M static/maps/mvc/history/hdca-model.js.map M static/maps/mvc/history/history-content-model.js.map M static/maps/mvc/history/history-contents.js.map M static/maps/mvc/history/history-model.js.map A static/maps/mvc/history/history-preferences.js.map M static/maps/mvc/history/history-structure-view.js.map M static/maps/mvc/history/history-view-annotated.js.map M static/maps/mvc/history/history-view-edit-current.js.map M static/maps/mvc/history/history-view-edit.js.map M static/maps/mvc/history/history-view.js.map M static/maps/mvc/history/multi-panel.js.map M static/maps/mvc/history/options-menu.js.map M static/maps/mvc/library/library-dataset-view.js.map M static/maps/mvc/library/library-folderrow-view.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/mvc/list/list-item.js.map M static/maps/mvc/list/list-view.js.map M static/maps/mvc/tool/tool-form-base.js.map M static/maps/mvc/tool/tool-form-composite.js.map M static/maps/mvc/tool/tool-form-workflow.js.map M static/maps/mvc/tool/tool-form.js.map A static/maps/mvc/tool/tool-webhooks.js.map M static/maps/mvc/tool/tools.js.map M static/maps/mvc/ui/error-modal.js.map M static/maps/mvc/ui/ui-buttons.js.map M static/maps/mvc/ui/ui-color-picker.js.map M static/maps/mvc/ui/ui-misc.js.map M static/maps/mvc/ui/ui-modal.js.map M static/maps/mvc/ui/ui-portlet.js.map M static/maps/mvc/ui/ui-select-content.js.map M static/maps/mvc/ui/ui-select-default.js.map M static/maps/mvc/ui/ui-tabs.js.map A static/maps/mvc/ui/ui-thumbnails.js.map M static/maps/mvc/upload/composite/composite-row.js.map M static/maps/mvc/upload/composite/composite-view.js.map M static/maps/mvc/upload/default/default-row.js.map M static/maps/mvc/upload/default/default-view.js.map M static/maps/mvc/upload/upload-button.js.map M static/maps/mvc/upload/upload-ftp.js.map M static/maps/mvc/upload/upload-model.js.map M static/maps/mvc/upload/upload-settings.js.map M static/maps/mvc/upload/upload-view.js.map A static/maps/mvc/user/user-preferences.js.map A static/maps/mvc/webhooks.js.map M static/maps/mvc/workflow/workflow-view.js.map M static/maps/ui/search-input.js.map M static/maps/utils/ajax-queue.js.map M static/maps/utils/utils.js.map A static/maps/viz/bbi-data-manager.js.map M static/maps/viz/trackster/painters.js.map M static/maps/viz/trackster/tracks.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map A static/scripts/layout/generic-nav-view.js M static/scripts/layout/menu.js M static/scripts/layout/page.js M static/scripts/layout/panel.js M static/scripts/layout/scratchbook.js A static/scripts/libs/bbi/bigwig.js A static/scripts/libs/bbi/jquery-ajax-native.js A static/scripts/libs/bbi/jszlib.js A static/scripts/libs/bbi/spans.js A static/scripts/libs/jquery.complexify.js M static/scripts/libs/jquery/jquery.js M static/scripts/libs/raven.js M static/scripts/mvc/annotation.js M static/scripts/mvc/base-mvc.js A static/scripts/mvc/base/controlled-fetch-collection.js M static/scripts/mvc/collection/collection-model.js M static/scripts/mvc/collection/collection-view.js M static/scripts/mvc/dataset/data.js M static/scripts/mvc/dataset/dataset-li-edit.js M static/scripts/mvc/dataset/dataset-li.js M static/scripts/mvc/dataset/dataset-model.js M static/scripts/mvc/form/form-data.js M static/scripts/mvc/form/form-input.js M static/scripts/mvc/form/form-parameters.js M static/scripts/mvc/form/form-repeat.js M static/scripts/mvc/form/form-section.js M static/scripts/mvc/form/form-view.js M static/scripts/mvc/history/copy-dialog.js M static/scripts/mvc/history/hda-model.js M static/scripts/mvc/history/hdca-model.js M static/scripts/mvc/history/history-content-model.js M static/scripts/mvc/history/history-contents.js M static/scripts/mvc/history/history-model.js A static/scripts/mvc/history/history-preferences.js M static/scripts/mvc/history/history-structure-view.js M static/scripts/mvc/history/history-view-annotated.js M static/scripts/mvc/history/history-view-edit-current.js M static/scripts/mvc/history/history-view-edit.js M static/scripts/mvc/history/history-view.js M static/scripts/mvc/history/multi-panel.js M static/scripts/mvc/history/options-menu.js M static/scripts/mvc/library/library-dataset-view.js M static/scripts/mvc/library/library-folderrow-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/list/list-item.js M static/scripts/mvc/list/list-view.js M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/tool/tool-form-composite.js M static/scripts/mvc/tool/tool-form-workflow.js M static/scripts/mvc/tool/tool-form.js A static/scripts/mvc/tool/tool-webhooks.js M static/scripts/mvc/tool/tools.js M static/scripts/mvc/ui/error-modal.js M static/scripts/mvc/ui/ui-buttons.js M static/scripts/mvc/ui/ui-misc.js M static/scripts/mvc/ui/ui-modal.js M static/scripts/mvc/ui/ui-portlet.js M static/scripts/mvc/ui/ui-select-content.js M static/scripts/mvc/ui/ui-select-default.js M static/scripts/mvc/ui/ui-tabs.js A static/scripts/mvc/ui/ui-thumbnails.js M static/scripts/mvc/upload/composite/composite-row.js M static/scripts/mvc/upload/composite/composite-view.js M static/scripts/mvc/upload/default/default-row.js M static/scripts/mvc/upload/default/default-view.js M static/scripts/mvc/upload/upload-ftp.js M static/scripts/mvc/upload/upload-view.js A static/scripts/mvc/user/user-preferences.js A static/scripts/mvc/webhooks.js M static/scripts/mvc/workflow/workflow-view.js M static/scripts/ui/search-input.js M static/scripts/utils/ajax-queue.js M static/scripts/utils/utils.js A static/scripts/viz/bbi-data-manager.js M static/scripts/viz/trackster/painters.js M static/scripts/viz/trackster/tracks.js A static/style/base.css M static/style/blue/base.css M static/style/blue/bootstrap-tour.css M static/style/blue/jquery.rating.css M static/style/blue/library.css R static/style/blue/tool_menu.css R templates/admin/tool_shed_repository/browse_categories.mako A templates/admin/tool_shed_repository/browse_toolsheds.mako M templates/admin/tool_shed_repository/common.mako M templates/admin/tool_shed_repository/manage_repository.mako R templates/admin/tool_shed_repository/preview_repository.mako M templates/admin/tool_shed_repository/reselect_tool_panel_section.mako M templates/admin/tool_shed_repository/select_shed_tool_panel_config.mako M templates/admin/tool_shed_repository/select_tool_panel_section.mako M templates/base.mako M templates/base/base_panels.mako M templates/js-app.mako M templates/show_params.mako M templates/user/change_password.mako A templates/user/communication_settings.mako M templates/user/index.mako M templates/user/info.mako M templates/user/register.mako M templates/user/username.mako M templates/webapps/galaxy/admin/index.mako M templates/webapps/galaxy/dataset/copy_view.mako M templates/webapps/galaxy/history/display.mako M templates/webapps/galaxy/history/embed.mako M templates/webapps/galaxy/history/view.mako M templates/webapps/galaxy/history/view_multiple.mako M templates/webapps/galaxy/library/common/common.mako M templates/webapps/galaxy/workflow/build_from_current_history.mako M templates/webapps/galaxy/workflow/display.mako M templates/webapps/galaxy/workflow/editor.mako R templates/webapps/galaxy/workflow/index.mako R templates/webapps/galaxy/workflow/missing_tools.mako R templates/webapps/galaxy/workflow/myexp_export_content.mako R templates/webapps/galaxy/workflow/rename.mako M templates/webapps/galaxy/workflow/run.mako R templates/webapps/galaxy/workflow/run_complete.mako A templates/webapps/reports/history_and_dataset_per_user.mako A templates/webapps/reports/history_and_dataset_type.mako A templates/webapps/reports/history_per_user.mako M templates/webapps/reports/index.mako A templates/webapps/reports/tool_error_messages.mako A templates/webapps/reports/tool_execution_time.mako A templates/webapps/reports/tool_execution_time_per_month.mako A templates/webapps/reports/tools_and_job_state.mako A templates/webapps/reports/tools_and_job_state_per_month.mako M templates/webapps/tool_shed/admin/index.mako M templates/webapps/tool_shed/group/index.mako M templates/webapps/tool_shed/index.mako M templates/webapps/tool_shed/repository/common.mako M templates/webapps/tool_shed/repository/export_repository.mako M templates/webapps/tool_shed/repository/tool_form.mako A test-data/neostore.zip M test/api/helpers.py A test/api/test_api_batch.py M test/api/test_authenticate.py M test/api/test_dataset_collections.py M test/api/test_histories.py M test/api/test_history_contents.py M test/api/test_libraries.py M test/api/test_page_revisions.py M test/api/test_pages.py M test/api/test_tool_data.py M test/api/test_tools.py M test/api/test_users.py A test/api/test_workflow_batch.ga M test/api/test_workflow_extraction.py M test/api/test_workflows.py M test/api/workflows_format_2/__init__.py M test/api/workflows_format_2/converter.py M test/api/workflows_format_2/main.py M test/base/api.py M test/base/driver_util.py M test/base/integration_util.py M test/base/interactor.py M test/base/test_logging.py M test/base/twilltestcase.py A test/casperjs/api-batch-tests.js M test/functional/test_data_managers.py M test/functional/test_library_templates.py M test/functional/test_toolbox.py A test/functional/tools/color_param.xml M test/functional/tools/column_multi_param.xml M test/functional/tools/column_param.xml A test/functional/tools/dbkey_output_action.xml M test/functional/tools/identifier_collection.xml M test/functional/tools/identifier_multiple.xml M test/functional/tools/identifier_single.xml M test/functional/tools/inputs_as_json.xml A test/functional/tools/metadata_column_names.xml A test/functional/tools/mulled_example_multi_1.xml A test/functional/tools/multi_data_optional.xml M test/functional/tools/multi_output.xml M test/functional/tools/multi_output_assign_primary.xml M test/functional/tools/multi_output_configured.xml R test/functional/tools/multi_page.xml M test/functional/tools/samples_tool_conf.xml M test/functional/tools/tool_directory.xml A test/functional/tools/tool_provided_metadata_1.xml A test/functional/tools/tool_provided_metadata_2.xml A test/functional/tools/tool_provided_metadata_3.xml M test/functional/tools/validation_repeat.xml A test/functional/tools/version_command.py A test/functional/tools/version_command_interpreter.xml A test/functional/tools/version_command_plain.xml A test/functional/tools/version_command_tool_dir.xml M test/functional/workflow.py A test/integration/test_resolvers.py M test/manual/workflows_scaling.py M test/qunit/package.json M test/qunit/test-data/fakeserver.js M test/qunit/tests/form_tests.js M test/qunit/tests/history_contents_model_tests.js M test/qunit/tests/ui_tests.js M test/qunit/tests/upload_dialog_tests.js M test/shed_functional/base/test_db_util.py M test/shed_functional/base/twilltestcase.py M test/shed_functional/functional/test_0300_reset_all_metadata.py M test/shed_functional/functional/test_0310_hg_api_features.py M test/shed_functional/functional/test_1010_install_repository_with_tool_dependencies.py M test/shed_functional/functional/test_1040_install_repository_basic_circular_dependencies.py M test/shed_functional/functional/test_1080_advanced_circular_dependency_installation.py M test/shed_functional/functional/test_1210_uninstall_reinstall_repository_with_tool_dependencies.py M test/shed_functional/functional/test_1300_reset_all_metadata.py M test/shed_functional/functional/test_1400_review_migration_stages.py M test/shed_functional/functional_tests.py M test/unit/jobs/test_job_wrapper.py M test/unit/jobs/test_runner_local.py M test/unit/managers/test_DatasetManager.py M test/unit/managers/test_HistoryManager.py M test/unit/managers/test_UserManager.py M test/unit/shed_unit/test_tool_panel_manager.py M test/unit/test_galaxy_mapping.py M test/unit/test_objectstore.py M test/unit/tools/test_data_parameters.py M test/unit/tools/test_parameter_parsing.py M test/unit/tools/test_parsing.py M test/unit/tools/test_tool_dependency_description.py M test/unit/tools/test_tool_deps.py M test/unit/tools/test_tool_loader.py M test/unit/tools/test_toolbox.py M test/unit/tools/test_toolbox_filters.py M test/unit/tools/test_watcher.py M test/unit/tools/test_wrappers.py M test/unit/tools_support.py M test/unit/unittest_utils/galaxy_mock.py M test/unit/unittest_utils/utility.py M test/unit/workflows/test_run_parameters.py M tool-data/shared/ucsc/ucsc_build_sites.txt.sample M tools/data_source/data_source.py M tools/data_source/hbvar_filter.py M tools/data_source/microbial_import_code.py M tools/data_source/upload.py M tools/data_source/upload.xml M tools/evolution/add_scores.py M tools/evolution/codingSnps_filter.py M tools/extract/extract_genomic_dna.py M tools/filters/axt_to_concat_fasta.py M tools/filters/axt_to_fasta.py M tools/filters/axt_to_lav.py M tools/filters/axt_to_lav_code.py M tools/filters/bed_to_gff_converter.py M tools/filters/convert_characters.py M tools/filters/gff/extract_GFF_Features.py M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_feature_count.py M tools/filters/gff/gtf_filter_by_attribute_values_list.py M tools/filters/gff_to_bed_converter.py M tools/filters/grep.py M tools/filters/gtf_to_bedgraph_converter.py M tools/filters/join.py M tools/filters/lav_to_bed.py M tools/filters/lav_to_bed_code.py M tools/filters/mergeCols.py M tools/filters/random_lines_two_pass.py M tools/filters/secure_hash_message_digest.py M tools/filters/sff_extract.py M tools/filters/trimmer.py M tools/filters/ucsc_gene_bed_to_exon_bed.py M tools/filters/ucsc_gene_bed_to_intron_bed.py M tools/filters/ucsc_gene_table_to_intervals.py M tools/filters/uniq.py M tools/filters/wiggle_to_simple.py M tools/genomespace/genomespace_exporter.py M tools/genomespace/genomespace_file_browser.py M tools/genomespace/genomespace_importer.py M tools/maf/interval2maf.py M tools/maf/interval_maf_to_merged_fasta.py M tools/maf/maf_by_block_number.py M tools/maf/maf_filter.py M tools/maf/maf_limit_size.py M tools/maf/maf_limit_to_species.py M tools/maf/maf_reverse_complement.py M tools/maf/maf_split_by_species.py M tools/maf/maf_stats.py M tools/maf/maf_thread_for_species.py M tools/maf/maf_to_bed.py M tools/maf/maf_to_bed_code.py M tools/maf/maf_to_fasta_concat.py M tools/maf/maf_to_fasta_multiple_sets.py M tools/maf/vcf_to_maf_customtrack.py M tools/metag_tools/shrimp_color_wrapper.py M tools/metag_tools/shrimp_wrapper.py M tools/next_gen_conversion/solid2fastq.py M tools/next_gen_conversion/solid_to_fastq.py M tools/ngs_simulation/ngs_simulation.py M tools/phenotype_association/pagetag.py M tools/phenotype_association/senatag.py M tools/solid_tools/maq_cs_wrapper.py M tools/solid_tools/solid_qual_stats.py M tools/sr_assembly/velvetg_wrapper.py M tools/sr_mapping/bfast_wrapper.py M tools/stats/filtering.py M tools/stats/grouping.py M tools/stats/gsummary.py M tools/visualization/LAJ_code.py M tox.ini Log Message: ----------- Merging with remove_mako_user_pref Commit: 22e465899029de9c2156d13b3f4325a83ff9e023 https://github.com/galaxyproject/galaxy/commit/22e465899029de9c2156d13b3f43… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2016-11-10 (Thu, 10 Nov 2016) Changed paths: M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Stashing changes before pulling from extra_user_preferences Commit: f3ecafd9b561b437c766651a6945067297313b2a https://github.com/galaxyproject/galaxy/commit/f3ecafd9b561b437c766651a6945… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2016-11-10 (Thu, 10 Nov 2016) Changed paths: R client/galaxy/scripts/mvc/user/extra-information.js M config/user_preferences_extra_conf.xml.sample M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Merging with remove_mako_user_pref Commit: 5327042e2f1b2f127fca13febcc1179740deab78 https://github.com/galaxyproject/galaxy/commit/5327042e2f1b2f127fca13febcc1… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2016-11-10 (Thu, 10 Nov 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/users.py M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/style/blue/base.css Log Message: ----------- Adding edit and save extra user preferences if present to manage info screen in User Preferences and merging base.css file in the static folder Commit: cc96000ba0a109dcb31300ca56927e5f07e3e775 https://github.com/galaxyproject/galaxy/commit/cc96000ba0a109dcb31300ca5692… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2016-11-11 (Fri, 11 Nov 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/users.py Log Message: ----------- Updating databse object of extra preferences to take dict() and not list() Commit: 9a114393a539cc4f9256784f852dffb4a94beb41 https://github.com/galaxyproject/galaxy/commit/9a114393a539cc4f9256784f852d… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2016-12-11 (Sun, 11 Dec 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/users.py Log Message: ----------- Adding error message for empty required fields for additional user preferences Commit: ba56bd56fd143ba5b19f1e598ad1533119a1ffd4 https://github.com/galaxyproject/galaxy/commit/ba56bd56fd143ba5b19f1e598ad1… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2016-12-11 (Sun, 11 Dec 2016) Changed paths: M config/galaxy.ini.sample M config/user_preferences_extra_conf.xml.sample Log Message: ----------- Adding changes to config files Commit: 887fe9c4ecac80e7b38fe99003c759727a1b3d15 https://github.com/galaxyproject/galaxy/commit/887fe9c4ecac80e7b38fe99003c7… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2016-12-11 (Sun, 11 Dec 2016) Changed paths: M .ci/flake8_lint_include_list.txt A .ci/jenkins/api/run_tests.sh A .ci/jenkins/framework/run_tests.sh A .ci/jenkins/integration/run_tests.sh A .ci/jenkins/selenium/Dockerfile A .ci/jenkins/selenium/docker-compose.yml A .ci/jenkins/selenium/galaxy.ini A .ci/jenkins/selenium/run_galaxy.bash A .ci/jenkins/selenium/run_tests.sh A .ci/jenkins/toolshed/run_tests.sh M .ci/py3_sources.txt M CONTRIBUTORS.md M Makefile M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/tool-panel.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/mvc/tool/tool-form-workflow.js M client/galaxy/scripts/mvc/tool/tools.js M client/galaxy/scripts/mvc/upload/composite/composite-row.js M client/galaxy/scripts/mvc/upload/default/default-row.js M client/galaxy/scripts/mvc/user/user-preferences.js M client/galaxy/style/less/base.less M client/galaxy/style/less/ui.less M client/galaxy/style/source_material/circle.py M config/datatypes_conf.xml.sample M config/job_conf.xml.sample_advanced M config/plugins/interactive_environments/rstudio/config/allowed_images.yml.sample M config/plugins/interactive_environments/rstudio/static/js/rstudio.js M config/plugins/interactive_environments/rstudio/templates/rstudio.mako M config/plugins/tours/core.galaxy_ui.yaml M config/tool_data_table_conf.xml.sample M contrib/galaxy_config_merger.py M contrib/nagios/check_galaxy.py M cron/add_manual_builds.py M cron/build_chrom_db.py M cron/parse_builds.py M cron/parse_builds_3_sites.py M doc/Makefile A doc/fix_schema_rst.sh M doc/parse_gx_xsd.py M doc/patch.py M doc/source/admin/index.rst M doc/source/admin/interactive_environments.rst M doc/source/admin/webhooks.rst M doc/source/project/organization.rst A doc/source/releases/16.10.rst M doc/source/releases/16.10_announce.rst A doc/source/releases/17.01_announce.rst M lib/galaxy/actions/admin.py M lib/galaxy/auth/__init__.py M lib/galaxy/auth/providers/ldap_ad.py M lib/galaxy/auth/providers/pam_auth.py M lib/galaxy/config.py M lib/galaxy/datatypes/assembly.py M lib/galaxy/datatypes/binary.py A lib/galaxy/datatypes/blast.py M lib/galaxy/datatypes/constructive_solid_geometry.py M lib/galaxy/datatypes/converters/bed_to_fli_converter.xml M lib/galaxy/datatypes/converters/bed_to_gff_converter.py M lib/galaxy/datatypes/converters/bed_to_gff_converter.xml M lib/galaxy/datatypes/converters/bed_to_tabix_converter.xml M lib/galaxy/datatypes/converters/bedgraph_to_array_tree_converter.py M lib/galaxy/datatypes/converters/bedgraph_to_array_tree_converter.xml M lib/galaxy/datatypes/converters/bedgraph_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/bgzip.py M lib/galaxy/datatypes/converters/cml_to_inchi_converter.xml M lib/galaxy/datatypes/converters/cml_to_mol2_converter.xml M lib/galaxy/datatypes/converters/cml_to_sdf_converter.xml M lib/galaxy/datatypes/converters/cml_to_smi_converter.xml M lib/galaxy/datatypes/converters/encodepeak_to_bgzip_converter.xml M lib/galaxy/datatypes/converters/encodepeak_to_tabix_converter.xml M lib/galaxy/datatypes/converters/fasta_to_2bit.xml M lib/galaxy/datatypes/converters/fasta_to_bowtie_base_index_converter.xml M lib/galaxy/datatypes/converters/fasta_to_bowtie_color_index_converter.xml M lib/galaxy/datatypes/converters/fasta_to_len.py M lib/galaxy/datatypes/converters/fasta_to_len.xml M lib/galaxy/datatypes/converters/fasta_to_tabular_converter.xml M lib/galaxy/datatypes/converters/fastq_to_fqtoc.xml M lib/galaxy/datatypes/converters/fastqsolexa_to_fasta_converter.py M lib/galaxy/datatypes/converters/fastqsolexa_to_fasta_converter.xml M lib/galaxy/datatypes/converters/fastqsolexa_to_qual_converter.py M lib/galaxy/datatypes/converters/fastqsolexa_to_qual_converter.xml M lib/galaxy/datatypes/converters/gff_to_bed_converter.py M lib/galaxy/datatypes/converters/gff_to_bed_converter.xml M lib/galaxy/datatypes/converters/gff_to_bgzip_converter.xml M lib/galaxy/datatypes/converters/gff_to_fli_converter.xml M lib/galaxy/datatypes/converters/gff_to_interval_index_converter.py M lib/galaxy/datatypes/converters/gff_to_interval_index_converter.xml M lib/galaxy/datatypes/converters/gff_to_tabix_converter.xml M lib/galaxy/datatypes/converters/inchi_to_cml_converter.xml M lib/galaxy/datatypes/converters/inchi_to_mol2_converter.xml M lib/galaxy/datatypes/converters/inchi_to_mol_converter.xml M lib/galaxy/datatypes/converters/inchi_to_sdf_converter.xml