galaxy-commits March 2017

galaxy-commits@lists.galaxyproject.org

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159 discussions

[galaxyproject/infrastructure-playbook] 6353ac: Redirect wiki pages to hub
by GitHub 09 Mar '17

09 Mar '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 6353ac6c8ebad10bcf8b72f144f0a4f7b9173b0f https://github.com/galaxyproject/infrastructure-playbook/commit/6353ac6c8eb… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-03-09 (Thu, 09 Mar 2017) Changed paths: M galaxyenv/host_vars/chouffe.galaxyproject.org.yml M galaxyenv/templates/nginx/wiki.j2 A galaxyenv/templates/nginx/wiki_hub_rewrites.conf.j2 Log Message: ----------- Redirect wiki pages to hub

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[galaxyproject/galaxy] 02f3a2: Bug fix for masthead webhook if Galaxy.page is und...
by GitHub 09 Mar '17

09 Mar '17

Branch: refs/heads/release_16.10 Home: https://github.com/galaxyproject/galaxy Commit: 02f3a2737dd1c48574df9bf8e51ce43e6789bf1e https://github.com/galaxyproject/galaxy/commit/02f3a2737dd1c48574df9bf8e51c… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-03-08 (Wed, 08 Mar 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: ----------- Bug fix for masthead webhook if Galaxy.page is undefined for workflow, data libraries etc pages Commit: 1b9a2868a17899787bf65181f96892596b16b51b https://github.com/galaxyproject/galaxy/commit/1b9a2868a17899787bf65181f968… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-03-09 (Thu, 09 Mar 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: ----------- Merge pull request #3728 from martenson/backport-masthead-fix [16.10] backport of webhook masthead fix for datalibs and workflows Compare: https://github.com/galaxyproject/galaxy/compare/b41b8e305bac...1b9a2868a178

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[galaxyproject/galaxy] 9928a7: Merge ConfiguresGalaxyMixin.reload_toolbox() in _c...
by GitHub 09 Mar '17

09 Mar '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 9928a74c6c1cb57edbfba4068616bd5b15f51093 https://github.com