M lib/galaxy/datatypes/converters/inchi_to_smi_converter.xml M lib/galaxy/datatypes/converters/interval_to_bed12_converter.xml M lib/galaxy/datatypes/converters/interval_to_bed6_converter.xml M lib/galaxy/datatypes/converters/interval_to_bed_converter.py M lib/galaxy/datatypes/converters/interval_to_bed_converter.xml M lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.py M lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.xml M lib/galaxy/datatypes/converters/interval_to_bgzip_converter.xml M lib/galaxy/datatypes/converters/interval_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/interval_to_coverage.py M lib/galaxy/datatypes/converters/interval_to_coverage.xml M lib/galaxy/datatypes/converters/interval_to_fli.py M lib/galaxy/datatypes/converters/interval_to_interval_index_converter.py M lib/galaxy/datatypes/converters/interval_to_interval_index_converter.xml M lib/galaxy/datatypes/converters/interval_to_tabix_converter.py M lib/galaxy/datatypes/converters/interval_to_tabix_converter.xml M lib/galaxy/datatypes/converters/len_to_linecount.xml M lib/galaxy/datatypes/converters/maf_to_fasta_converter.xml M lib/galaxy/datatypes/converters/maf_to_interval_converter.xml M lib/galaxy/datatypes/converters/mol2_to_cml_converter.xml M lib/galaxy/datatypes/converters/mol2_to_inchi_converter.xml M lib/galaxy/datatypes/converters/mol2_to_mol_converter.xml M lib/galaxy/datatypes/converters/mol2_to_sdf_converter.xml M lib/galaxy/datatypes/converters/mol2_to_smi_converter.xml M lib/galaxy/datatypes/converters/mol_to_cml_converter.xml M lib/galaxy/datatypes/converters/mol_to_inchi_converter.xml M lib/galaxy/datatypes/converters/mol_to_mol2_converter.xml M lib/galaxy/datatypes/converters/picard_interval_list_to_bed6_converter.py M lib/galaxy/datatypes/converters/picard_interval_list_to_bed6_converter.xml M lib/galaxy/datatypes/converters/pileup_to_interval_index_converter.py M lib/galaxy/datatypes/converters/pileup_to_interval_index_converter.xml M lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.py M lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.xml M lib/galaxy/datatypes/converters/sam_to_bam.py M lib/galaxy/datatypes/converters/sam_to_bam.xml M lib/galaxy/datatypes/converters/sam_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/sdf_to_cml_converter.xml M lib/galaxy/datatypes/converters/sdf_to_inchi_converter.xml M lib/galaxy/datatypes/converters/sdf_to_mol2_converter.xml M lib/galaxy/datatypes/converters/sdf_to_smi_converter.xml M lib/galaxy/datatypes/converters/smi_to_cml_converter.xml M lib/galaxy/datatypes/converters/smi_to_inchi_converter.xml M lib/galaxy/datatypes/converters/smi_to_mol2_converter.xml M lib/galaxy/datatypes/converters/smi_to_mol_converter.xml M lib/galaxy/datatypes/converters/smi_to_sdf_converter.xml M lib/galaxy/datatypes/converters/smi_to_smi_converter.xml M lib/galaxy/datatypes/converters/tabular_to_dbnsfp.py M lib/galaxy/datatypes/converters/tabular_to_dbnsfp.xml M lib/galaxy/datatypes/converters/vcf_to_bgzip_converter.xml M lib/galaxy/datatypes/converters/vcf_to_interval_index_converter.py M lib/galaxy/datatypes/converters/vcf_to_interval_index_converter.xml M lib/galaxy/datatypes/converters/vcf_to_tabix_converter.xml M lib/galaxy/datatypes/converters/vcf_to_vcf_bgzip.py M lib/galaxy/datatypes/converters/wig_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/wiggle_to_array_tree_converter.py M lib/galaxy/datatypes/converters/wiggle_to_array_tree_converter.xml M lib/galaxy/datatypes/converters/wiggle_to_simple_converter.py M lib/galaxy/datatypes/converters/wiggle_to_simple_converter.xml M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/display_applications/parameters.py M lib/galaxy/datatypes/images.py M lib/galaxy/datatypes/msa.py M lib/galaxy/datatypes/neo4j.py M lib/galaxy/datatypes/proteomics.py M lib/galaxy/datatypes/sniff.py A lib/galaxy/datatypes/test/tblastn_four_human_vs_rhodopsin.xml M lib/galaxy/datatypes/triples.py M lib/galaxy/dependencies/dev-requirements.txt M lib/galaxy/exceptions/error_codes.py M lib/galaxy/external_services/actions.py M lib/galaxy/external_services/parameters.py M lib/galaxy/external_services/result_handlers/basic.py M lib/galaxy/external_services/service.py M lib/galaxy/forms/forms.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/actions/post.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/dynamic_tool_destination.py M lib/galaxy/jobs/handler.py M lib/galaxy/jobs/metrics/__init__.py M lib/galaxy/jobs/metrics/collectl/cli.py M lib/galaxy/jobs/metrics/collectl/subsystems.py M lib/galaxy/jobs/metrics/instrumenters/core.py M lib/galaxy/jobs/metrics/instrumenters/cpuinfo.py M lib/galaxy/jobs/metrics/instrumenters/env.py M lib/galaxy/jobs/metrics/instrumenters/meminfo.py M lib/galaxy/jobs/runners/cli.py M lib/galaxy/jobs/runners/slurm.py M lib/galaxy/jobs/runners/util/cli/job/slurm_torque.py M lib/galaxy/jobs/splitters/basic.py M lib/galaxy/managers/collections_util.py M lib/galaxy/managers/configuration.py M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py M lib/galaxy/model/metadata.py M lib/galaxy/model/migrate/versions/0007_sharing_histories.py M lib/galaxy/model/migrate/versions/0008_galaxy_forms.py M lib/galaxy/model/migrate/versions/0010_hda_display_at_authz_table.py M lib/galaxy/model/migrate/versions/0011_v0010_mysql_index_fix.py M lib/galaxy/model/migrate/versions/0012_user_address.py M lib/galaxy/model/migrate/versions/0013_change_lib_item_templates_to_forms.py M lib/galaxy/model/migrate/versions/0016_v0015_mysql_index_fix.py M lib/galaxy/model/migrate/versions/0018_ordered_tags_and_page_tags.py M lib/galaxy/model/migrate/versions/0020_library_upload_job.py M lib/galaxy/model/migrate/versions/0026_cloud_tables.py M lib/galaxy/model/migrate/versions/0050_drop_cloud_tables.py M lib/galaxy/model/migrate/versions/0052_sample_dataset_table.py M lib/galaxy/model/migrate/versions/0091_add_tool_version_tables.py M lib/galaxy/objectstore/pulsar.py M lib/galaxy/objectstore/rods.py M lib/galaxy/queue_worker.py M lib/galaxy/quota/__init__.py M lib/galaxy/sample_tracking/data_transfer.py M lib/galaxy/sample_tracking/request_types.py M lib/galaxy/sample_tracking/sample.py M lib/galaxy/security/__init__.py M lib/galaxy/security/passwords.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/actions/data_manager.py M lib/galaxy/tools/actions/data_source.py M lib/galaxy/tools/actions/history_imp_exp.py M lib/galaxy/tools/actions/metadata.py M lib/galaxy/tools/actions/model_operations.py M lib/galaxy/tools/actions/upload.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/tools/cwl/runtime_actions.py M lib/galaxy/tools/cwl/schema.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/commands.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/deps/mulled/_cli.py M lib/galaxy/tools/deps/mulled/mulled_build.py M lib/galaxy/tools/deps/mulled/mulled_build_channel.py M lib/galaxy/tools/deps/requirements.py M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/deps/resolvers/modules.py M lib/galaxy/tools/deps/views.py M lib/galaxy/tools/execute.py M lib/galaxy/tools/imp_exp/exp_history_to_archive.xml M lib/galaxy/tools/imp_exp/export_history.py M lib/galaxy/tools/lint.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/dataset_matcher.py M lib/galaxy/tools/parameters/input_translation.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/parameters/sanitize.py M lib/galaxy/tools/parameters/validation.py M lib/galaxy/tools/parser/output_actions.py M lib/galaxy/tools/parser/output_collection_def.py M lib/galaxy/tools/test.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/integrated_panel.py M lib/galaxy/tools/toolbox/lineages/tool_shed.py M lib/galaxy/tools/toolbox/parser.py M lib/galaxy/tools/toolbox/watcher.py M lib/galaxy/tools/util/galaxyops/__init__.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/util/__init__.py M lib/galaxy/util/aliaspickler.py M lib/galaxy/util/dbkeys.py M lib/galaxy/util/hash_util.py M lib/galaxy/util/object_wrapper.py M lib/galaxy/util/pastescript/loadwsgi.py M lib/galaxy/util/pastescript/serve.py M lib/galaxy/version.py M lib/galaxy/web/framework/base.py M lib/galaxy/web/framework/middleware/error.py M lib/galaxy/web/framework/middleware/statsd.py M lib/galaxy/web/framework/middleware/translogger.py M lib/galaxy/web/framework/openid_manager.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/webapps/galaxy/api/configuration.py M lib/galaxy/webapps/galaxy/api/tool_dependencies.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/api/users.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/external_services.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/galaxy/controllers/search.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/webapps/reports/config.py M lib/galaxy/webapps/tool_shed/config.py M lib/galaxy/webapps/tool_shed/controllers/groups.py M lib/galaxy/webapps/tool_shed/controllers/user.py M lib/galaxy/webapps/tool_shed/framework/middleware/remoteuser.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0013_add_review_tables.py M lib/galaxy/webapps/tool_shed/util/ratings_util.py M lib/galaxy/workflow/extract.py M lib/galaxy/workflow/run.py M lib/galaxy/workflow/schedulers/core.py M lib/galaxy/workflow/steps.py M lib/galaxy_utils/sequence/fastq.py M lib/galaxy_utils/sequence/vcf.py M lib/mimeparse.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/env_file_builder.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M lib/tool_shed/repository_types/unrestricted.py M lib/tool_shed/tools/tool_validator.py M lib/tool_shed/util/shed_util_common.py M lib/tool_shed/util/tool_util.py M lib/tool_shed/util/web_util.py M lib/tool_shed/util/workflow_util.py M run_tests.sh M scripts/api/data_manager_example_execute.py M scripts/api/example_watch_folder.py M scripts/api/filter_failed_datasets_from_collection.py M scripts/api/form_create_from_xml.py M scripts/api/history_create_history.py M scripts/api/history_delete_history.py M scripts/api/import_library_dataset_to_history.py M scripts/api/import_workflows_from_installed_tool_shed_repository.py M scripts/api/install_tool_shed_repositories.py M scripts/api/library_create_folder.py M scripts/api/library_create_library.py M scripts/api/library_upload_from_import_dir.py M scripts/api/load_data_with_metadata.py M scripts/api/repair_tool_shed_repository.py M scripts/api/request_type_create_from_xml.py M scripts/api/requests_update_state.py M scripts/api/reset_metadata_on_installed_repositories.py M scripts/api/sample_dataset_update_status.py M scripts/api/sample_update_state.py M scripts/api/search.py M scripts/api/sequencer_configuration_create.py M scripts/api/upload_to_history.py M scripts/api/workflow_delete.py M scripts/api/workflow_execute.py M scripts/api/workflow_execute_parameters.py M scripts/api/workflow_import.py M scripts/api/workflow_import_from_file_rpark.py M scripts/auth/pam_auth_helper.py M scripts/bootstrap_history.py M scripts/build_toolbox.py M scripts/build_universe_config.py M scripts/check_galaxy.py M scripts/check_python.py M scripts/cleanup_datasets/admin_cleanup_datasets.py M scripts/cleanup_datasets/cleanup_datasets.py M scripts/cleanup_datasets/pgcleanup.py M scripts/cleanup_datasets/populate_uuid.py M scripts/cleanup_datasets/remove_renamed_datasets_from_disk.py M scripts/cleanup_datasets/rename_purged_datasets.py M scripts/cleanup_datasets/update_dataset_size.py M scripts/cleanup_datasets/update_metadata.py M scripts/common_startup.sh M scripts/communication/communication_server.py M scripts/create_db.py M scripts/data_libraries/build_lucene_index.py M scripts/data_libraries/build_whoosh_index.py M scripts/drmaa_external_killer.py M scripts/drmaa_external_runner.py A scripts/dump_tour.py M scripts/external_chown_script.py M scripts/extract_dataset_part.py M scripts/extract_toolbox_sections.py M scripts/functional_tests.py M scripts/grt.py M scripts/loc_files/create_all_fasta_loc.py M scripts/manage_db.py M scripts/microbes/BeautifulSoup.py M scripts/microbes/create_bacteria_loc_file.py M scripts/microbes/create_bacteria_table.py M scripts/microbes/get_builds_lengths.py M scripts/microbes/harvest_bacteria.py M scripts/others/incorrect_gops_jobs.py M scripts/others/incorrect_gops_join_jobs.py M scripts/set_dataset_sizes.py M scripts/set_user_disk_usage.py M scripts/slideshow/build_slideshow.py M scripts/summarize_timings.py M scripts/sync_reports_config.py M scripts/tool_shed/api/add_repository_registry_entry.py M scripts/tool_shed/api/create_categories.py M scripts/tool_shed/api/create_users.py M scripts/tool_shed/api/export.py M scripts/tool_shed/api/get_filtered_repository_revisions.py M scripts/tool_shed/api/import_capsule.py M scripts/tool_shed/api/remove_repository_registry_entry.py M scripts/tool_shed/api/reset_metadata_on_repositories.py M scripts/tool_shed/bootstrap_tool_shed/bootstrap_util.py M scripts/tool_shed/bootstrap_tool_shed/create_user_with_api_key.py M scripts/tool_shed/build_ts_whoosh_index.py M scripts/tool_shed/check_download_urls.py M scripts/tool_shed/check_filesystem_for_empty_tool_dependency_installation_paths.py M scripts/tool_shed/check_s3_for_empty_tool_dependency_installation_paths.py M scripts/tool_shed/clean_up_tool_dependency_directory.py M scripts/tool_shed/deprecate_repositories_without_metadata.py M scripts/tool_shed/migrate_tools_to_repositories.py M scripts/tool_shed/show_tool_dependency_installation_dir_contents.py M scripts/tools/maf/check_loc_file.py M scripts/tools/re_escape_output.py M scripts/transfer.py M scripts/update_shed_config_path.py M static/maps/layout/menu.js.map M static/maps/mvc/dataset/dataset-li-edit.js.map M static/maps/mvc/dataset/dataset-li.js.map M static/maps/mvc/form/form-section.js.map M static/maps/mvc/history/options-menu.js.map M static/maps/mvc/tool/tool-form-workflow.js.map M static/maps/mvc/tool/tools.js.map M static/maps/mvc/upload/composite/composite-row.js.map M static/maps/mvc/upload/default/default-row.js.map M static/maps/mvc/user/user-preferences.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/layout/menu.js M static/scripts/mvc/dataset/dataset-li-edit.js M static/scripts/mvc/form/form-section.js M static/scripts/mvc/history/options-menu.js M static/scripts/mvc/tool/tool-form-workflow.js M static/scripts/mvc/tool/tools.js M static/scripts/mvc/upload/composite/composite-row.js M static/scripts/mvc/upload/default/default-row.js M static/scripts/mvc/user/user-preferences.js M static/style/blue/base.css M static/welcome.html.sample M templates/admin/tool_shed_repository/common.mako M templates/admin/tool_shed_repository/select_tool_panel_section.mako M templates/show_params.mako R templates/user/change_password.mako R templates/user/communication_settings.mako R templates/user/edit_address.mako R templates/user/new_address.mako R templates/user/permissions.mako M templates/user/register.mako R templates/user/toolbox_filters.mako R templates/user/username.mako R templates/webapps/galaxy/user/api_keys.mako M templates/webapps/galaxy/user/list_users.mako R templates/webapps/galaxy/user/manage_info.mako M templates/webapps/galaxy/workflow/editor.mako M templates/webapps/galaxy/workflow/list.mako M templates/webapps/tool_shed/repository/common.mako A templates/webapps/tool_shed/user/api_keys.mako A templates/webapps/tool_shed/user/change_password.mako A templates/webapps/tool_shed/user/index.mako A templates/webapps/tool_shed/user/username.mako A test-data/bam_from_sam.bam A test-data/sam_with_header.sam M test/api/test_api_batch.py A test/api/test_configuration.py M test/api/test_datasets.py M test/api/test_histories.py M test/api/test_history_contents_provenance.py M test/api/test_users.py M test/api/test_workflows.py M test/api/workflows_format_2/main.py M test/base/api.py M test/base/api_asserts.py M test/base/driver_util.py M test/base/interactor.py M test/base/twilltestcase.py R test/casperjs/anon-history-tests.js R test/casperjs/api-batch-tests.js R test/casperjs/api-configuration-tests.js R test/casperjs/api-history-tests.js R test/casperjs/api-tool-tests.js R test/casperjs/api-user-tests.js R test/casperjs/hda-state-tests.js R test/casperjs/history-options-tests.js R test/casperjs/history-panel-tests.js R test/casperjs/history-share-tests.js R test/casperjs/login-tests.js R test/casperjs/registration-tests.js R test/casperjs/upload-tests.js M test/functional/test_library_templates.py A test/functional/tools/for_tours/filtering.py A test/functional/tools/for_tours/filtering.xml A test/functional/tools/sam_to_bam.xml M test/functional/tools/sample_datatypes_conf.xml M test/functional/tools/samples_tool_conf.xml A test/galaxy_selenium/__init__.py A test/galaxy_selenium/cli.py A test/galaxy_selenium/data.py A test/galaxy_selenium/driver_factory.py A test/galaxy_selenium/has_driver.py A test/galaxy_selenium/navigates_galaxy.py A test/galaxy_selenium/navigation-data.yml A test/galaxy_selenium/sizzle.py M test/integration/test_resolvers.py M test/manual/workflows_scaling.py A test/selenium_tests/__init__.py A test/selenium_tests/framework.py A test/selenium_tests/test_anon_history.py A test/selenium_tests/test_history_dataset_state.py A test/selenium_tests/test_history_options.py A test/selenium_tests/test_history_panel.py A test/selenium_tests/test_history_sharing.py A test/selenium_tests/test_login.py A test/selenium_tests/test_registration.py A test/selenium_tests/test_stock_tours.py A test/selenium_tests/test_uploads.py A test/selenium_tests/test_workflow_editor.py M test/shed_functional/base/twilltestcase.py M test/shed_functional/functional/test_1010_install_repository_with_tool_dependencies.py M test/shed_functional/functional/test_1140_simple_repository_dependency_multiple_owners.py M test/shed_functional/functional/test_1210_uninstall_reinstall_repository_with_tool_dependencies.py M test/unit/dataset_collections/test_matching.py M test/unit/datatypes/dataproviders/test_base_dataproviders.py M test/unit/datatypes/dataproviders/test_line_dataproviders.py M test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py M test/unit/jobs/test_command_factory.py M test/unit/jobs/test_job_configuration.py M test/unit/jobs/test_job_output_checker.py M test/unit/jobs/test_job_wrapper.py M test/unit/jobs/test_mapper.py M test/unit/jobs/test_rule_helper.py M test/unit/jobs/test_runner_local.py M test/unit/managers/base.py M test/unit/managers/test_CollectionManager.py M test/unit/managers/test_DatasetManager.py M test/unit/managers/test_HDAManager.py M test/unit/managers/test_HDCAManager.py M test/unit/managers/test_HistoryContentsManager.py M test/unit/managers/test_HistoryManager.py M test/unit/managers/test_UserManager.py M test/unit/shed_unit/test_fabric_util.py M test/unit/shed_unit/test_td_common_util.py M test/unit/shed_unit/test_tool_panel_manager.py M test/unit/test_galaxy_transactions.py M test/unit/test_routes.py M test/unit/test_sockets.py M test/unit/tools/test_actions.py M test/unit/tools/test_citations.py M test/unit/tools/test_collect_primary_datasets.py M test/unit/tools/test_column_parameters.py M test/unit/tools/test_conda_resolution.py M test/unit/tools/test_data_parameters.py M test/unit/tools/test_dataset_matcher.py M test/unit/tools/test_evaluation.py M test/unit/tools/test_execution.py M test/unit/tools/test_history_imp_exp.py M test/unit/tools/test_parameter_parsing.py M test/unit/tools/test_select_parameters.py M test/unit/tools/test_tool_external_files.py M test/unit/tools/test_toolbox.py M test/unit/tools/test_wrappers.py M test/unit/unittest_utils/galaxy_mock.py M test/unit/unittest_utils/tempfilecache.py M test/unit/unittest_utils/utility.py M test/unit/visualizations/plugins/test_VisualizationPlugin.py M test/unit/visualizations/plugins/test_VisualizationsRegistry.py M test/unit/web/base/test_HookPluginManager.py M test/unit/web/base/test_PageServingPluginManager.py M test/unit/web/base/test_PluginManager.py M test/unit/web/framework/test_webapp.py M test/unit/workflows/test_modules.py M test/unit/workflows/test_run_parameters.py M test/unit/workflows/test_workflow_progress.py M test/unit/workflows/workflow_support.py A tool-data/blastdb.loc.sample A tool-data/blastdb_d.loc.sample A tool-data/blastdb_p.loc.sample M tools/data_source/data_source.py M tools/data_source/fetch.py M tools/data_source/genbank.py M tools/data_source/upload.py M tools/evolution/add_scores.py M tools/extract/extract_genomic_dna.py M tools/extract/liftOver_wrapper.py M tools/filters/axt_to_fasta.py M tools/filters/bed_to_gff_converter.py M tools/filters/catWrapper.py M tools/filters/convert_characters.py M tools/filters/gff/extract_GFF_Features.py M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_feature_count.py M tools/filters/gff/gtf_filter_by_attribute_values_list.py M tools/filters/gff_to_bed_converter.py M tools/filters/grep.py M tools/filters/gtf_to_bedgraph_converter.py M tools/filters/join.py M tools/filters/joinWrapper.py M tools/filters/lav_to_bed.py M tools/filters/mergeCols.py M tools/filters/random_lines_two_pass.py M tools/filters/randomlines.py M tools/filters/secure_hash_message_digest.py M tools/filters/sorter.py M tools/filters/trimmer.py M tools/filters/ucsc_gene_bed_to_exon_bed.py M tools/filters/ucsc_gene_bed_to_intron_bed.py M tools/filters/ucsc_gene_table_to_intervals.py M tools/filters/uniq.py M tools/filters/wiggle_to_simple.py M tools/genomespace/genomespace_exporter.py M tools/genomespace/genomespace_file_browser.py M tools/genomespace/genomespace_importer.py M tools/maf/interval2maf.py M tools/maf/interval_maf_to_merged_fasta.py M tools/maf/maf_by_block_number.py M tools/maf/maf_filter.py M tools/maf/maf_limit_size.py M tools/maf/maf_limit_to_species.py M tools/maf/maf_reverse_complement.py M tools/maf/maf_split_by_species.py M tools/maf/maf_stats.py M tools/maf/maf_thread_for_species.py M tools/maf/maf_to_bed.py M tools/maf/maf_to_fasta_multiple_sets.py M tools/maf/maf_to_interval.py M tools/maf/vcf_to_maf_customtrack.py M tools/meme/fimo_wrapper.py M tools/metag_tools/blat_wrapper.py M tools/next_gen_conversion/fastq_conversions.py M tools/next_gen_conversion/fastq_gen_conv.py M tools/next_gen_conversion/solid2fastq.py M tools/next_gen_conversion/solid_to_fastq.py M tools/ngs_simulation/ngs_simulation.py M tools/phenotype_association/pagetag.py M tools/phenotype_association/senatag.py M tools/solid_tools/maq_cs_wrapper.py M tools/solid_tools/solid_qual_stats.py M tools/sr_assembly/velveth_wrapper.py M tools/sr_mapping/bfast_wrapper.py M tools/sr_mapping/srma_wrapper.py M tools/stats/aggregate_scores_in_intervals.py M tools/stats/filtering.py M tools/stats/grouping.py M tools/stats/gsummary.py Log Message: ----------- Merging with dev Commit: 748f85e700f6a23d681edc74f2e375130e4b38e8 https://github.com/galaxyproject/galaxy/commit/748f85e700f6a23d681edc74f2e3… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2016-12-11 (Sun, 11 Dec 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/users.py Log Message: ----------- Handling malformed additional preferences config xml Commit: 0c95a7a2b281f3399e2bf7a8c6dd2c35fb781b0b https://github.com/galaxyproject/galaxy/commit/0c95a7a2b281f3399e2bf7a8c6dd… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2016-12-13 (Tue, 13 Dec 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/users.py Log Message: ----------- Updating a for loop Commit: 6d70e92c9c71d40cccbefb69466afca1188e40a3 https://github.com/galaxyproject/galaxy/commit/6d70e92c9c71d40cccbefb69466a… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2017-01-04 (Wed, 04 Jan 2017) Changed paths: M client/galaxy/style/less/base.less Log Message: ----------- revert style changes Commit: 4b43a1fb68bc5ed49e4c46ee231337f800fbe2e4 https://github.com/galaxyproject/galaxy/commit/4b43a1fb68bc5ed49e4c46ee2313… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2017-01-04 (Wed, 04 Jan 2017) Changed paths: M .ci/flake8_lint_include_list.txt A .ci/jenkins/api/run_tests.sh A .ci/jenkins/framework/run_tests.sh A .ci/jenkins/integration/run_tests.sh A .ci/jenkins/selenium/Dockerfile A .ci/jenkins/selenium/docker-compose.yml A .ci/jenkins/selenium/galaxy.ini A .ci/jenkins/selenium/run_galaxy.bash A .ci/jenkins/selenium/run_tests.sh A .ci/jenkins/toolshed/run_tests.sh M .ci/py3_sources.txt M CONTRIBUTORS.md M Makefile M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/tool-panel.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/tool/tool-form-workflow.js M client/galaxy/scripts/mvc/tool/tools.js M client/galaxy/scripts/mvc/upload/composite/composite-row.js M client/galaxy/scripts/mvc/upload/default/default-row.js M client/galaxy/scripts/mvc/user/user-preferences.js M client/galaxy/style/less/dataset.less M client/galaxy/style/less/ui.less M client/galaxy/style/source_material/circle.py M config/datatypes_conf.xml.sample M config/galaxy.ini.sample M config/job_conf.xml.sample_advanced M config/plugins/interactive_environments/jupyter/config/jupyter.ini.sample M config/plugins/interactive_environments/rstudio/config/allowed_images.yml.sample M config/plugins/interactive_environments/rstudio/static/js/rstudio.js M config/plugins/interactive_environments/rstudio/templates/rstudio.mako M config/plugins/tours/core.galaxy_ui.yaml M config/plugins/tours/core.history.yaml M config/plugins/visualizations/charts/static/repository/build/registry.js M config/plugins/visualizations/charts/static/repository/build/registry.js.map M config/plugins/visualizations/charts/static/repository/visualizations/utilities/tabular-form.js M config/plugins/visualizations/charts/webpack.config.js M config/tool_data_table_conf.xml.sample M contrib/galaxy_config_merger.py M contrib/nagios/check_galaxy.py M cron/add_manual_builds.py M cron/build_chrom_db.py M cron/parse_builds.py M cron/parse_builds_3_sites.py A display_applications/igv/genome_fasta.xml M doc/Makefile A doc/fix_schema_rst.sh M doc/parse_gx_xsd.py M doc/patch.py M doc/source/admin/dependency_resolvers.rst M doc/source/admin/index.rst M doc/source/admin/interactive_environments.rst M doc/source/admin/interactive_environments.svg M doc/source/admin/webhooks.rst M doc/source/dev/faq.rst M doc/source/dev/interactive_environments.rst M doc/source/project/organization.rst A doc/source/releases/16.10.rst M doc/source/releases/16.10_announce.rst A doc/source/releases/17.01_announce.rst M lib/galaxy/actions/admin.py M lib/galaxy/auth/__init__.py M lib/galaxy/auth/providers/ldap_ad.py M lib/galaxy/auth/providers/pam_auth.py M lib/galaxy/config.py M lib/galaxy/datatypes/assembly.py M lib/galaxy/datatypes/binary.py A lib/galaxy/datatypes/blast.py M lib/galaxy/datatypes/constructive_solid_geometry.py M lib/galaxy/datatypes/converters/bam_to_bai.xml M lib/galaxy/datatypes/converters/bcf_bgzip_to_bcf_converter.xml M lib/galaxy/datatypes/converters/bcf_to_bcf_bgzip_converter.xml M lib/galaxy/datatypes/converters/bed_gff_or_vcf_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/bed_to_bgzip_converter.xml M lib/galaxy/datatypes/converters/bed_to_fli_converter.xml M lib/galaxy/datatypes/converters/bed_to_gff_converter.py M lib/galaxy/datatypes/converters/bed_to_gff_converter.xml M lib/galaxy/datatypes/converters/bed_to_interval_index_converter.xml M lib/galaxy/datatypes/converters/bed_to_tabix_converter.xml M lib/galaxy/datatypes/converters/bedgraph_to_array_tree_converter.py M lib/galaxy/datatypes/converters/bedgraph_to_array_tree_converter.xml M lib/galaxy/datatypes/converters/bedgraph_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/bgzip.py M lib/galaxy/datatypes/converters/cml_to_inchi_converter.xml M lib/galaxy/datatypes/converters/cml_to_mol2_converter.xml M lib/galaxy/datatypes/converters/cml_to_sdf_converter.xml M lib/galaxy/datatypes/converters/cml_to_smi_converter.xml M lib/galaxy/datatypes/converters/encodepeak_to_bgzip_converter.xml M lib/galaxy/datatypes/converters/encodepeak_to_tabix_converter.xml M lib/galaxy/datatypes/converters/fasta_to_2bit.xml M lib/galaxy/datatypes/converters/fasta_to_bowtie_base_index_converter.xml M lib/galaxy/datatypes/converters/fasta_to_bowtie_color_index_converter.xml A lib/galaxy/datatypes/converters/fasta_to_fai.xml M lib/galaxy/datatypes/converters/fasta_to_len.py M lib/galaxy/datatypes/converters/fasta_to_len.xml M lib/galaxy/datatypes/converters/fasta_to_tabular_converter.xml M lib/galaxy/datatypes/converters/fastq_to_fqtoc.xml M lib/galaxy/datatypes/converters/fastqsolexa_to_fasta_converter.py M lib/galaxy/datatypes/converters/fastqsolexa_to_fasta_converter.xml M lib/galaxy/datatypes/converters/fastqsolexa_to_qual_converter.py M lib/galaxy/datatypes/converters/fastqsolexa_to_qual_converter.xml M lib/galaxy/datatypes/converters/gff_to_bed_converter.py M lib/galaxy/datatypes/converters/gff_to_bed_converter.xml M lib/galaxy/datatypes/converters/gff_to_bgzip_converter.xml M lib/galaxy/datatypes/converters/gff_to_fli_converter.xml M lib/galaxy/datatypes/converters/gff_to_interval_index_converter.py M lib/galaxy/datatypes/converters/gff_to_interval_index_converter.xml M lib/galaxy/datatypes/converters/gff_to_tabix_converter.xml M lib/galaxy/datatypes/converters/inchi_to_cml_converter.xml M lib/galaxy/datatypes/converters/inchi_to_mol2_converter.xml M lib/galaxy/datatypes/converters/inchi_to_mol_converter.xml M lib/galaxy/datatypes/converters/inchi_to_sdf_converter.xml M lib/galaxy/datatypes/converters/inchi_to_smi_converter.xml M lib/galaxy/datatypes/converters/interval_to_bed12_converter.xml M lib/galaxy/datatypes/converters/interval_to_bed6_converter.xml M lib/galaxy/datatypes/converters/interval_to_bed_converter.py M lib/galaxy/datatypes/converters/interval_to_bed_converter.xml M lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.py M lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.xml M lib/galaxy/datatypes/converters/interval_to_bgzip_converter.xml M lib/galaxy/datatypes/converters/interval_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/interval_to_coverage.py M lib/galaxy/datatypes/converters/interval_to_coverage.xml M lib/galaxy/datatypes/converters/interval_to_fli.py M lib/galaxy/datatypes/converters/interval_to_interval_index_converter.py M lib/galaxy/datatypes/converters/interval_to_interval_index_converter.xml M lib/galaxy/datatypes/converters/interval_to_tabix_converter.py M lib/galaxy/datatypes/converters/interval_to_tabix_converter.xml M lib/galaxy/datatypes/converters/len_to_linecount.xml M lib/galaxy/datatypes/converters/lped_to_fped_converter.py M lib/galaxy/datatypes/converters/lped_to_fped_converter.xml M lib/galaxy/datatypes/converters/lped_to_pbed_converter.py M lib/galaxy/datatypes/converters/lped_to_pbed_converter.xml M lib/galaxy/datatypes/converters/maf_to_fasta_converter.xml M lib/galaxy/datatypes/converters/maf_to_interval_converter.xml M lib/galaxy/datatypes/converters/mol2_to_cml_converter.xml M lib/galaxy/datatypes/converters/mol2_to_inchi_converter.xml M lib/galaxy/datatypes/converters/mol2_to_mol_converter.xml M lib/galaxy/datatypes/converters/mol2_to_sdf_converter.xml M lib/galaxy/datatypes/converters/mol2_to_smi_converter.xml M lib/galaxy/datatypes/converters/mol_to_cml_converter.xml M lib/galaxy/datatypes/converters/mol_to_inchi_converter.xml M lib/galaxy/datatypes/converters/mol_to_mol2_converter.xml M lib/galaxy/datatypes/converters/pbed_ldreduced_converter.py M lib/galaxy/datatypes/converters/pbed_ldreduced_converter.xml M lib/galaxy/datatypes/converters/pbed_to_lped_converter.py M lib/galaxy/datatypes/converters/pbed_to_lped_converter.xml M lib/galaxy/datatypes/converters/picard_interval_list_to_bed6_converter.py M lib/galaxy/datatypes/converters/picard_interval_list_to_bed6_converter.xml M lib/galaxy/datatypes/converters/pileup_to_interval_index_converter.py M lib/galaxy/datatypes/converters/pileup_to_interval_index_converter.xml M lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.py M lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.xml M lib/galaxy/datatypes/converters/sam_to_bam.py M lib/galaxy/datatypes/converters/sam_to_bam.xml M lib/galaxy/datatypes/converters/sam_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/sdf_to_cml_converter.xml M lib/galaxy/datatypes/converters/sdf_to_inchi_converter.xml M lib/galaxy/datatypes/converters/sdf_to_mol2_converter.xml M lib/galaxy/datatypes/converters/sdf_to_smi_converter.xml M lib/galaxy/datatypes/converters/smi_to_cml_converter.xml M lib/galaxy/datatypes/converters/smi_to_inchi_converter.xml M lib/galaxy/datatypes/converters/smi_to_mol2_converter.xml M lib/galaxy/datatypes/converters/smi_to_mol_converter.xml M lib/galaxy/datatypes/converters/smi_to_sdf_converter.xml M lib/galaxy/datatypes/converters/smi_to_smi_converter.xml M lib/galaxy/datatypes/converters/tabular_to_dbnsfp.py M lib/galaxy/datatypes/converters/tabular_to_dbnsfp.xml M lib/galaxy/datatypes/converters/vcf_bgzip_to_tabix_converter.xml M lib/galaxy/datatypes/converters/vcf_to_bgzip_converter.xml M lib/galaxy/datatypes/converters/vcf_to_interval_index_converter.py M lib/galaxy/datatypes/converters/vcf_to_interval_index_converter.xml M lib/galaxy/datatypes/converters/vcf_to_tabix_converter.xml M lib/galaxy/datatypes/converters/vcf_to_vcf_bgzip.py M lib/galaxy/datatypes/converters/vcf_to_vcf_bgzip_converter.xml M lib/galaxy/datatypes/converters/wig_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/wiggle_to_array_tree_converter.py M lib/galaxy/datatypes/converters/wiggle_to_array_tree_converter.xml M lib/galaxy/datatypes/converters/wiggle_to_simple_converter.py M lib/galaxy/datatypes/converters/wiggle_to_simple_converter.xml M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/display_applications/parameters.py M lib/galaxy/datatypes/genetics.py M lib/galaxy/datatypes/images.py M lib/galaxy/datatypes/msa.py M lib/galaxy/datatypes/neo4j.py M lib/galaxy/datatypes/proteomics.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py A lib/galaxy/datatypes/test/1.smat A lib/galaxy/datatypes/test/tblastn_four_human_vs_rhodopsin.xml M lib/galaxy/datatypes/text.py M lib/galaxy/datatypes/triples.py M lib/galaxy/dependencies/dev-requirements.txt M lib/galaxy/exceptions/error_codes.py M lib/galaxy/external_services/actions.py M lib/galaxy/external_services/parameters.py M lib/galaxy/external_services/result_handlers/basic.py M lib/galaxy/external_services/service.py M lib/galaxy/forms/forms.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/actions/post.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/dynamic_tool_destination.py M lib/galaxy/jobs/handler.py M lib/galaxy/jobs/mapper.py M lib/galaxy/jobs/metrics/__init__.py M lib/galaxy/jobs/metrics/collectl/cli.py M lib/galaxy/jobs/metrics/collectl/subsystems.py M lib/galaxy/jobs/metrics/instrumenters/core.py M lib/galaxy/jobs/metrics/instrumenters/cpuinfo.py M lib/galaxy/jobs/metrics/instrumenters/env.py M lib/galaxy/jobs/metrics/instrumenters/meminfo.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/cli.py M lib/galaxy/jobs/runners/local.py M lib/galaxy/jobs/runners/slurm.py A lib/galaxy/jobs/runners/state_handlers/_safe_eval.py M lib/galaxy/jobs/runners/state_handlers/resubmit.py M lib/galaxy/jobs/runners/util/cli/job/slurm_torque.py M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh M lib/galaxy/jobs/runners/util/job_script/__init__.py M lib/galaxy/jobs/splitters/basic.py M lib/galaxy/managers/collections.py M lib/galaxy/managers/collections_util.py M lib/galaxy/managers/configuration.py M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py M lib/galaxy/model/metadata.py M lib/galaxy/model/migrate/versions/0007_sharing_histories.py M lib/galaxy/model/migrate/versions/0008_galaxy_forms.py M lib/galaxy/model/migrate/versions/0010_hda_display_at_authz_table.py M lib/galaxy/model/migrate/versions/0011_v0010_mysql_index_fix.py M lib/galaxy/model/migrate/versions/0012_user_address.py M lib/galaxy/model/migrate/versions/0013_change_lib_item_templates_to_forms.py M lib/galaxy/model/migrate/versions/0016_v0015_mysql_index_fix.py M lib/galaxy/model/migrate/versions/0018_ordered_tags_and_page_tags.py M lib/galaxy/model/migrate/versions/0020_library_upload_job.py M lib/galaxy/model/migrate/versions/0026_cloud_tables.py M lib/galaxy/model/migrate/versions/0050_drop_cloud_tables.py M lib/galaxy/model/migrate/versions/0052_sample_dataset_table.py M lib/galaxy/model/migrate/versions/0091_add_tool_version_tables.py M lib/galaxy/objectstore/pulsar.py M lib/galaxy/objectstore/rods.py M lib/galaxy/queue_worker.py M lib/galaxy/quota/__init__.py M lib/galaxy/sample_tracking/data_transfer.py M lib/galaxy/sample_tracking/request_types.py M lib/galaxy/sample_tracking/sample.py M lib/galaxy/security/__init__.py M lib/galaxy/security/passwords.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/actions/data_manager.py M lib/galaxy/tools/actions/data_source.py M lib/galaxy/tools/actions/history_imp_exp.py M lib/galaxy/tools/actions/metadata.py M lib/galaxy/tools/actions/model_operations.py M lib/galaxy/tools/actions/upload.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/tools/cwl/runtime_actions.py M lib/galaxy/tools/cwl/schema.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/commands.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/container_resolvers/explicit.py M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/deps/installable.py M lib/galaxy/tools/deps/mulled/_cli.py M lib/galaxy/tools/deps/mulled/invfile.lua M lib/galaxy/tools/deps/mulled/mulled_build.py M lib/galaxy/tools/deps/mulled/mulled_build_channel.py M lib/galaxy/tools/deps/requirements.py M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/deps/resolvers/modules.py M lib/galaxy/tools/deps/views.py M lib/galaxy/tools/execute.py M lib/galaxy/tools/imp_exp/exp_history_to_archive.xml M lib/galaxy/tools/imp_exp/export_history.py M lib/galaxy/tools/lint.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/dataset_matcher.py M lib/galaxy/tools/parameters/input_translation.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/parameters/sanitize.py M lib/galaxy/tools/parameters/validation.py M lib/galaxy/tools/parser/output_actions.py M lib/galaxy/tools/parser/output_collection_def.py M lib/galaxy/tools/test.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/integrated_panel.py M lib/galaxy/tools/toolbox/lineages/tool_shed.py M lib/galaxy/tools/toolbox/parser.py M lib/galaxy/tools/toolbox/watcher.py M lib/galaxy/tools/util/galaxyops/__init__.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/util/__init__.py M lib/galaxy/util/aliaspickler.py M lib/galaxy/util/dbkeys.py M lib/galaxy/util/hash_util.py M lib/galaxy/util/object_wrapper.py M lib/galaxy/util/pastescript/loadwsgi.py M lib/galaxy/util/pastescript/serve.py M lib/galaxy/version.py M lib/galaxy/visualization/plugins/plugin.py M lib/galaxy/visualization/plugins/registry.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/web/framework/base.py M lib/galaxy/web/framework/middleware/error.py M lib/galaxy/web/framework/middleware/remoteuser.py M lib/galaxy/web/framework/middleware/sentry.py M lib/galaxy/web/framework/middleware/statsd.py M lib/galaxy/web/framework/middleware/translogger.py M lib/galaxy/web/framework/openid_manager.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/web/proxy/js/Dockerfile M lib/galaxy/webapps/galaxy/api/configuration.py M lib/galaxy/webapps/galaxy/api/tool_dependencies.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/api/users.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/external_services.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/galaxy/controllers/search.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/webapps/reports/config.py M lib/galaxy/webapps/tool_shed/config.py M lib/galaxy/webapps/tool_shed/controllers/groups.py M lib/galaxy/webapps/tool_shed/controllers/user.py M lib/galaxy/webapps/tool_shed/framework/middleware/remoteuser.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0013_add_review_tables.py M lib/galaxy/webapps/tool_shed/util/ratings_util.py M lib/galaxy/workflow/extract.py M lib/galaxy/workflow/run.py M lib/galaxy/workflow/schedulers/core.py M lib/galaxy/workflow/steps.py M lib/galaxy_utils/sequence/fastq.py M lib/galaxy_utils/sequence/vcf.py M lib/mimeparse.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/env_file_builder.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M lib/tool_shed/repository_types/unrestricted.py M lib/tool_shed/tools/tool_validator.py M lib/tool_shed/util/shed_util_common.py M lib/tool_shed/util/tool_util.py M lib/tool_shed/util/web_util.py M lib/tool_shed/util/workflow_util.py M run_tests.sh M scripts/api/data_manager_example_execute.py M scripts/api/example_watch_folder.py M scripts/api/filter_failed_datasets_from_collection.py M scripts/api/form_create_from_xml.py M scripts/api/history_create_history.py M scripts/api/history_delete_history.py M scripts/api/import_library_dataset_to_history.py M scripts/api/import_workflows_from_installed_tool_shed_repository.py M scripts/api/install_tool_shed_repositories.py M scripts/api/library_create_folder.py M scripts/api/library_create_library.py M scripts/api/library_upload_from_import_dir.py M scripts/api/load_data_with_metadata.py M scripts/api/repair_tool_shed_repository.py M scripts/api/request_type_create_from_xml.py M scripts/api/requests_update_state.py M scripts/api/reset_metadata_on_installed_repositories.py M scripts/api/sample_dataset_update_status.py M scripts/api/sample_update_state.py M scripts/api/search.py M scripts/api/sequencer_configuration_create.py M scripts/api/upload_to_history.py M scripts/api/workflow_delete.py M scripts/api/workflow_execute.py M scripts/api/workflow_execute_parameters.py M scripts/api/workflow_import.py M scripts/api/workflow_import_from_file_rpark.py M scripts/auth/pam_auth_helper.py M scripts/bootstrap_history.py M scripts/build_toolbox.py M scripts/build_universe_config.py M scripts/check_galaxy.py M scripts/check_python.py M scripts/cleanup_datasets/admin_cleanup_datasets.py M scripts/cleanup_datasets/cleanup_datasets.py M scripts/cleanup_datasets/pgcleanup.py M scripts/cleanup_datasets/populate_uuid.py M scripts/cleanup_datasets/remove_renamed_datasets_from_disk.py M scripts/cleanup_datasets/rename_purged_datasets.py M scripts/cleanup_datasets/update_dataset_size.py M scripts/cleanup_datasets/update_metadata.py M scripts/common_startup.sh M scripts/communication/communication_server.py M scripts/create_db.py M scripts/data_libraries/build_lucene_index.py M scripts/data_libraries/build_whoosh_index.py M scripts/drmaa_external_killer.py M scripts/drmaa_external_runner.py A scripts/dump_tour.py M scripts/external_chown_script.py M scripts/extract_dataset_part.py M scripts/extract_toolbox_sections.py M scripts/functional_tests.py M scripts/grt.py M scripts/loc_files/create_all_fasta_loc.py M scripts/manage_db.py M scripts/microbes/BeautifulSoup.py M scripts/microbes/create_bacteria_loc_file.py M scripts/microbes/create_bacteria_table.py M scripts/microbes/get_builds_lengths.py M scripts/microbes/harvest_bacteria.py M scripts/others/incorrect_gops_jobs.py M scripts/others/incorrect_gops_join_jobs.py R scripts/run_selenium_tests.sh M scripts/set_dataset_sizes.py M scripts/set_user_disk_usage.py M scripts/slideshow/build_slideshow.py M scripts/summarize_timings.py M scripts/sync_reports_config.py M scripts/tool_shed/api/add_repository_registry_entry.py M scripts/tool_shed/api/create_categories.py M scripts/tool_shed/api/create_users.py M scripts/tool_shed/api/export.py M scripts/tool_shed/api/get_filtered_repository_revisions.py M scripts/tool_shed/api/import_capsule.py M scripts/tool_shed/api/remove_repository_registry_entry.py M scripts/tool_shed/api/reset_metadata_on_repositories.py M scripts/tool_shed/bootstrap_tool_shed/bootstrap_util.py M scripts/tool_shed/bootstrap_tool_shed/create_user_with_api_key.py M scripts/tool_shed/build_ts_whoosh_index.py M scripts/tool_shed/check_download_urls.py M scripts/tool_shed/check_filesystem_for_empty_tool_dependency_installation_paths.py M scripts/tool_shed/check_s3_for_empty_tool_dependency_installation_paths.py M scripts/tool_shed/clean_up_tool_dependency_directory.py M scripts/tool_shed/deprecate_repositories_without_metadata.py M scripts/tool_shed/migrate_tools_to_repositories.py M scripts/tool_shed/show_tool_dependency_installation_dir_contents.py M scripts/tools/maf/check_loc_file.py M scripts/tools/re_escape_output.py M scripts/transfer.py M scripts/update_shed_config_path.py M static/maps/layout/menu.js.map M static/maps/mvc/dataset/dataset-li-edit.js.map M static/maps/mvc/dataset/dataset-li.js.map M static/maps/mvc/form/form-section.js.map M static/maps/mvc/history/options-menu.js.map M static/maps/mvc/tool/tool-form-composite.js.map M static/maps/mvc/tool/tool-form-workflow.js.map M static/maps/mvc/tool/tools.js.map M static/maps/mvc/upload/composite/composite-row.js.map M static/maps/mvc/upload/default/default-row.js.map A static/maps/mvc/user/change-password.js.map A static/maps/mvc/user/extra-information.js.map A static/maps/mvc/user/manage-user-information.js.map M static/maps/mvc/user/user-preferences.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/layout/menu.js M static/scripts/mvc/dataset/dataset-li-edit.js M static/scripts/mvc/form/form-section.js M static/scripts/mvc/history/options-menu.js M static/scripts/mvc/tool/tool-form-composite.js M static/scripts/mvc/tool/tool-form-workflow.js M static/scripts/mvc/tool/tools.js M static/scripts/mvc/upload/composite/composite-row.js M static/scripts/mvc/upload/default/default-row.js A static/scripts/mvc/user/change-password.js A static/scripts/mvc/user/extra-information.js A static/scripts/mvc/user/manage-user-information.js M static/scripts/mvc/user/user-preferences.js M static/style/blue/base.css M static/welcome.html.sample M templates/admin/tool_shed_repository/common.mako M templates/admin/tool_shed_repository/select_tool_panel_section.mako M templates/show_params.mako R templates/user/change_password.mako R templates/user/communication_settings.mako R templates/user/edit_address.mako R templates/user/new_address.mako R templates/user/permissions.mako M templates/user/register.mako R templates/user/toolbox_filters.mako R templates/user/username.mako M templates/webapps/galaxy/galaxy.masthead.mako R templates/webapps/galaxy/user/api_keys.mako M templates/webapps/galaxy/user/list_users.mako R templates/webapps/galaxy/user/manage_info.mako M templates/webapps/galaxy/workflow/editor.mako M templates/webapps/galaxy/workflow/list.mako M templates/webapps/tool_shed/repository/common.mako A templates/webapps/tool_shed/user/api_keys.mako A templates/webapps/tool_shed/user/change_password.mako A templates/webapps/tool_shed/user/index.mako A templates/webapps/tool_shed/user/username.mako A test-data/bam_from_sam.bam A test-data/sam_with_header.sam M test/api/test_api_batch.py A test/api/test_configuration.py M test/api/test_datasets.py M test/api/test_histories.py M test/api/test_history_contents_provenance.py M test/api/test_tools.py M test/api/test_users.py M test/api/test_workflows.py M test/api/workflows_format_2/main.py M test/base/api.py M test/base/api_asserts.py M test/base/driver_util.py M test/base/integration_util.py M test/base/interactor.py M test/base/twilltestcase.py R test/casperjs/anon-history-tests.js R test/casperjs/api-batch-tests.js R test/casperjs/api-configuration-tests.js R test/casperjs/api-history-tests.js R test/casperjs/api-tool-tests.js R test/casperjs/api-user-tests.js R test/casperjs/hda-state-tests.js R test/casperjs/history-options-tests.js R test/casperjs/history-panel-tests.js R test/casperjs/history-share-tests.js R test/casperjs/login-tests.js R test/casperjs/registration-tests.js R test/casperjs/upload-tests.js M test/functional/test_library_templates.py M test/functional/test_toolbox.py A test/functional/tools/for_tours/filtering.py A test/functional/tools/for_tours/filtering.xml A test/functional/tools/paired_collection_map_over_structured_like.xml A test/functional/tools/python_environment_problem.py A test/functional/tools/python_environment_problem.xml A test/functional/tools/sam_to_bam.xml M test/functional/tools/sample_datatypes_conf.xml M test/functional/tools/samples_tool_conf.xml R test/functional/workflow.py A test/galaxy_selenium/__init__.py A test/galaxy_selenium/cli.py A test/galaxy_selenium/data.py A test/galaxy_selenium/driver_factory.py A test/galaxy_selenium/has_driver.py A test/galaxy_selenium/navigates_galaxy.py A test/galaxy_selenium/navigation-data.yml A test/galaxy_selenium/sizzle.py A test/integration/resubmission_job_conf.xml A test/integration/resubmission_job_resource_parameters_conf.xml A test/integration/resubmission_rules/__init__.py A test/integration/resubmission_rules/rules.py A test/integration/resubmission_runners.py A test/integration/test_job_resubmission.py M test/integration/test_resolvers.py M test/manual/workflows_scaling.py A test/selenium_tests/__init__.py A test/selenium_tests/framework.py A test/selenium_tests/test_anon_history.py A test/selenium_tests/test_history_dataset_state.py A test/selenium_tests/test_history_options.py A test/selenium_tests/test_history_panel.py A test/selenium_tests/test_history_sharing.py A test/selenium_tests/test_login.py A test/selenium_tests/test_registration.py A test/selenium_tests/test_stock_tours.py A test/selenium_tests/test_tool_form.py A test/selenium_tests/test_uploads.py A test/selenium_tests/test_workflow_editor.py M test/shed_functional/base/twilltestcase.py M test/shed_functional/functional/test_1010_install_repository_with_tool_dependencies.py M test/shed_functional/functional/test_1140_simple_repository_dependency_multiple_owners.py M test/shed_functional/functional/test_1210_uninstall_reinstall_repository_with_tool_dependencies.py M test/unit/dataset_collections/test_matching.py M test/unit/datatypes/dataproviders/test_base_dataproviders.py M test/unit/datatypes/dataproviders/test_line_dataproviders.py M test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py M test/unit/jobs/test_command_factory.py M test/unit/jobs/test_job_configuration.py M test/unit/jobs/test_job_output_checker.py M test/unit/jobs/test_job_wrapper.py M test/unit/jobs/test_mapper.py M test/unit/jobs/test_rule_helper.py M test/unit/jobs/test_runner_local.py M test/unit/managers/base.py M test/unit/managers/test_CollectionManager.py M test/unit/managers/test_DatasetManager.py M test/unit/managers/test_HDAManager.py M test/unit/managers/test_HDCAManager.py M test/unit/managers/test_HistoryContentsManager.py M test/unit/managers/test_HistoryManager.py M test/unit/managers/test_UserManager.py M test/unit/shed_unit/test_fabric_util.py M test/unit/shed_unit/test_td_common_util.py M test/unit/shed_unit/test_tool_panel_manager.py M test/unit/test_galaxy_transactions.py M test/unit/test_routes.py M test/unit/test_sockets.py M test/unit/tools/test_actions.py M test/unit/tools/test_citations.py M test/unit/tools/test_collect_primary_datasets.py M test/unit/tools/test_column_parameters.py M test/unit/tools/test_conda_resolution.py M test/unit/tools/test_data_parameters.py M test/unit/tools/test_dataset_matcher.py M test/unit/tools/test_evaluation.py M test/unit/tools/test_execution.py M test/unit/tools/test_history_imp_exp.py M test/unit/tools/test_parameter_parsing.py M test/unit/tools/test_select_parameters.py M test/unit/tools/test_tool_external_files.py M test/unit/tools/test_toolbox.py M test/unit/tools/test_wrappers.py M test/unit/tools_support.py M test/unit/unittest_utils/galaxy_mock.py M test/unit/unittest_utils/tempfilecache.py M test/unit/unittest_utils/utility.py M test/unit/visualizations/plugins/test_VisualizationPlugin.py M test/unit/visualizations/plugins/test_VisualizationsRegistry.py M test/unit/web/base/test_HookPluginManager.py M test/unit/web/base/test_PageServingPluginManager.py M test/unit/web/base/test_PluginManager.py M test/unit/web/framework/test_webapp.py M test/unit/workflows/test_modules.py M test/unit/workflows/test_run_parameters.py M test/unit/workflows/test_workflow_progress.py M test/unit/workflows/workflow_support.py A tool-data/blastdb.loc.sample A tool-data/blastdb_d.loc.sample A tool-data/blastdb_p.loc.sample M tools/data_source/data_source.py M tools/data_source/fetch.py M tools/data_source/genbank.py M tools/data_source/upload.py M tools/evolution/add_scores.py M tools/extract/extract_genomic_dna.py M tools/extract/liftOver_wrapper.py M tools/filters/axt_to_fasta.py M tools/filters/bed_to_gff_converter.py M tools/filters/catWrapper.py M tools/filters/convert_characters.py M tools/filters/gff/extract_GFF_Features.py M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_attribute.xml M tools/filters/gff/gff_filter_by_feature_count.py M tools/filters/gff/gff_filter_by_feature_count.xml M tools/filters/gff/gtf_filter_by_attribute_values_list.py R tools/filters/gff/sort_gtf.py M tools/filters/gff_to_bed_converter.py M tools/filters/grep.py M tools/filters/gtf_to_bedgraph_converter.py M tools/filters/join.py M tools/filters/joinWrapper.py M tools/filters/lav_to_bed.py M tools/filters/mergeCols.py M tools/filters/random_lines_two_pass.py M tools/filters/randomlines.py M tools/filters/secure_hash_message_digest.py M tools/filters/sorter.py M tools/filters/trimmer.py M tools/filters/ucsc_gene_bed_to_exon_bed.py M tools/filters/ucsc_gene_bed_to_intron_bed.py M tools/filters/ucsc_gene_table_to_intervals.py M tools/filters/uniq.py M tools/filters/wiggle_to_simple.py M tools/genomespace/genomespace_exporter.py M tools/genomespace/genomespace_file_browser.py M tools/genomespace/genomespace_importer.py M tools/maf/interval2maf.py M tools/maf/interval_maf_to_merged_fasta.py M tools/maf/maf_by_block_number.py M tools/maf/maf_filter.py M tools/maf/maf_limit_size.py M tools/maf/maf_limit_to_species.py M tools/maf/maf_reverse_complement.py M tools/maf/maf_split_by_species.py M tools/maf/maf_stats.py M tools/maf/maf_thread_for_species.py M tools/maf/maf_to_bed.py M tools/maf/maf_to_fasta_multiple_sets.py M tools/maf/maf_to_interval.py M tools/maf/vcf_to_maf_customtrack.py M tools/meme/fimo_wrapper.py M tools/metag_tools/blat_wrapper.py M tools/next_gen_conversion/fastq_conversions.py M tools/next_gen_conversion/fastq_gen_conv.py M tools/next_gen_conversion/solid2fastq.py M tools/next_gen_conversion/solid_to_fastq.py M tools/ngs_simulation/ngs_simulation.py M tools/phenotype_association/pagetag.py M tools/phenotype_association/senatag.py M tools/solid_tools/maq_cs_wrapper.py M tools/solid_tools/solid_qual_stats.py M tools/sr_assembly/velveth_wrapper.py M tools/sr_mapping/bfast_wrapper.py M tools/sr_mapping/srma_wrapper.py M tools/stats/aggregate_scores_in_intervals.py M tools/stats/filtering.py M tools/stats/grouping.py M tools/stats/gsummary.py Log Message: ----------- Merge branch 'dev' into extra_user_preferences Commit: 24d52054adf43b55d50d0fca10c6cbab0a041983 https://github.com/galaxyproject/galaxy/commit/24d52054adf43b55d50d0fca10c6… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2017-01-04 (Wed, 04 Jan 2017) Changed paths: M config/user_preferences_extra_conf.xml.sample M lib/galaxy/webapps/galaxy/api/users.py M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Merge branch 'extra_user_preferences' of https://github.com/bgruening/galaxy into extra_user_preferences Commit: 22dba016be3ca3753a1b2ee8769e506864f8770b https://github.com/galaxyproject/galaxy/commit/22dba016be3ca3753a1b2ee8769e… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2017-01-04 (Wed, 04 Jan 2017) Changed paths: M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- static build Commit: 5a86e3c5ca09932a67957afe44d9444dff8474f0 https://github.com/galaxyproject/galaxy/commit/5a86e3c5ca09932a67957afe44d9… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-01-05 (Thu, 05 Jan 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/users.py Log Message: ----------- linting fixes Commit: 94b2184f897cf19ab5d884708fe484451d199219 https://github.com/galaxyproject/galaxy/commit/94b2184f897cf19ab5d884708fe4… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2017-08-07 (Mon, 07 Aug 2017) Changed paths: M .ci/flake8_blacklist.txt M .ci/flake8_docstrings_include_list.txt M .ci/flake8_lint_include_list.txt M .ci/flake8_wrapper_docstrings.sh M .ci/jenkins/selenium/run_galaxy.bash M .ci/jenkins/selenium/run_tests.sh M .ci/py3_sources.txt M .gitignore M .travis.yml M CITATION M CONTRIBUTING.md M CONTRIBUTORS.md M Makefile M README.rst A SECURITY_POLICY.md A client/galaxy/scripts/admin.toolshed.js A client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/analysis.js R client/galaxy/scripts/apps/history-panel.js M client/galaxy/scripts/apps/login.js A client/galaxy/scripts/apps/panels/admin-panel.js A client/galaxy/scripts/apps/panels/history-panel.js A client/galaxy/scripts/apps/panels/tool-panel.js R client/galaxy/scripts/apps/tool-panel.js M client/galaxy/scripts/galaxy.interactive_environments.js M client/galaxy/scripts/galaxy.js M client/galaxy/scripts/galaxy.library.js M client/galaxy/scripts/galaxy.pages.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/layout/panel.js M client/galaxy/scripts/layout/scratchbook.js M client/galaxy/scripts/libs/jquery/jquery.autocomplete.js M client/galaxy/scripts/mvc/citation/citation-view.js A client/galaxy/scripts/mvc/collection/base-creator.js M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/collection/collection-view-edit.js M client/galaxy/scripts/mvc/collection/collection-view.js M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/collection/pair-collection-creator.js M client/galaxy/scripts/mvc/dataset/data.js A client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/dataset/dataset-model.js M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/grid/grid-model.js A client/galaxy/scripts/mvc/grid/grid-shared.js M client/galaxy/scripts/mvc/grid/grid-template.js M client/galaxy/scripts/mvc/grid/grid-view.js M client/galaxy/scripts/mvc/history/hda-li.js M client/galaxy/scripts/mvc/history/hdca-li.js M client/galaxy/scripts/mvc/history/history-contents.js A client/galaxy/scripts/mvc/history/history-list.js M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/history-view-edit-current.js M client/galaxy/scripts/mvc/history/history-view-edit.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/mvc/library/library-folderlist-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-librarylist-view.js M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js M client/galaxy/scripts/mvc/tag.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js R client/galaxy/scripts/mvc/tool/tool-form-workflow.js M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/scripts/mvc/tool/tools.js A client/galaxy/scripts/mvc/toolshed/categories-view.js A client/galaxy/scripts/mvc/toolshed/repo-queue-view.js A client/galaxy/scripts/mvc/toolshed/repo-status-view.js A client/galaxy/scripts/mvc/toolshed/repositories-view.js A client/galaxy/scripts/mvc/toolshed/repository-queue-view.js A client/galaxy/scripts/mvc/toolshed/repository-view.js A client/galaxy/scripts/mvc/toolshed/shed-list-view.js A client/galaxy/scripts/mvc/toolshed/toolshed-model.js A client/galaxy/scripts/mvc/toolshed/util.js A client/galaxy/scripts/mvc/toolshed/workflows-view.js M client/galaxy/scripts/mvc/tours.js M client/galaxy/scripts/mvc/ui/ui-buttons.js M client/galaxy/scripts/mvc/ui/ui-color-picker.js M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/mvc/ui/ui-options.js M client/galaxy/scripts/mvc/ui/ui-portlet.js M client/galaxy/scripts/mvc/ui/ui-select-content.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/scripts/mvc/ui/ui-slider.js M client/galaxy/scripts/mvc/ui/ui-table.js A client/galaxy/scripts/mvc/upload/collection/collection-row.js A client/galaxy/scripts/mvc/upload/collection/collection-view.js M client/galaxy/scripts/mvc/upload/upload-ftp.js M client/galaxy/scripts/mvc/upload/upload-view.js A client/galaxy/scripts/mvc/user/user-custom-builds.js M client/galaxy/scripts/mvc/user/user-preferences.js M client/galaxy/scripts/mvc/user/user-quotameter.js M client/galaxy/scripts/mvc/webhooks.js M client/galaxy/scripts/mvc/workflow/workflow-canvas.js A client/galaxy/scripts/mvc/workflow/workflow-forms.js A client/galaxy/scripts/mvc/workflow/workflow-icons.js M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-node.js M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M client/galaxy/scripts/mvc/workflow/workflow-view-node.js M client/galaxy/scripts/mvc/workflow/workflow-view.js A client/galaxy/scripts/mvc/workflow/workflow.js A client/galaxy/scripts/nls/de/locale.js A client/galaxy/scripts/nls/es/locale.js A client/galaxy/scripts/nls/fr/locale.js M client/galaxy/scripts/nls/ja/locale.js M client/galaxy/scripts/nls/locale.js M client/galaxy/scripts/nls/zh/locale.js M client/galaxy/scripts/onload.js M client/galaxy/scripts/ui/autocom_tagging.js M client/galaxy/scripts/utils/utils.js M client/galaxy/scripts/viz/circster.js M client/galaxy/scripts/viz/phyloviz.js M client/galaxy/scripts/viz/trackster.js M client/galaxy/scripts/viz/trackster/tracks.js M client/galaxy/scripts/viz/visualization.js M client/galaxy/style/less/base.less M client/galaxy/style/less/galaxy_bootstrap/overrides.less M client/galaxy/style/less/history.less M client/galaxy/style/less/ui.less M client/galaxy/style/less/ui/paired-collection-creator.less M client/galaxy/style/less/upload.less A client/package-lock.json M client/package.json M client/webpack.config.js A config/build_sites.yml.sample A config/containers_conf.yml.sample M config/datatypes_conf.xml.sample M config/dependency_resolvers_conf.xml.sample M config/galaxy.ini.sample M config/job_conf.xml.sample_advanced A config/local_conda_mapping.yml.sample M config/openid_conf.xml.sample M config/plugins/interactive_environments/bam_iobio/config/bam_iobio.ini.sample M config/plugins/interactive_environments/bam_iobio/static/js/bam_iobio.js M config/plugins/interactive_environments/bam_iobio/templates/bam_iobio.mako M config/plugins/interactive_environments/common/templates/ie.mako A config/plugins/interactive_environments/ethercalc/config/allowed_images.yml.sample A config/plugins/interactive_environments/ethercalc/config/ethercalc.ini.sample A config/plugins/interactive_environments/ethercalc/config/ethercalc.xml A config/plugins/interactive_environments/ethercalc/static/js/ethercalc.js A config/plugins/interactive_environments/ethercalc/templates/ethercalc.mako M config/plugins/interactive_environments/jupyter/config/allowed_images.yml.sample M config/plugins/interactive_environments/jupyter/config/jupyter.ini.sample M config/plugins/interactive_environments/jupyter/config/jupyter.xml M config/plugins/interactive_environments/jupyter/static/js/jupyter.js M config/plugins/interactive_environments/jupyter/templates/jupyter.mako M config/plugins/interactive_environments/neo/config/allowed_images.yml.sample M config/plugins/interactive_environments/neo/config/neo.ini.sample M config/plugins/interactive_environments/neo/config/neo.xml M config/plugins/interactive_environments/neo/static/js/neo.js M config/plugins/interactive_environments/neo/templates/neo.mako M config/plugins/interactive_environments/phinch/config/phinch.ini.sample M config/plugins/interactive_environments/phinch/static/js/phinch.js M config/plugins/interactive_environments/phinch/templates/phinch.mako M config/plugins/interactive_environments/rstudio/config/allowed_images.yml.sample M config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample M config/plugins/interactive_environments/rstudio/config/rstudio.xml M config/plugins/interactive_environments/rstudio/static/js/rstudio.js M config/plugins/interactive_environments/rstudio/templates/rstudio.mako M config/plugins/tours/core.galaxy_ui.yaml M config/plugins/tours/core.history.yaml A config/plugins/visualizations/charts/static/repository/build/biojs_phylocanvas.js A config/plugins/visualizations/charts/static/repository/build/biojs_phylocanvas.js.map R config/plugins/visualizations/charts/static/repository/build/cytoscape_basic.js R config/plugins/visualizations/charts/static/repository/build/cytoscape_basic.js.map A config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js A config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js.map A config/plugins/visualizations/charts/static/repository/build/ngl_viewer.js A config/plugins/visualizations/charts/static/repository/build/ngl_viewer.js.map M config/plugins/visualizations/charts/static/repository/build/registry.js M config/plugins/visualizations/charts/static/repository/build/registry.js.map M config/plugins/visualizations/charts/static/repository/build/registry.tmp.js A config/plugins/visualizations/charts/static/repository/plugins/biojs/phylocanvas/phylocanvas.js A config/plugins/visualizations/charts/static/repository/plugins/ngl/viewer.js M config/plugins/visualizations/charts/static/repository/registry.json A config/plugins/visualizations/charts/static/repository/utilities/sifjson.js M config/plugins/visualizations/charts/static/repository/utilities/utils.js A config/plugins/visualizations/charts/static/repository/visualizations/biojs/phylocanvas/config.js A config/plugins/visualizations/charts/static/repository/visualizations/biojs/phylocanvas/logo.png A config/plugins/visualizations/charts/static/repository/visualizations/biojs/phylocanvas/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/basic/config.js R config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/basic/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/basic/wrapper.js A config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/config.js A config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/logo.png A config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/wrapper.js A config/plugins/visualizations/charts/static/repository/visualizations/ngl/viewer/config.js A config/plugins/visualizations/charts/static/repository/visualizations/ngl/viewer/logo.png A config/plugins/visualizations/charts/static/repository/visualizations/ngl/viewer/wrapper.js M config/plugins/visualizations/charts/templates/charts.mako M config/plugins/visualizations/csg/templates/csg.mako M config/plugins/visualizations/graphviz/templates/graphviz.mako M config/plugins/visualizations/scatterplot/templates/scatterplot.mako A config/plugins/visualizations/unipept/README.md A config/plugins/visualizations/unipept/config/unipept.xml A config/plugins/visualizations/unipept/static/style.css A config/plugins/visualizations/unipept/static/tooltip.css A config/plugins/visualizations/unipept/static/unipept-visualizations.es5.js A config/plugins/visualizations/unipept/static/unipept-visualizations.es5.js.map A config/plugins/visualizations/unipept/static/unipept_viz.js A config/plugins/visualizations/unipept/templates/glyphicons-86-repeat.png A config/plugins/visualizations/unipept/templates/unipept.mako R config/plugins/webhooks/demo/history_test1/config/history_test1.yml R config/plugins/webhooks/demo/history_test2/config/history_test2.yml R config/plugins/webhooks/demo/masthead_test/config/masthead_test.yml R config/plugins/webhooks/demo/phdcomics/config/phdcomics.yaml R config/plugins/webhooks/demo/phdcomics/helper/__init__.py R config/plugins/webhooks/demo/phdcomics/static/script.js R config/plugins/webhooks/demo/phdcomics/static/styles.css A config/plugins/webhooks/demo/search/config/searchover.yaml A config/plugins/webhooks/demo/search/static/script.js A config/plugins/webhooks/demo/search/static/styles.css A config/plugins/webhooks/demo/tool_list/config/tool_list.yml A config/plugins/webhooks/demo/tool_list/helper/__init__.py A config/plugins/webhooks/demo/tour_generator/config/tour_generator.yml A config/plugins/webhooks/demo/tour_generator/helper/__init__.py A config/plugins/webhooks/demo/tour_generator/static/script.js A config/plugins/webhooks/demo/tour_generator/static/styles.css R config/plugins/webhooks/demo/trans_object/config/trans_object.yaml R config/plugins/webhooks/demo/trans_object/helper/__init__.py R config/plugins/webhooks/demo/xkcd/config/xkcd.yml R config/plugins/webhooks/demo/xkcd/static/script.js R config/plugins/webhooks/demo/xkcd/static/styles.css A config/swarm_manager_conf.yml.sample M config/tool_conf.xml.main M config/tool_conf.xml.sample M config/tool_destinations.yml.sample M config/tool_shed.ini.sample M contrib/galaxy.debian-init M contrib/galaxy_supervisor.conf M contrib/nagios/check_galaxy M contrib/nagios/check_galaxy.py M cron/updateucsc.sh.sample M display_applications/igv/bigwig.xml M doc/Makefile R doc/patch.py M doc/schema_template.md A doc/source/admin/authentication.md R doc/source/admin/chat-0.png R doc/source/admin/chat-1.png R doc/source/admin/chat-2.png R doc/source/admin/chat-3.png R doc/source/admin/chat-4.png R doc/source/admin/chat.rst R doc/source/admin/communication_server.png R doc/source/admin/communication_server_rooms.png M doc/source/admin/conda_faq.rst M doc/source/admin/dependency_resolvers.rst M doc/source/admin/framework_dependencies.rst R doc/source/admin/grt.rst R doc/source/admin/images_webhooks/history-menu.png R doc/source/admin/images_webhooks/masthead.png R doc/source/admin/images_webhooks/masthead_trans_object.png R doc/source/admin/images_webhooks/tool.png R doc/source/admin/images_webhooks/workflow.png M doc/source/admin/index.rst R doc/source/admin/interactive_environments.png R doc/source/admin/interactive_environments.rst R doc/source/admin/interactive_environments.svg R doc/source/admin/mulled_containers.rst A doc/source/admin/reports.md A doc/source/admin/special_topics/chat-0.png A doc/source/admin/special_topics/chat-1.png A doc/source/admin/special_topics/chat-2.png A doc/source/admin/special_topics/chat-3.png A doc/source/admin/special_topics/chat-4.png A doc/source/admin/special_topics/chat.rst A doc/source/admin/special_topics/communication_server.png A doc/source/admin/special_topics/communication_server_rooms.png A doc/source/admin/special_topics/grafana.png A doc/source/admin/special_topics/grt.rst A doc/source/admin/special_topics/images_webhooks/history-menu.png A doc/source/admin/special_topics/images_webhooks/masthead.png A doc/source/admin/special_topics/images_webhooks/masthead_trans_object.png A doc/source/admin/special_topics/images_webhooks/tool.png A doc/source/admin/special_topics/images_webhooks/workflow.png A doc/source/admin/special_topics/index.rst A doc/source/admin/special_topics/interactive_environments.png A doc/source/admin/special_topics/interactive_environments.rst A doc/source/admin/special_topics/interactive_environments.svg A doc/source/admin/special_topics/mulled_containers.rst A doc/source/admin/special_topics/performance_tracking.rst A doc/source/admin/special_topics/webhooks.rst A doc/source/admin/tool_panel.rst M doc/source/admin/useful_scripts.rst R doc/source/admin/webhooks.rst M doc/source/api/guidelines.rst M doc/source/api_doc.rst M doc/source/conf.py M doc/source/dev/build_a_job_runner.rst M doc/source/dev/index.rst M doc/source/dev/interactive_environments.rst M doc/source/index.rst M doc/source/lib/galaxy.actions.rst M doc/source/lib/galaxy.auth.providers.rst M doc/source/lib/galaxy.auth.rst A doc/source/lib/galaxy.containers.rst M doc/source/lib/galaxy.dataset_collections.rst M doc/source/lib/galaxy.dataset_collections.types.rst M doc/source/lib/galaxy.datatypes.converters.rst M doc/source/lib/galaxy.datatypes.dataproviders.rst M doc/source/lib/galaxy.datatypes.display_applications.rst M doc/source/lib/galaxy.datatypes.rst M doc/source/lib/galaxy.datatypes.util.rst M doc/source/lib/galaxy.dependencies.rst M doc/source/lib/galaxy.eggs.rst M doc/source/lib/galaxy.exceptions.rst M doc/source/lib/galaxy.external_services.result_handlers.rst M doc/source/lib/galaxy.external_services.rst M doc/source/lib/galaxy.forms.rst M doc/source/lib/galaxy.jobs.actions.rst M doc/source/lib/galaxy.jobs.deferred.rst M doc/source/lib/galaxy.jobs.metrics.collectl.rst M doc/source/lib/galaxy.jobs.metrics.instrumenters.rst M doc/source/lib/galaxy.jobs.metrics.rst M doc/source/lib/galaxy.jobs.rst M doc/source/lib/galaxy.jobs.runners.rst M doc/source/lib/galaxy.jobs.runners.state_handlers.rst M doc/source/lib/galaxy.jobs.runners.util.cli.job.rst M doc/source/lib/galaxy.jobs.runners.util.cli.rst M doc/source/lib/galaxy.jobs.runners.util.cli.shell.rst M doc/source/lib/galaxy.jobs.runners.util.condor.rst A doc/source/lib/galaxy.jobs.runners.util.drmaa.rst M doc/source/lib/galaxy.jobs.runners.util.job_script.rst M doc/source/lib/galaxy.jobs.runners.util.rst M doc/source/lib/galaxy.jobs.splitters.rst M doc/source/lib/galaxy.managers.rst M doc/source/lib/galaxy.model.migrate.rst M doc/source/lib/galaxy.model.orm.rst M doc/source/lib/galaxy.model.rst M doc/source/lib/galaxy.model.tool_shed_install.migrate.rst M doc/source/lib/galaxy.model.tool_shed_install.rst M doc/source/lib/galaxy.objectstore.rst M doc/source/lib/galaxy.openid.rst M doc/source/lib/galaxy.quota.rst M doc/source/lib/galaxy.rst M doc/source/lib/galaxy.sample_tracking.rst M doc/source/lib/galaxy.security.rst R doc/source/lib/galaxy.tags.rst M doc/source/lib/galaxy.tools.actions.rst A doc/source/lib/galaxy.tools.cwl.rst M doc/source/lib/galaxy.tools.data.rst M doc/source/lib/galaxy.tools.data_manager.rst A doc/source/lib/galaxy.tools.deps.container_resolvers.rst A doc/source/lib/galaxy.tools.deps.mulled.rst M doc/source/lib/galaxy.tools.deps.resolvers.rst M doc/source/lib/galaxy.tools.deps.rst M doc/source/lib/galaxy.tools.filters.rst M doc/source/lib/galaxy.tools.imp_exp.rst M doc/source/lib/galaxy.tools.linters.rst A doc/source/lib/galaxy.tools.locations.rst M doc/source/lib/galaxy.tools.parameters.rst M doc/source/lib/galaxy.tools.parser.rst M doc/source/lib/galaxy.tools.rst M doc/source/lib/galaxy.tools.search.rst M doc/source/lib/galaxy.tools.toolbox.filters.rst M doc/source/lib/galaxy.tools.toolbox.lineages.rst M doc/source/lib/galaxy.tools.toolbox.rst M doc/source/lib/galaxy.tools.util.galaxyops.rst M doc/source/lib/galaxy.tools.util.rst A doc/source/lib/galaxy.tools.verify.asserts.rst A doc/source/lib/galaxy.tools.verify.rst A doc/source/lib/galaxy.tours.rst M doc/source/lib/galaxy.util.backports.rst M doc/source/lib/galaxy.util.log.rst M doc/source/lib/galaxy.util.pastescript.rst M doc/source/lib/galaxy.util.rst M doc/source/lib/galaxy.visualization.data_providers.phyloviz.rst M doc/source/lib/galaxy.visualization.data_providers.rst M doc/source/lib/galaxy.visualization.genome.rst M doc/source/lib/galaxy.visualization.plugins.rst M doc/source/lib/galaxy.visualization.rst M doc/source/lib/galaxy.visualization.tracks.rst M doc/source/lib/galaxy.web.base.controllers.rst M doc/source/lib/galaxy.web.base.rst M doc/source/lib/galaxy.web.framework.helpers.rst M doc/source/lib/galaxy.web.framework.middleware.rst M doc/source/lib/galaxy.web.framework.rst M doc/source/lib/galaxy.web.proxy.rst M doc/source/lib/galaxy.web.rst M doc/source/lib/galaxy.web.security.rst A doc/source/lib/galaxy.web.stack.rst M doc/source/lib/galaxy.webapps.galaxy.api.rst M doc/source/lib/galaxy.webapps.galaxy.controllers.rst M doc/source/lib/galaxy.webapps.galaxy.rst M doc/source/lib/galaxy.webapps.reports.controllers.rst M doc/source/lib/galaxy.webapps.reports.rst M doc/source/lib/galaxy.webapps.rst M doc/source/lib/galaxy.webapps.tool_shed.api.rst M doc/source/lib/galaxy.webapps.tool_shed.controllers.rst M doc/source/lib/galaxy.webapps.tool_shed.framework.middleware.rst M doc/source/lib/galaxy.webapps.tool_shed.framework.rst M doc/source/lib/galaxy.webapps.tool_shed.model.migrate.rst M doc/source/lib/galaxy.webapps.tool_shed.model.rst M doc/source/lib/galaxy.webapps.tool_shed.rst M doc/source/lib/galaxy.webapps.tool_shed.search.rst M doc/source/lib/galaxy.webapps.tool_shed.security.rst M doc/source/lib/galaxy.webapps.tool_shed.util.rst A doc/source/lib/galaxy.webhooks.rst M doc/source/lib/galaxy.work.rst M doc/source/lib/galaxy.workflow.rst M doc/source/lib/galaxy.workflow.schedulers.rst M doc/source/lib/galaxy_ext.metadata.rst M doc/source/lib/galaxy_ext.rst R doc/source/lib/galaxy_utils.rst R doc/source/lib/galaxy_utils.sequence.rst M doc/source/lib/log_tempfile.rst M doc/source/lib/modules.rst M doc/source/lib/psyco_full.rst M doc/source/lib/tool_shed.capsule.rst M doc/source/lib/tool_shed.dependencies.repository.rst M doc/source/lib/tool_shed.dependencies.rst M doc/source/lib/tool_shed.dependencies.tool.rst M doc/source/lib/tool_shed.galaxy_install.datatypes.rst M doc/source/lib/tool_shed.galaxy_install.grids.rst M doc/source/lib/tool_shed.galaxy_install.metadata.rst M doc/source/lib/tool_shed.galaxy_install.migrate.rst M doc/source/lib/tool_shed.galaxy_install.repository_dependencies.rst M doc/source/lib/tool_shed.galaxy_install.rst M doc/source/lib/tool_shed.galaxy_install.tool_dependencies.recipe.rst M doc/source/lib/tool_shed.galaxy_install.tool_dependencies.rst M doc/source/lib/tool_shed.galaxy_install.tools.rst M doc/source/lib/tool_shed.galaxy_install.utility_containers.rst M doc/source/lib/tool_shed.grids.rst M doc/source/lib/tool_shed.managers.rst M doc/source/lib/tool_shed.metadata.rst M doc/source/lib/tool_shed.repository_types.rst M doc/source/lib/tool_shed.rst M doc/source/lib/tool_shed.tools.rst M doc/source/lib/tool_shed.util.rst M doc/source/lib/tool_shed.utility_containers.rst M doc/source/project/issues.rst M doc/source/project/organization.rst M doc/source/releases/13.01_announce.rst M doc/source/releases/13.02_announce.rst M doc/source/releases/13.04_announce.rst M doc/source/releases/13.06_announce.rst M doc/source/releases/13.08_announce.rst M doc/source/releases/13.11_announce.rst M doc/source/releases/14.02_announce.rst M doc/source/releases/14.04_announce.rst M doc/source/releases/14.06_announce.rst M doc/source/releases/14.08_announce.rst M doc/source/releases/14.10_announce.rst M doc/source/releases/15.01_announce.rst M doc/source/releases/15.03_announce.rst M doc/source/releases/15.05.rst M doc/source/releases/15.05_announce.rst M doc/source/releases/15.07_announce.rst M doc/source/releases/15.10_announce.rst M doc/source/releases/16.01_announce.rst M doc/source/releases/16.04_announce.rst M doc/source/releases/16.07_announce.rst M doc/source/releases/16.10_announce.rst A doc/source/releases/17.01.rst M doc/source/releases/17.01_announce.rst A doc/source/releases/17.05.rst A doc/source/releases/17.05_announce.rst A doc/source/releases/17.09_announce.rst M doc/source/releases/_header.rst M doc/source/releases/_thanks.rst M doc/source/releases/index.rst M doc/source/releases/older_releases.rst M doc/source/slideshow/architecture/galaxy_architecture.md M doc/source/slideshow/architecture/images/hda_dataset.plantuml.svg M doc/source/slideshow/architecture/images/hda_hdca.plantuml.svg M doc/source/slideshow/architecture/images/objectstore.plantuml.svg M doc/source/slideshow/architecture/images/plantuml_options.txt M doc/source/slideshow/architecture/images/server_client.plantuml.svg M doc/source/slideshow/architecture/images/server_client_old.plantuml.svg M doc/source/slideshow/architecture/images/webapp.plantuml.svg M doc/source/slideshow/architecture/style.css M doc/source/ts_api_doc.rst M lib/galaxy/app.py M lib/galaxy/auth/__init__.py M lib/galaxy/auth/providers/__init__.py M lib/galaxy/auth/providers/ldap_ad.py M lib/galaxy/config.py A lib/galaxy/containers/__init__.py A lib/galaxy/containers/docker.py A lib/galaxy/containers/docker_decorators.py A lib/galaxy/containers/docker_model.py A lib/galaxy/containers/docker_swarm.py A lib/galaxy/containers/docker_swarm_manager.py M lib/galaxy/dataset_collections/matching.py M lib/galaxy/dataset_collections/registry.py M lib/galaxy/dataset_collections/structure.py M lib/galaxy/dataset_collections/types/__init__.py M lib/galaxy/dataset_collections/types/list.py M lib/galaxy/dataset_collections/types/paired.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/blast.py M lib/galaxy/datatypes/chrominfo.py M lib/galaxy/datatypes/constructive_solid_geometry.py M lib/galaxy/datatypes/converters/bedgraph_to_array_tree_converter.py M lib/galaxy/datatypes/converters/cml_to_inchi_converter.xml M lib/galaxy/datatypes/converters/cml_to_mol2_converter.xml M lib/galaxy/datatypes/converters/cml_to_sdf_converter.xml M lib/galaxy/datatypes/converters/cml_to_smi_converter.xml M lib/galaxy/datatypes/converters/fasta_to_tabular_converter.py A lib/galaxy/datatypes/converters/fastqbz2_to_fastq.xml A lib/galaxy/datatypes/converters/fastqcssangerbz2_to_fastqcssanger.xml A lib/galaxy/datatypes/converters/fastqcssangergz_to_fastqcssanger.xml A lib/galaxy/datatypes/converters/fastqgz_to_fastq.xml A lib/galaxy/datatypes/converters/fastqilluminabz2_to_fastqillumina.xml A lib/galaxy/datatypes/converters/fastqilluminagz_to_fastqillumina.xml A lib/galaxy/datatypes/converters/fastqsangerbz2_to_fastqsanger.xml A lib/galaxy/datatypes/converters/fastqsangergz_to_fastqsanger.xml A lib/galaxy/datatypes/converters/fastqsolexabz2_to_fastqsolexa.xml A lib/galaxy/datatypes/converters/fastqsolexagz_to_fastqsolexa.xml M lib/galaxy/datatypes/converters/inchi_to_cml_converter.xml M lib/galaxy/datatypes/converters/inchi_to_mol2_converter.xml M lib/galaxy/datatypes/converters/inchi_to_mol_converter.xml M lib/galaxy/datatypes/converters/inchi_to_sdf_converter.xml M lib/galaxy/datatypes/converters/inchi_to_smi_converter.xml M lib/galaxy/datatypes/converters/interval_to_fli.py M lib/galaxy/datatypes/converters/mol2_to_cml_converter.xml M lib/galaxy/datatypes/converters/mol2_to_inchi_converter.xml M lib/galaxy/datatypes/converters/mol2_to_mol_converter.xml M lib/galaxy/datatypes/converters/mol2_to_sdf_converter.xml M lib/galaxy/datatypes/converters/mol2_to_smi_converter.xml M lib/galaxy/datatypes/converters/mol_to_cml_converter.xml M lib/galaxy/datatypes/converters/mol_to_inchi_converter.xml M lib/galaxy/datatypes/converters/mol_to_mol2_converter.xml M lib/galaxy/datatypes/converters/mol_to_smi_converter.xml M lib/galaxy/datatypes/converters/pbed_ldreduced_converter.py M lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.py M lib/galaxy/datatypes/converters/sam_to_bam.py M lib/galaxy/datatypes/converters/sdf_to_cml_converter.xml M lib/galaxy/datatypes/converters/sdf_to_inchi_converter.xml M lib/galaxy/datatypes/converters/sdf_to_mol2_converter.xml M lib/galaxy/datatypes/converters/sdf_to_smi_converter.xml M lib/galaxy/datatypes/converters/smi_to_cml_converter.xml M lib/galaxy/datatypes/converters/smi_to_inchi_converter.xml M lib/galaxy/datatypes/converters/smi_to_mol2_converter.xml M lib/galaxy/datatypes/converters/smi_to_mol_converter.xml M lib/galaxy/datatypes/converters/smi_to_sdf_converter.xml M lib/galaxy/datatypes/converters/smi_to_smi_converter.xml M lib/galaxy/datatypes/converters/vcf_to_interval_index_converter.py M lib/galaxy/datatypes/converters/wiggle_to_array_tree_converter.py M lib/galaxy/datatypes/converters/wiggle_to_simple_converter.py M lib/galaxy/datatypes/coverage.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/dataproviders/chunk.py M lib/galaxy/datatypes/dataproviders/column.py M lib/galaxy/datatypes/dataproviders/dataset.py M lib/galaxy/datatypes/dataproviders/decorators.py M lib/galaxy/datatypes/dataproviders/external.py M lib/galaxy/datatypes/dataproviders/hierarchy.py M lib/galaxy/datatypes/dataproviders/line.py M lib/galaxy/datatypes/display_applications/application.py M lib/galaxy/datatypes/display_applications/parameters.py M lib/galaxy/datatypes/genetics.py M lib/galaxy/datatypes/graph.py M lib/galaxy/datatypes/images.py M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/molecules.py M lib/galaxy/datatypes/mothur.py M lib/galaxy/datatypes/neo4j.py A lib/galaxy/datatypes/plant_tribes.py M lib/galaxy/datatypes/proteomics.py M lib/galaxy/datatypes/qualityscore.py M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/tabular.py A lib/galaxy/datatypes/test/1.ptkscmp A lib/galaxy/datatypes/test/diamond_db.dmnd M lib/galaxy/datatypes/text.py M lib/galaxy/datatypes/triples.py M lib/galaxy/datatypes/util/gff_util.py M lib/galaxy/datatypes/xml.py M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conda-environment.txt M lib/galaxy/dependencies/conditional-requirements.txt M lib/galaxy/dependencies/dev-requirements.txt M lib/galaxy/dependencies/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt M lib/galaxy/exceptions/__init__.py M lib/galaxy/exceptions/error_codes.json M lib/galaxy/exceptions/error_codes.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/actions/post.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/datasets.py M lib/galaxy/jobs/deferred/__init__.py M lib/galaxy/jobs/dynamic_tool_destination.py M lib/galaxy/jobs/handler.py M lib/galaxy/jobs/metrics/__init__.py M lib/galaxy/jobs/metrics/instrumenters/__init__.py M lib/galaxy/jobs/rule_helper.py M lib/galaxy/jobs/runners/__init__.py A lib/galaxy/jobs/runners/chronos.py M lib/galaxy/jobs/runners/cli.py M lib/galaxy/jobs/runners/condor.py M lib/galaxy/jobs/runners/drmaa.py M lib/galaxy/jobs/runners/kubernetes.py M lib/galaxy/jobs/runners/local.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/jobs/runners/tasks.py M lib/galaxy/jobs/runners/util/cli/__init__.py M lib/galaxy/jobs/runners/util/cli/job/__init__.py M lib/galaxy/jobs/runners/util/cli/job/slurm.py M lib/galaxy/jobs/runners/util/cli/shell/__init__.py M lib/galaxy/jobs/runners/util/cli/shell/local.py M lib/galaxy/jobs/runners/util/cli/shell/rsh.py M lib/galaxy/jobs/runners/util/condor/__init__.py M lib/galaxy/jobs/runners/util/kill.py M lib/galaxy/jobs/runners/util/retry.py M lib/galaxy/jobs/runners/util/sudo.py M lib/galaxy/managers/citations.py M lib/galaxy/managers/collections.py M lib/galaxy/managers/collections_util.py M lib/galaxy/managers/configuration.py M lib/galaxy/managers/datasets.py M lib/galaxy/managers/deletable.py M lib/galaxy/managers/hdas.py M lib/galaxy/managers/hdcas.py M lib/galaxy/managers/tags.py M lib/galaxy/managers/users.py M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/model/base.py M lib/galaxy/model/custom_types.py M lib/galaxy/model/mapping.py M lib/galaxy/model/metadata.py M lib/galaxy/model/migrate/check.py M lib/galaxy/model/migrate/versions/0003_security_and_libraries.py M lib/galaxy/model/migrate/versions/0004_indexes_and_defaults.py M lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py M lib/galaxy/model/migrate/versions/0006_change_qual_datatype.py M lib/galaxy/model/migrate/versions/0007_sharing_histories.py M lib/galaxy/model/migrate/versions/0008_galaxy_forms.py M lib/galaxy/model/migrate/versions/0009_request_table.py M lib/galaxy/model/migrate/versions/0010_hda_display_at_authz_table.py M lib/galaxy/model/migrate/versions/0011_v0010_mysql_index_fix.py M lib/galaxy/model/migrate/versions/0012_user_address.py M lib/galaxy/model/migrate/versions/0013_change_lib_item_templates_to_forms.py M lib/galaxy/model/migrate/versions/0014_pages.py M lib/galaxy/model/migrate/versions/0015_tagging.py M lib/galaxy/model/migrate/versions/0016_v0015_mysql_index_fix.py M lib/galaxy/model/migrate/versions/0017_library_item_indexes.py M lib/galaxy/model/migrate/versions/0018_ordered_tags_and_page_tags.py M lib/galaxy/model/migrate/versions/0019_request_library_folder.py M lib/galaxy/model/migrate/versions/0020_library_upload_job.py M lib/galaxy/model/migrate/versions/0021_user_prefs.py M lib/galaxy/model/migrate/versions/0022_visualization_tables.py M lib/galaxy/model/migrate/versions/0024_page_slug_unique_constraint.py M lib/galaxy/model/migrate/versions/0025_user_info.py M lib/galaxy/model/migrate/versions/0026_cloud_tables.py M lib/galaxy/model/migrate/versions/0027_request_events.py M lib/galaxy/model/migrate/versions/0028_external_metadata_file_override.py M lib/galaxy/model/migrate/versions/0029_user_actions.py M lib/galaxy/model/migrate/versions/0031_community_and_workflow_tags.py M lib/galaxy/model/migrate/versions/0033_published_cols_for_histories_and_workflows.py M lib/galaxy/model/migrate/versions/0034_page_user_share_association.py M lib/galaxy/model/migrate/versions/0035_item_annotations_and_workflow_step_tags.py M lib/galaxy/model/migrate/versions/0036_add_deleted_column_to_library_template_assoc_tables.py M lib/galaxy/model/migrate/versions/0037_samples_library.py M lib/galaxy/model/migrate/versions/0038_add_inheritable_column_to_library_template_assoc_tables.py M lib/galaxy/model/migrate/versions/0039_add_synopsis_column_to_library_table.py M lib/galaxy/model/migrate/versions/0040_page_annotations.py M lib/galaxy/model/migrate/versions/0041_workflow_invocation.py M lib/galaxy/model/migrate/versions/0043_visualization_sharing_tagging_annotating.py M lib/galaxy/model/migrate/versions/0044_add_notify_column_to_request_table.py M lib/galaxy/model/migrate/versions/0045_request_type_permissions_table.py M lib/galaxy/model/migrate/versions/0046_post_job_actions.py M lib/galaxy/model/migrate/versions/0047_job_table_user_id_column.py M lib/galaxy/model/migrate/versions/0048_dataset_instance_state_column.py M lib/galaxy/model/migrate/versions/0049_api_keys_table.py M lib/galaxy/model/migrate/versions/0050_drop_cloud_tables.py M lib/galaxy/model/migrate/versions/0051_imported_col_for_jobs_table.py M lib/galaxy/model/migrate/versions/0052_sample_dataset_table.py M lib/galaxy/model/migrate/versions/0053_item_ratings.py M lib/galaxy/model/migrate/versions/0055_add_pja_assoc_for_jobs.py M lib/galaxy/model/migrate/versions/0057_request_notify.py M lib/galaxy/model/migrate/versions/0058_history_import_export.py M lib/galaxy/model/migrate/versions/0059_sample_dataset_file_path.py M lib/galaxy/model/migrate/versions/0060_history_archive_import.py M lib/galaxy/model/migrate/versions/0062_user_openid_table.py M lib/galaxy/model/migrate/versions/0063_sequencer_table.py M lib/galaxy/model/migrate/versions/0064_add_run_and_sample_run_association_tables.py M lib/galaxy/model/migrate/versions/0065_add_name_to_form_fields_and_values.py M lib/galaxy/model/migrate/versions/0066_deferred_job_and_transfer_job_tables.py M lib/galaxy/model/migrate/versions/0067_populate_sequencer_table.py M lib/galaxy/model/migrate/versions/0068_rename_sequencer_to_external_services.py M lib/galaxy/model/migrate/versions/0069_rename_sequencer_form_type.py M lib/galaxy/model/migrate/versions/0070_add_info_column_to_deferred_job_table.py M lib/galaxy/model/migrate/versions/0071_add_history_and_workflow_to_sample.py M lib/galaxy/model/migrate/versions/0072_add_pid_and_socket_columns_to_transfer_job_table.py M lib/galaxy/model/migrate/versions/0073_add_ldda_to_implicit_conversion_table.py M lib/galaxy/model/migrate/versions/0074_add_purged_column_to_library_dataset_table.py M lib/galaxy/model/migrate/versions/0075_add_subindex_column_to_run_table.py M lib/galaxy/model/migrate/versions/0077_create_tool_tag_association_table.py M lib/galaxy/model/migrate/versions/0078_add_columns_for_disk_usage_accounting.py M lib/galaxy/model/migrate/versions/0079_input_library_to_job_table.py M lib/galaxy/model/migrate/versions/0080_quota_tables.py M lib/galaxy/model/migrate/versions/0081_add_tool_version_to_hda_ldda.py M lib/galaxy/model/migrate/versions/0082_add_tool_shed_repository_table.py M lib/galaxy/model/migrate/versions/0083_add_prepare_files_to_task.py M lib/galaxy/model/migrate/versions/0084_add_ldda_id_to_implicit_conversion_table.py M lib/galaxy/model/migrate/versions/0085_add_task_info.py M lib/galaxy/model/migrate/versions/0086_add_tool_shed_repository_table_columns.py M lib/galaxy/model/migrate/versions/0087_tool_id_guid_map_table.py M lib/galaxy/model/migrate/versions/0088_add_installed_changeset_revison_column.py M lib/galaxy/model/migrate/versions/0089_add_object_store_id_columns.py M lib/galaxy/model/migrate/versions/0090_add_tool_shed_repository_table_columns.py M lib/galaxy/model/migrate/versions/0091_add_tool_version_tables.py M lib/galaxy/model/migrate/versions/0092_add_migrate_tools_table.py M lib/galaxy/model/migrate/versions/0093_add_job_params_col.py M lib/galaxy/model/migrate/versions/0094_add_job_handler_col.py M lib/galaxy/model/migrate/versions/0095_hda_subsets.py M lib/galaxy/model/migrate/versions/0096_openid_provider.py M lib/galaxy/model/migrate/versions/0097_add_ctx_rev_column.py M lib/galaxy/model/migrate/versions/0098_genome_index_tool_data_table.py M lib/galaxy/model/migrate/versions/0099_add_tool_dependency_table.py M lib/galaxy/model/migrate/versions/0100_alter_tool_dependency_table_version_column.py M lib/galaxy/model/migrate/versions/0101_drop_installed_changeset_revision_column.py M lib/galaxy/model/migrate/versions/0102_add_tool_dependency_status_columns.py M lib/galaxy/model/migrate/versions/0103_add_tool_shed_repository_status_columns.py M lib/galaxy/model/migrate/versions/0104_update_genome_downloader_job_parameters.py M lib/galaxy/model/migrate/versions/0105_add_cleanup_event_table.py M lib/galaxy/model/migrate/versions/0106_add_missing_indexes.py M lib/galaxy/model/migrate/versions/0107_add_exit_code_to_job_and_task.py M lib/galaxy/model/migrate/versions/0108_add_extended_metadata.py M lib/galaxy/model/migrate/versions/0109_add_repository_dependency_tables.py M lib/galaxy/model/migrate/versions/0110_add_dataset_uuid.py M lib/galaxy/model/migrate/versions/0111_add_job_destinations.py M lib/galaxy/model/migrate/versions/0112_add_data_manager_history_association_and_data_manager_job_association_tables.py M lib/galaxy/model/migrate/versions/0113_update_migrate_tools_table.py M lib/galaxy/model/migrate/versions/0114_update_migrate_tools_table_again.py M lib/galaxy/model/migrate/versions/0115_longer_user_password_field.py M lib/galaxy/model/migrate/versions/0116_drop_update_available_col_add_tool_shed_status_col.py M lib/galaxy/model/migrate/versions/0117_add_user_activation.py M lib/galaxy/model/migrate/versions/0118_add_hda_extended_metadata.py M lib/galaxy/model/migrate/versions/0119_job_metrics.py M lib/galaxy/model/migrate/versions/0120_dataset_collections.py M lib/galaxy/model/migrate/versions/0121_workflow_uuids.py M lib/galaxy/model/migrate/versions/0122_grow_mysql_blobs.py M lib/galaxy/model/migrate/versions/0123_add_workflow_request_tables.py M lib/galaxy/model/migrate/versions/0124_job_state_history.py M lib/galaxy/model/migrate/versions/0125_workflow_step_tracking.py M lib/galaxy/model/migrate/versions/0126_password_reset.py M lib/galaxy/model/migrate/versions/0127_output_collection_adjustments.py M lib/galaxy/model/migrate/versions/0128_session_timeout.py M lib/galaxy/model/migrate/versions/0129_job_external_output_metadata_validity.py M lib/galaxy/model/migrate/versions/0130_change_pref_datatype.py M lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_parameter_modules.py M lib/galaxy/model/migrate/versions/0132_add_lastpasswordchange_to_user.py M lib/galaxy/model/migrate/versions/0133_add_dependency_column_to_job.py A lib/galaxy/model/migrate/versions/0134_hda_set_deleted_if_purged.py M lib/galaxy/model/orm/engine_factory.py M lib/galaxy/model/orm/scripts.py M lib/galaxy/model/search.py M lib/galaxy/model/tool_shed_install/__init__.py M lib/galaxy/model/tool_shed_install/mapping.py M lib/galaxy/model/tool_shed_install/migrate/check.py M lib/galaxy/objectstore/__init__.py M lib/galaxy/objectstore/azure_blob.py A lib/galaxy/objectstore/pithos.py M lib/galaxy/objectstore/s3.py M lib/galaxy/objectstore/s3_multipart_upload.py M lib/galaxy/queue_worker.py M lib/galaxy/queues.py M lib/galaxy/sample_tracking/external_service_types.py M lib/galaxy/security/__init__.py M lib/galaxy/security/passwords.py R lib/galaxy/tags/__init__.py R lib/galaxy/tags/tag_handler.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/actions/model_operations.py M lib/galaxy/tools/actions/upload_common.py A lib/galaxy/tools/cache.py M lib/galaxy/tools/cwl/cwltool_deps.py M lib/galaxy/tools/cwl/parser.py M lib/galaxy/tools/cwl/representation.py M lib/galaxy/tools/cwl/runtime_actions.py M lib/galaxy/tools/cwl/schema.py M lib/galaxy/tools/data/__init__.py M lib/galaxy/tools/data_manager/manager.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/container_resolvers/__init__.py M lib/galaxy/tools/deps/container_resolvers/explicit.py M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/deps/dependencies.py M lib/galaxy/tools/deps/docker_util.py M lib/galaxy/tools/deps/installable.py M lib/galaxy/tools/deps/mulled/invfile.lua M lib/galaxy/tools/deps/mulled/mulled_build.py M lib/galaxy/tools/deps/mulled/mulled_build_channel.py M lib/galaxy/tools/deps/mulled/mulled_build_files.py M lib/galaxy/tools/deps/mulled/mulled_build_tool.py M lib/galaxy/tools/deps/mulled/mulled_search.py M lib/galaxy/tools/deps/mulled/util.py M lib/galaxy/tools/deps/requirements.py M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/deps/resolvers/brewed_tool_shed_packages.py M lib/galaxy/tools/deps/resolvers/conda.py A lib/galaxy/tools/deps/resolvers/default_conda_mapping.yml M lib/galaxy/tools/deps/resolvers/galaxy_packages.py M lib/galaxy/tools/deps/resolvers/homebrew.py M lib/galaxy/tools/deps/resolvers/modules.py M lib/galaxy/tools/deps/resolvers/resolver_mixins.py A lib/galaxy/tools/deps/singularity_util.py M lib/galaxy/tools/deps/views.py M lib/galaxy/tools/errors.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/execute.py A lib/galaxy/tools/fetcher.py M lib/galaxy/tools/filter_failed_collection.xml A lib/galaxy/tools/filter_from_file.xml M lib/galaxy/tools/flatten_collection.xml M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/imp_exp/export_history.py M lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py M lib/galaxy/tools/linters/general.py M lib/galaxy/tools/linters/inputs.py M lib/galaxy/tools/linters/outputs.py M lib/galaxy/tools/linters/stdio.py M lib/galaxy/tools/linters/tests.py M lib/galaxy/tools/loader_directory.py A lib/galaxy/tools/locations/__init__.py A lib/galaxy/tools/locations/dockstore.py A lib/galaxy/tools/locations/file.py A lib/galaxy/tools/locations/http.py M lib/galaxy/tools/merge_collection.xml M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/dynamic_options.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/tools/parameters/meta.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/parameters/validation.py M lib/galaxy/tools/parameters/wrapped.py M lib/galaxy/tools/parser/cwl.py M lib/galaxy/tools/parser/factory.py M lib/galaxy/tools/parser/interface.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/parser/yaml.py A lib/galaxy/tools/relabel_from_file.xml M lib/galaxy/tools/search/__init__.py M lib/galaxy/tools/toolbox/base.py R lib/galaxy/tools/toolbox/cache.py M lib/galaxy/tools/toolbox/filters/examples.py.sample M lib/galaxy/tools/toolbox/lineages/__init__.py M lib/galaxy/tools/toolbox/lineages/factory.py M lib/galaxy/tools/toolbox/lineages/interface.py R lib/galaxy/tools/toolbox/lineages/stock.py R lib/galaxy/tools/toolbox/lineages/tool_shed.py M lib/galaxy/tools/toolbox/parser.py M lib/galaxy/tools/toolbox/tags.py M lib/galaxy/tools/toolbox/watcher.py M lib/galaxy/tools/unzip_collection.xml M lib/galaxy/tools/util/galaxyops/__init__.py M lib/galaxy/tools/util/maf_utilities.py M lib/galaxy/tools/verify/__init__.py M lib/galaxy/tools/verify/asserts/__init__.py M lib/galaxy/tools/verify/asserts/text.py M lib/galaxy/tools/verify/asserts/xml.py M lib/galaxy/tools/verify/test_data.py M lib/galaxy/tools/wrappers.py M lib/galaxy/tools/xsd/README.md M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/tools/zip_collection.xml M lib/galaxy/tours/__init__.py M lib/galaxy/util/__init__.py A lib/galaxy/util/compression_utils.py A lib/galaxy/util/handlers.py M lib/galaxy/util/json.py M lib/galaxy/util/object_wrapper.py A lib/galaxy/util/oset.py M lib/galaxy/util/plugin_config.py R lib/galaxy/util/postfork.py M lib/galaxy/util/properties.py M lib/galaxy/util/submodules.py A lib/galaxy/util/tool_version.py M lib/galaxy/version.py M lib/galaxy/visualization/genomes.py M lib/galaxy/visualization/plugins/plugin.py M lib/galaxy/web/base/controller.py R lib/galaxy/web/base/controllers/__init__.py R lib/galaxy/web/base/controllers/admin.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/web/framework/base.py M lib/galaxy/web/framework/decorators.py M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/web/framework/middleware/batch.py A lib/galaxy/web/framework/middleware/graphite.py M lib/galaxy/web/framework/middleware/remoteuser.py M lib/galaxy/web/framework/middleware/sentry.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/web/proxy/__init__.py M lib/galaxy/web/proxy/js/lib/mapper.js M lib/galaxy/web/proxy/js/package.json A lib/galaxy/web/stack/__init__.py M lib/galaxy/webapps/galaxy/api/configuration.py M lib/galaxy/webapps/galaxy/api/folder_contents.py M lib/galaxy/webapps/galaxy/api/histories.py M lib/galaxy/webapps/galaxy/api/history_contents.py M lib/galaxy/webapps/galaxy/api/jobs.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py M lib/galaxy/webapps/galaxy/api/library_contents.py M lib/galaxy/webapps/galaxy/api/quotas.py M lib/galaxy/webapps/galaxy/api/tool_dependencies.py M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/api/tools.py A lib/galaxy/webapps/galaxy/api/toolshed.py M lib/galaxy/webapps/galaxy/api/users.py M lib/galaxy/webapps/galaxy/api/webhooks.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/buildapp.py A lib/galaxy/webapps/galaxy/config_watchers.py M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/history.py A lib/galaxy/webapps/galaxy/controllers/interactive_environments.py M lib/galaxy/webapps/galaxy/controllers/library.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/webapps/galaxy/controllers/page.py R lib/galaxy/webapps/galaxy/controllers/search.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/reports/app.py M lib/galaxy/webapps/reports/buildapp.py M lib/galaxy/webapps/reports/config.py M lib/galaxy/webapps/tool_shed/api/categories.py M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/api/tools.py M lib/galaxy/webapps/tool_shed/app.py M lib/galaxy/webapps/tool_shed/buildapp.py M lib/galaxy/webapps/tool_shed/config.py M lib/galaxy/webapps/tool_shed/controllers/admin.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0024_password_reset.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0025_session_timeout.py M lib/galaxy/webapps/util.py M lib/galaxy/webhooks/__init__.py M lib/galaxy/work/context.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/render.py M lib/galaxy/workflow/run.py M lib/galaxy/workflow/run_request.py M lib/galaxy/workflow/schedulers/__init__.py M lib/galaxy/workflow/scheduling_manager.py M lib/galaxy/workflow/steps.py R lib/galaxy_utils/__init__.py R lib/galaxy_utils/sequence/__init__.py R lib/galaxy_utils/sequence/fasta.py R lib/galaxy_utils/sequence/fastq.py R lib/galaxy_utils/sequence/sequence.py R lib/galaxy_utils/sequence/transform.py R lib/galaxy_utils/sequence/vcf.py M lib/log_tempfile.py M lib/tool_shed/capsule/capsule_manager.py M lib/tool_shed/galaxy_install/datatypes/custom_datatype_manager.py M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/galaxy_install/installed_repository_manager.py M lib/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/env_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py M lib/tool_shed/galaxy_install/tool_migration_manager.py M lib/tool_shed/galaxy_install/tools/data_manager.py M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py M lib/tool_shed/galaxy_install/update_repository_manager.py M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/metadata/repository_metadata_manager.py M lib/tool_shed/repository_registry.py M lib/tool_shed/tools/tool_version_manager.py A lib/tool_shed/util/admin_util.py M lib/tool_shed/util/commit_util.py M lib/tool_shed/util/common_util.py M lib/tool_shed/util/readme_util.py M lib/tool_shed/util/repository_util.py M lib/tool_shed/util/shed_util_common.py M lib/tool_shed/util/tool_dependency_util.py M lib/tool_shed/util/tool_util.py M lib/tool_shed/util/workflow_util.py M lib/tool_shed/utility_containers/__init__.py R openid/google.xml M run.sh M run_tests.sh M scripts/api/README M scripts/api/library_upload_dir.py M scripts/bootstrap_history.py M scripts/common_startup.sh M scripts/drmaa_external_runner.py M scripts/external_chown_script.py R scripts/grt.py R scripts/grt.yml.sample A scripts/grt/export.py A scripts/grt/grt.yml.sample A scripts/grt/upload.py A scripts/manage_tool_dependencies.py M scripts/runtime_stats.py A scripts/secret_decoder_ring.py M scripts/slideshow/slideshow_template.html M setup.cfg A static/GruntFile.js A static/GruntFile.js.map A static/maps/admin.toolshed.js.map A static/maps/analysis.js.map A static/maps/app.js.map A static/maps/app/analysis.js.map M static/maps/galaxy.interactive_environments.js.map M static/maps/galaxy.js.map M static/maps/galaxy.library.js.map M static/maps/galaxy.pages.js.map M static/maps/layout/menu.js.map M static/maps/layout/page.js.map M static/maps/layout/panel.js.map M static/maps/layout/scratchbook.js.map M static/maps/libs/jquery/jquery.autocomplete.js.map A static/maps/libs/showdown.js.map M static/maps/mvc/citation/citation-view.js.map A static/maps/mvc/collection/base-creator.js.map M static/maps/mvc/collection/collection-model.js.map M static/maps/mvc/collection/collection-view-edit.js.map M static/maps/mvc/collection/collection-view.js.map M static/maps/mvc/collection/list-collection-creator.js.map M static/maps/mvc/collection/list-of-pairs-collection-creator.js.map M static/maps/mvc/collection/pair-collection-creator.js.map M static/maps/mvc/dataset/data.js.map A static/maps/mvc/dataset/dataset-edit-attributes.js.map M static/maps/mvc/dataset/dataset-li-edit.js.map M static/maps/mvc/dataset/dataset-li.js.map M static/maps/mvc/dataset/dataset-model.js.map M static/maps/mvc/form/form-input.js.map M static/maps/mvc/form/form-parameters.js.map M static/maps/mvc/form/form-section.js.map M static/maps/mvc/form/form-view.js.map M static/maps/mvc/grid/grid-model.js.map A static/maps/mvc/grid/grid-shared.js.map M static/maps/mvc/grid/grid-template.js.map M static/maps/mvc/grid/grid-view.js.map M static/maps/mvc/history/hda-li.js.map M static/maps/mvc/history/hdca-li.js.map M static/maps/mvc/history/history-contents.js.map A static/maps/mvc/history/history-list.js.map M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/history-view-edit-current.js.map M static/maps/mvc/history/history-view-edit.js.map M static/maps/mvc/history/history-view.js.map M static/maps/mvc/history/options-menu.js.map M static/maps/mvc/library/library-folderlist-view.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/mvc/library/library-librarylist-view.js.map M static/maps/mvc/library/library-librarytoolbar-view.js.map M static/maps/mvc/tag.js.map M static/maps/mvc/tool/tool-form-base.js.map M static/maps/mvc/tool/tool-form-composite.js.map R static/maps/mvc/tool/tool-form-workflow.js.map M static/maps/mvc/tool/tool-form.js.map M static/maps/mvc/tool/tools.js.map A static/maps/mvc/toolshed/categories-view.js.map A static/maps/mvc/toolshed/repo-queue-view.js.map A static/maps/mvc/toolshed/repo-status-view.js.map A static/maps/mvc/toolshed/repositories-view.js.map A static/maps/mvc/toolshed/repository-queue-view.js.map A static/maps/mvc/toolshed/repository-view.js.map A static/maps/mvc/toolshed/shed-category-view.js.map A static/maps/mvc/toolshed/shed-list-view.js.map A static/maps/mvc/toolshed/shed-repo-details-view.js.map A static/maps/mvc/toolshed/shed-repo-list-view.js.map A static/maps/mvc/toolshed/sheds-list-view.js.map A static/maps/mvc/toolshed/toolshed-model.js.map A static/maps/mvc/toolshed/util.js.map A static/maps/mvc/toolshed/workflows-view.js.map M static/maps/mvc/tours.js.map M static/maps/mvc/ui/ui-buttons.js.map M static/maps/mvc/ui/ui-color-picker.js.map M static/maps/mvc/ui/ui-misc.js.map M static/maps/mvc/ui/ui-options.js.map M static/maps/mvc/ui/ui-portlet.js.map M static/maps/mvc/ui/ui-select-content.js.map M static/maps/mvc/ui/ui-select-default.js.map M static/maps/mvc/ui/ui-slider.js.map M static/maps/mvc/ui/ui-table.js.map A static/maps/mvc/upload/collection/collection-row.js.map A static/maps/mvc/upload/collection/collection-view.js.map M static/maps/mvc/upload/upload-ftp.js.map M static/maps/mvc/upload/upload-view.js.map A static/maps/mvc/user/user-custom-builds.js.map M static/maps/mvc/user/user-preferences.js.map M static/maps/mvc/user/user-quotameter.js.map M static/maps/mvc/webhooks.js.map M static/maps/mvc/workflow/workflow-canvas.js.map A static/maps/mvc/workflow/workflow-configure-menu.js.map A static/maps/mvc/workflow/workflow-forms.js.map A static/maps/mvc/workflow/workflow-icons.js.map M static/maps/mvc/workflow/workflow-manager.js.map M static/maps/mvc/workflow/workflow-node.js.map M static/maps/mvc/workflow/workflow-terminals.js.map M static/maps/mvc/workflow/workflow-view-node.js.map M static/maps/mvc/workflow/workflow-view.js.map M static/maps/mvc/workflow/workflow.js.map A static/maps/nls/de/locale.js.map A static/maps/nls/es/locale.js.map A static/maps/nls/fr/locale.js.map M static/maps/nls/ja/locale.js.map M static/maps/nls/locale.js.map M static/maps/nls/zh/locale.js.map M static/maps/onload.js.map M static/maps/ui/autocom_tagging.js.map M static/maps/utils/utils.js.map M static/maps/viz/circster.js.map M static/maps/viz/phyloviz.js.map M static/maps/viz/trackster.js.map M static/maps/viz/trackster/tracks.js.map M static/maps/viz/visualization.js.map A static/scripts/admin.toolshed.js A static/scripts/analysis.js A static/scripts/app.js A static/scripts/app/analysis.js A static/scripts/bundled/admin.bundled.js A static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/galaxy.interactive_environments.js M static/scripts/galaxy.js M static/scripts/galaxy.library.js M static/scripts/galaxy.pages.js M static/scripts/layout/menu.js M static/scripts/layout/page.js M static/scripts/layout/panel.js M static/scripts/layout/scratchbook.js M static/scripts/libs/jquery/jquery.autocomplete.js A static/scripts/libs/showdown.js M static/scripts/mvc/citation/citation-view.js A static/scripts/mvc/collection/base-creator.js M static/scripts/mvc/collection/collection-model.js M static/scripts/mvc/collection/collection-view-edit.js M static/scripts/mvc/collection/collection-view.js M static/scripts/mvc/collection/list-collection-creator.js M static/scripts/mvc/collection/list-of-pairs-collection-creator.js M static/scripts/mvc/collection/pair-collection-creator.js M static/scripts/mvc/dataset/data.js A static/scripts/mvc/dataset/dataset-edit-attributes.js M static/scripts/mvc/dataset/dataset-li-edit.js M static/scripts/mvc/dataset/dataset-li.js M static/scripts/mvc/dataset/dataset-model.js M static/scripts/mvc/form/form-input.js M static/scripts/mvc/form/form-parameters.js M static/scripts/mvc/form/form-section.js M static/scripts/mvc/form/form-view.js A static/scripts/mvc/grid/grid-shared.js M static/scripts/mvc/grid/grid-template.js M static/scripts/mvc/grid/grid-view.js M static/scripts/mvc/history/hda-li.js M static/scripts/mvc/history/hdca-li.js M static/scripts/mvc/history/history-contents.js A static/scripts/mvc/history/history-list.js M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/history-view-edit-current.js M static/scripts/mvc/history/history-view-edit.js M static/scripts/mvc/history/history-view.js M static/scripts/mvc/history/options-menu.js M static/scripts/mvc/library/library-folderlist-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/library/library-librarylist-view.js M static/scripts/mvc/library/library-librarytoolbar-view.js M static/scripts/mvc/tag.js M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/tool/tool-form-composite.js R static/scripts/mvc/tool/tool-form-workflow.js M static/scripts/mvc/tool/tool-form.js M static/scripts/mvc/tool/tools.js A static/scripts/mvc/toolshed/categories-view.js A static/scripts/mvc/toolshed/repo-queue-view.js A static/scripts/mvc/toolshed/repo-status-view.js A static/scripts/mvc/toolshed/repositories-view.js A static/scripts/mvc/toolshed/repository-queue-view.js A static/scripts/mvc/toolshed/repository-view.js A static/scripts/mvc/toolshed/shed-category-view.js A static/scripts/mvc/toolshed/shed-list-view.js A static/scripts/mvc/toolshed/shed-repo-details-view.js A static/scripts/mvc/toolshed/shed-repo-list-view.js A static/scripts/mvc/toolshed/sheds-list-view.js A static/scripts/mvc/toolshed/toolshed-model.js A static/scripts/mvc/toolshed/util.js A static/scripts/mvc/toolshed/workflows-view.js M static/scripts/mvc/tours.js M static/scripts/mvc/ui/ui-buttons.js M static/scripts/mvc/ui/ui-color-picker.js M static/scripts/mvc/ui/ui-misc.js M static/scripts/mvc/ui/ui-options.js M static/scripts/mvc/ui/ui-portlet.js M static/scripts/mvc/ui/ui-select-content.js M static/scripts/mvc/ui/ui-select-default.js M static/scripts/mvc/ui/ui-slider.js M static/scripts/mvc/ui/ui-table.js A static/scripts/mvc/upload/collection/collection-row.js A static/scripts/mvc/upload/collection/collection-view.js M static/scripts/mvc/upload/upload-ftp.js M static/scripts/mvc/upload/upload-view.js A static/scripts/mvc/user/user-custom-builds.js M static/scripts/mvc/user/user-preferences.js M static/scripts/mvc/user/user-quotameter.js M static/scripts/mvc/webhooks.js M static/scripts/mvc/workflow/workflow-canvas.js A static/scripts/mvc/workflow/workflow-configure-menu.js A static/scripts/mvc/workflow/workflow-forms.js A static/scripts/mvc/workflow/workflow-icons.js M static/scripts/mvc/workflow/workflow-manager.js M static/scripts/mvc/workflow/workflow-node.js M static/scripts/mvc/workflow/workflow-terminals.js M static/scripts/mvc/workflow/workflow-view-node.js M static/scripts/mvc/workflow/workflow-view.js A static/scripts/mvc/workflow/workflow.js A static/scripts/nls/de/locale.js A static/scripts/nls/es/locale.js A static/scripts/nls/fr/locale.js M static/scripts/nls/ja/locale.js M static/scripts/nls/locale.js M static/scripts/nls/zh/locale.js M static/scripts/onload.js M static/scripts/ui/autocom_tagging.js M static/scripts/utils/utils.js M static/scripts/viz/circster.js M static/scripts/viz/phyloviz.js M static/scripts/viz/trackster.js M static/scripts/viz/trackster/tracks.js M static/scripts/viz/visualization.js M static/style/blue/base.css M static/welcome.html.sample M templates/admin/reload_tool.mako R templates/admin/tool_shed_repository/browse_toolsheds.mako R templates/admin/tool_shed_repository/select_shed_tool_panel_config.mako M templates/admin/tool_shed_repository/select_tool_panel_section.mako M templates/base.mako M templates/base/base_panels.mako M templates/display_base.mako M templates/galaxy_client_app.mako M templates/grid_base.mako M templates/ind_share_base.mako M templates/js-app.mako M templates/sharing_base.mako M templates/show_params.mako R templates/user/dbkeys.mako M templates/user/index.mako M templates/user/login.mako M templates/user/logout.mako M templates/user/register.mako M templates/webapps/galaxy/admin/center.mako R templates/webapps/galaxy/admin/index.mako A templates/webapps/galaxy/admin/manage_dependencies.mako M templates/webapps/galaxy/base_panels.mako M templates/webapps/galaxy/data_manager/index.mako M templates/webapps/galaxy/dataset/display.mako R templates/webapps/galaxy/dataset/edit_attributes.mako M templates/webapps/galaxy/dataset/errors.mako R templates/webapps/galaxy/dataset/grid.mako M templates/webapps/galaxy/galaxy.masthead.mako M templates/webapps/galaxy/galaxy.panels.mako M templates/webapps/galaxy/history/display_structured.mako R templates/webapps/galaxy/history/grid.mako R templates/webapps/galaxy/history/grid_js.mako R templates/webapps/galaxy/history/list_published.mako M templates/webapps/galaxy/history/share.mako R templates/webapps/galaxy/history/shared_grid.mako M templates/webapps/galaxy/mobile/form.mako M templates/webapps/galaxy/mobile/index.mako M templates/webapps/galaxy/page/editor.mako R templates/webapps/galaxy/page/index.mako R templates/webapps/galaxy/page/list_published.mako R templates/webapps/galaxy/page/select_items_grid.mako M templates/webapps/galaxy/requests/common/common.mako M templates/webapps/galaxy/root/tool_runner.mako R templates/webapps/galaxy/tracks/add_to_viz.mako R templates/webapps/galaxy/tracks/add_tracks.mako R templates/webapps/galaxy/tracks/history_datasets_select_grid.mako R templates/webapps/galaxy/tracks/history_select_grid.mako R templates/webapps/galaxy/tracks/library_datasets_select_grid.mako R templates/webapps/galaxy/visualization/list.mako R templates/webapps/galaxy/visualization/list_published.mako M templates/webapps/galaxy/workflow/build_from_current_history.mako R templates/webapps/galaxy/workflow/configure_menu.mako M templates/webapps/galaxy/workflow/display.mako M templates/webapps/galaxy/workflow/editor.mako R templates/webapps/galaxy/workflow/editor_generic_form.mako R templates/webapps/galaxy/workflow/editor_tool_form.mako R templates/webapps/galaxy/workflow/import.mako R templates/webapps/galaxy/workflow/list.mako R templates/webapps/galaxy/workflow/list_for_run.mako R templates/webapps/galaxy/workflow/list_published.mako R templates/webapps/galaxy/workflow/run.mako M templates/webapps/reports/base_panels.mako M templates/webapps/tool_shed/admin/center.mako M templates/webapps/tool_shed/base_panels.mako M templates/webapps/tool_shed/repository/common.mako M templates/webapps/tool_shed/repository/tool_form.mako A test-data/1.fastqsanger.bz2 A test-data/1.fastqsanger.gz A test-data/5_Ig-like.gff A test-data/filter_labels_1.txt A test-data/new_labels_1.txt A test-data/new_labels_2.txt A test-data/new_labels_bad_1.txt A test-data/new_labels_bad_2.txt A test-data/simple.xml M test/TESTING.md R test/api/helpers.py M test/api/test_dataset_collections.py M test/api/test_datasets.py M test/api/test_datatypes.py M test/api/test_histories.py M test/api/test_history_contents.py M test/api/test_history_contents_provenance.py M test/api/test_jobs.py M test/api/test_libraries.py M test/api/test_search.py M test/api/test_tools.py M test/api/test_users.py A test/api/test_visualizations.py A test/api/test_webhooks.py R test/api/test_workflow_1.ga R test/api/test_workflow_2.ga R test/api/test_workflow_batch.ga M test/api/test_workflow_extraction.py R test/api/test_workflow_map_reduce_pause.ga R test/api/test_workflow_matching_lists.ga R test/api/test_workflow_missing_tool.ga R test/api/test_workflow_pause.ga R test/api/test_workflow_topoambigouity.ga R test/api/test_workflow_topoambigouity_auto_laidout.ga R test/api/test_workflow_validation_1.ga R test/api/test_workflow_with_runtime_input.ga M test/api/test_workflows.py M test/api/test_workflows_from_yaml.py R test/api/workflows_format_2/README.txt R test/api/workflows_format_2/__init__.py R test/api/workflows_format_2/converter.py R test/api/workflows_format_2/interface.py R test/api/workflows_format_2/main.py M test/base/api_asserts.py A test/base/data/test_workflow_1.ga A test/base/data/test_workflow_2.ga A test/base/data/test_workflow_batch.ga A test/base/data/test_workflow_map_reduce_pause.ga A test/base/data/test_workflow_matching_lists.ga A test/base/data/test_workflow_missing_tool.ga A test/base/data/test_workflow_pause.ga A test/base/data/test_workflow_topoambigouity.ga A test/base/data/test_workflow_topoambigouity_auto_laidout.ga A test/base/data/test_workflow_validation_1.ga A test/base/data/test_workflow_with_runtime_input.ga M test/base/driver_util.py A test/base/populators.py A test/base/workflows_format_2/README.txt A test/base/workflows_format_2/__init__.py A test/base/workflows_format_2/converter.py A test/base/workflows_format_2/interface.py A test/base/workflows_format_2/main.py R test/casperjs/api-dataset-tests.js R test/casperjs/api-visualizations-tests.js M test/docker/README.md M test/docker/base/Dockerfile M test/docker/base/ansible_vars.yml M test/docker/base/run_test_wrapper.sh M test/functional/tools/checksum.xml A test/functional/tools/collection_creates_dynamic_nested_fail.xml A test/functional/tools/collection_creates_list_fail.xml M test/functional/tools/column_param.xml A test/functional/tools/compressed_bz2_fastq_conversion.xml A test/functional/tools/compressed_bz2_fastq_no_conversion.xml A test/functional/tools/compressed_gz_fastq_conversion.xml A test/functional/tools/compressed_gz_fastq_no_conversion.xml M test/functional/tools/create_10.xml A test/functional/tools/create_2.xml A test/functional/tools/explicit_conversion.xml A test/functional/tools/for_workflows/mapper2.xml A test/functional/tools/identifier_multiple_in_conditional.xml A test/functional/tools/identifier_multiple_in_repeat.xml A test/functional/tools/implicit_conversion.xml A test/functional/tools/is_valid_xml.xml A test/functional/tools/legacy_r.xml M test/functional/tools/md5sum.xml A test/functional/tools/mulled_example_conflict.xml A test/functional/tools/mulled_example_multi_incomplete.xml A test/functional/tools/mulled_example_multi_versionless.xml A test/functional/tools/output_format_deprecated_when.xml A test/functional/tools/param_text_option.xml M test/functional/tools/sample_datatypes_conf.xml M test/functional/tools/samples_tool_conf.xml A test/functional/webhooks/history_test1/config/history_test1.yml A test/functional/webhooks/history_test2/config/history_test2.yml A test/functional/webhooks/masthead_test/config/masthead_test.yml A test/functional/webhooks/phdcomics/config/phdcomics.yaml A test/functional/webhooks/phdcomics/helper/__init__.py A test/functional/webhooks/phdcomics/static/script.js A test/functional/webhooks/phdcomics/static/styles.css A test/functional/webhooks/trans_object/config/trans_object.yaml A test/functional/webhooks/trans_object/helper/__init__.py A test/functional/webhooks/xkcd/config/xkcd.yml A test/functional/webhooks/xkcd/static/script.js A test/functional/webhooks/xkcd/static/styles.css M test/galaxy_selenium/has_driver.py M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation-data.yml M test/galaxy_selenium/sizzle.py A test/integration/resubmission_default_job_conf.xml M test/integration/resubmission_runners.py A test/integration/test_config_options_users.py M test/integration/test_job_resubmission.py A test/integration/test_maximum_worklfow_invocation_duration.py M test/integration/test_resolvers.py A test/integration/test_workflow_handler_configuration.py A test/integration/workflow_handler_configuration_job_conf.xml A test/integration/workflow_handler_configuration_workflow_scheduler_conf.xml M test/manual/workflows_scaling.py M test/qunit/package.json M test/qunit/test-data/bootstrapped.js M test/qunit/test-data/paired-collection-creator.data.js M test/qunit/tests/form_tests.js M test/qunit/tests/galaxy-app-base.js M test/qunit/tests/page_tests.js M test/qunit/tests/ui_tests.html M test/qunit/tests/ui_tests.js M test/qunit/tests/workflow_editor_tests.js A test/selenium_tests/_workflow_fixtures.py M test/selenium_tests/framework.py A test/selenium_tests/test_collection_builders.py M test/selenium_tests/test_history_dataset_state.py M test/selenium_tests/test_history_sharing.py M test/selenium_tests/test_login.py M test/selenium_tests/test_registration.py M test/selenium_tests/test_stock_tours.py M test/selenium_tests/test_tool_form.py M test/selenium_tests/test_uploads.py M test/selenium_tests/test_workflow_editor.py A test/selenium_tests/test_workflow_management.py A test/selenium_tests/test_workflow_run.py M test/shed_functional/base/twilltestcase.py M test/shed_functional/functional/test_1090_repository_dependency_handling.py M test/shed_functional/functional/test_1150_datatype_converters.py A test/unit/jobs/conditional_runners_job_conf.xml M test/unit/jobs/test_job_configuration.py M test/unit/managers/test_HDAManager.py M test/unit/managers/test_HistoryManager.py A test/unit/shed_unit/test_installed_repository_manager.py M test/unit/shed_unit/test_tool_panel_manager.py M test/unit/tools/test_conda_resolution.py M test/unit/tools/test_data_parameters.py M test/unit/tools/test_execution.py M test/unit/tools/test_tool_deps.py M test/unit/tools/test_toolbox.py M test/unit/tools/test_watcher.py M test/unit/tools/test_wrappers.py M test/unit/tools_support.py M test/unit/unittest_utils/galaxy_mock.py M test/unit/workflows/test_modules.py M test/unit/workflows/test_workflow_progress.py M test/unit/workflows/workflow_support.py M tool-data/shared/ucsc/builds.txt.sample M tool-data/shared/ucsc/ucsc_build_sites.txt.sample M tools/evolution/add_scores.xml M tools/extract/extract_genomic_dna.xml M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_attribute.xml M tools/filters/pasteWrapper.xml M tools/filters/trimmer.py M tools/filters/trimmer.xml M tools/filters/wc_gnu.xml M tools/maf/genebed_maf_to_fasta.xml M tools/maf/interval2maf.xml M tools/maf/interval2maf_pairwise.xml M tools/maf/interval_maf_to_merged_fasta.xml M tools/maf/macros.xml M tools/maf/maf_by_block_number.xml M tools/maf/maf_filter.xml M tools/maf/maf_limit_size.xml M tools/maf/maf_limit_to_species.xml M tools/maf/maf_reverse_complement.xml M tools/maf/maf_split_by_species.xml M tools/maf/maf_stats.xml M tools/maf/maf_thread_for_species.xml M tools/maf/maf_to_bed.xml M tools/maf/maf_to_fasta.xml M tools/maf/maf_to_interval.xml M tools/maf/vcf_to_maf_customtrack.xml M tools/metag_tools/shrimp_color_wrapper.xml M tools/metag_tools/shrimp_wrapper.xml M tools/next_gen_conversion/fastq_gen_conv.xml M tools/plotting/bar_chart.xml M tools/stats/aggregate_binned_scores_in_intervals.xml M tox.ini Log Message: ----------- merge with master Commit: 045039da95cf0cb86160e2da18450209ee7409c5 https://github.com/galaxyproject/galaxy/commit/045039da95cf0cb86160e2da1845… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2017-08-07 (Mon, 07 Aug 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/users.py Log Message: ----------- merge with master, address Aysams comments Commit: c0a00890551f3241a17ebd280c71a58880907589 https://github.com/galaxyproject/galaxy/commit/c0a00890551f3241a17ebd280c71… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2017-08-07 (Mon, 07 Aug 2017) Log Message: ----------- merge with master Commit: 82ce70ee67f139cfa1775c9a7be58d1d88c13830 https://github.com/galaxyproject/galaxy/commit/82ce70ee67f139cfa1775c9a7be5… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2017-08-07 (Mon, 07 Aug 2017) Changed paths: M config/user_preferences_extra_conf.xml.sample Log Message: ----------- address Erics comments Commit: 913bf293dba532cae696c4c1fbeea27307e686e3 https://github.com/galaxyproject/galaxy/commit/913bf293dba532cae696c4c1fbee… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2017-08-07 (Mon, 07 Aug 2017) Changed paths: M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map Log Message: ----------- update client Commit: 40071e2949bb4217e10f225d0d9cbf976f76c67f https://github.com/galaxyproject/galaxy/commit/40071e2949bb4217e10f225d0d9c… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2017-08-07 (Mon, 07 Aug 2017) Changed paths: M config/user_preferences_extra_conf.xml.sample Log Message: ----------- remove another password field Commit: 4aa8d631d97e3c253d6f4c1398a599039aa52acf https://github.com/galaxyproject/galaxy/commit/4aa8d631d97e3c253d6f4c1398a5… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2017-08-07 (Mon, 07 Aug 2017) Changed paths: M lib/galaxy/config.py Log Message: ----------- register user_preference config file Commit: 54fb8487d25e2964ca9f7ad02b3b2fc45ed591fb https://github.com/galaxyproject/galaxy/commit/54fb8487d25e2964ca9f7ad02b3b… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2017-08-07 (Mon, 07 Aug 2017) Changed paths: R config/user_preferences_extra_conf.xml.sample A config/user_preferences_extra_conf.yml.sample Log Message: ----------- rename config file Commit: 1ca8f2c927c91d467d160af81081a89073a36b5a https://github.com/galaxyproject/galaxy/commit/1ca8f2c927c91d467d160af81081… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2017-08-07 (Mon, 07 Aug 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/users.py Log Message: ----------- use yml instead of XML and reorder the preference panels Commit: dc9c71f7575450f5100ae538000ac0232e4ead52 https://github.com/galaxyproject/galaxy/commit/dc9c71f7575450f5100ae538000a… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2017-08-07 (Mon, 07 Aug 2017) Changed paths: M lib/galaxy/config.py Log Message: ----------- rename the config files from XML to YML Commit: 03bbbe96a9df6fdfd6ea7599b3cc7a8484a22660 https://github.com/galaxyproject/galaxy/commit/03bbbe96a9df6fdfd6ea7599b3cc… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2017-08-07 (Mon, 07 Aug 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/users.py Log Message: ----------- fix linting error Commit: 305f9f94c04579a8414e0034e0ec90311119431b https://github.com/galaxyproject/galaxy/commit/305f9f94c04579a8414e0034e0ec… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2017-08-08 (Tue, 08 Aug 2017) Changed paths: M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map Log Message: ----------- revert static files Commit: a06ec3e58dc1c53a8bcf515f38c89976eae1a074 https://github.com/galaxyproject/galaxy/commit/a06ec3e58dc1c53a8bcf515f38c8… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-08-08 (Tue, 08 Aug 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/users.py Log Message: ----------- change xml to yml Commit: a71f64c8da2427b6f5808b9f4e91612fe82efe10 https://github.com/galaxyproject/galaxy/commit/a71f64c8da2427b6f5808b9f4e91… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-08-08 (Tue, 08 Aug 2017) Changed paths: M config/user_preferences_extra_conf.yml.sample Log Message: ----------- fix apollo spelling Commit: 338fffad0bcaea709cc552dcab5310e4b73ea4c7 https://github.com/galaxyproject/galaxy/commit/338fffad0bcaea709cc552dcab53… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-08-08 (Tue, 08 Aug 2017) Changed paths: M lib/galaxy/config.py Log Message: ----------- Remove user_preferences_extra_conf.yml sample file from the default list Commit: eb8f7f0da328b0fd440f67bdf0c6f9c5e366a32d https://github.com/galaxyproject/galaxy/commit/eb8f7f0da328b0fd440f67bdf0c6… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-08-08 (Tue, 08 Aug 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/users.py Log Message: ----------- remove debug statement Commit: 196a2bbcf50c4f9fa41588d8e087e5b5cee9da65 https://github.com/galaxyproject/galaxy/commit/196a2bbcf50c4f9fa41588d8e087… Author: Eric Rasche <hxr(a)hx42.org> Date: 2017-08-08 (Tue, 08 Aug 2017) Changed paths: A config/user_preferences_extra_conf.yml.sample M lib/galaxy/config.py M lib/galaxy/webapps/galaxy/api/users.py Log Message: ----------- Merge pull request #3383 from bgruening/extra_user_preferences Add extension point for user preferences Compare: https://github.com/galaxyproject/galaxy/compare/4a35bd3532ce...196a2bbcf50c

1 0

[galaxyproject/infrastructure-playbook] 3e18d5: Increase max walltime for Jetstream jobs for Du No...
by GitHub 08 Aug '17

08 Aug '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 3e18d57835e51c48d17366fed93027a536d41e05 https://github.com/galaxyproject/infrastructure-playbook/commit/3e18d57835e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-08-08 (Tue, 08 Aug 2017) Changed paths: M jetstream_common/templates/slurm/slurm.conf.j2 Log Message: ----------- Increase max walltime for Jetstream jobs for Du Novo: Align Families (how did this work before)?

1 0

[galaxyproject/usegalaxy-playbook] 4d11e2: Main integrated tool panel
by GitHub 08 Aug '17

08 Aug '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 4d11e2dadd455daba11c24eae5a039d7e488717a https://github.com/galaxyproject/usegalaxy-playbook/commit/4d11e2dadd455dab… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-08-08 (Tue, 08 Aug 2017) Changed paths: M env/main/files/galaxy/var/integrated_tool_panel.xml Log Message: ----------- Main integrated tool panel Commit: 2d2db24e8d099282666f5acda432305aeb887a04 https://github.com/galaxyproject/usegalaxy-playbook/commit/2d2db24e8d099282… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-08-08 (Tue, 08 Aug 2017) Changed paths: M env/common/stack.yml M env/main/_inc_config_post_tasks.yml M env/main/group_vars/galaxyservers/vars.yml A env/test/files/nginx/tacc-protected/index.html M env/test/group_vars/webservers/vars.yml M env/test/group_vars/webservers/vault.yml A env/test/templates/nginx/nginx_galaxy.pam.j2 M env/test/templates/nginx/tacc_protected.j2 Log Message: ----------- Fix Main impersonation and other protected stuff Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/f0726c237e5c...…

1 0

[galaxyproject/galaxy] bf6896: Fix get_tool returning list when it shouldn't.
by GitHub 08 Aug '17

08 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: bf68966accd18af2da1e4fa518d01119f5a696f2 https://github.com/galaxyproject/galaxy/commit/bf68966accd18af2da1e4fa518d0… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-08 (Tue, 08 Aug 2017) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Fix get_tool returning list when it shouldn't. Commit: 4a35bd3532ce3a9e0af84c3a86ee33585e9e0ba3 https://github.com/galaxyproject/galaxy/commit/4a35bd3532ce3a9e0af84c3a86ee… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-08-08 (Tue, 08 Aug 2017) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Merge pull request #4390 from jmchilton/toollist Fix get_tool returning list when it shouldn't. Compare: https://github.com/galaxyproject/galaxy/compare/d53a5424967e...4a35bd3532ce

1 0

[galaxyproject/galaxy] ecad39: Refactor ToolOutputCollectionStructure to allow it...
by GitHub 08 Aug '17

08 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ecad3996f1f4715db5ff326f9f6ae5067cd2e0fc https://github.com/galaxyproject/galaxy/commit/ecad3996f1f4715db5ff326f9f6a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-08 (Tue, 08 Aug 2017) Changed paths: M lib/galaxy/tools/parser/output_objects.py Log Message: ----------- Refactor ToolOutputCollectionStructure to allow it be more easily consumed. Make complex arguments optional. Commit: e8112210429d710a9eb9702f541cfaed6e219454 https://github.com/galaxyproject/galaxy/commit/e8112210429d710a9eb9702f541c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-08 (Tue, 08 Aug 2017) Changed paths: M lib/galaxy/tools/parser/output_objects.py Log Message: ----------- Improve cohesion of interaction between ToolOutputCollectionStructure and ToolOutputCollection. Shield more of ToolOutputCollectionStructure internals from ToolOutputCollection. Commit: d53a5424967e46d683f7baafe06cb53703e86adf https://github.com/galaxyproject/galaxy/commit/d53a5424967e46d683f7baafe06c… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-08-08 (Tue, 08 Aug 2017) Changed paths: M lib/galaxy/tools/parser/output_objects.py Log Message: ----------- Merge pull request #4389 from jmchilton/output_collect_refactor Refactor ToolOutputCollectionStructure... Compare: https://github.com/galaxyproject/galaxy/compare/d2394aa172e2...d53a5424967e

1 0

[galaxyproject/galaxy] 15cc6e: Async update 20170615
by GitHub 07 Aug '17

07 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 15cc6e461a9d921c9762a54a112f74abc9353309 https://github.com/galaxyproject/galaxy/commit/15cc6e461a9d921c9762a54a112f… Author: Fabio Cumbo <fabio.cumbo(a)gmail.com> Date: 2017-06-15 (Thu, 15 Jun 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/async.py Log Message: ----------- Async update 20170615 The asynchronous procedure expects that only one output is defined in the tool XML schema. This improvement permits to define also collections. This feature is useful in conjunction with tools like [galaxy-json-collect-data-source](https://github.com/fabio-cumbo/galaxy- json-collect-data-source) (please see the README of the tool for more information). It does not affect the behaviour of the asynchronous data sources previously developed. Commit: b4fdc27f533a0a204f9eedfcd265a15ef0fb469e https://github.com/galaxyproject/galaxy/commit/b4fdc27f533a0a204f9eedfcd265… Author: Fabio Cumbo <fabio.cumbo(a)gmail.com> Date: 2017-06-16 (Fri, 16 Jun 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/async.py Log Message: ----------- Blank line contains whitespace: fixed Commit: d5409500aebe1c5798ae632977be64b8f71a85a8 https://github.com/galaxyproject/galaxy/commit/d5409500aebe1c5798ae632977be… Author: Fabio Cumbo <fabio.cumbo(a)gmail.com> Date: 2017-07-11 (Tue, 11 Jul 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/async.py Log Message: ----------- minor update 20170711 if GALAXY_TYPE is provided, we do not need to loop over tool.outputs.values() Commit: e516ba738ecbb13f29d072fd0ad707f8470369de https://github.com/galaxyproject/galaxy/commit/e516ba738ecbb13f29d072fd0ad7… Author: Fabio Cumbo <fabio.cumbo(a)gmail.com> Date: 2017-07-11 (Tue, 11 Jul 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/async.py Log Message: ----------- except Exception: fixed Commit: 835e4fb0ae09c12a8db80ca6f3d339275f3881f0 https://github.com/galaxyproject/galaxy/commit/835e4fb0ae09c12a8db80ca6f3d3… Author: Fabio Cumbo <fabio.cumbo(a)gmail.com> Date: 2017-07-12 (Wed, 12 Jul 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/async.py Log Message: ----------- outputs count: fixed Commit: d2394aa172e2030c301f7b50863fb3d96664a2db https://github.com/galaxyproject/galaxy/commit/d2394aa172e2030c301f7b50863f… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-08-07 (Mon, 07 Aug 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/async.py Log Message: ----------- Merge pull request #4198 from fabio-cumbo/data-source-async Async update: support to collections Compare: https://github.com/galaxyproject/galaxy/compare/6e37bc05c1d5...d2394aa172e2

1 0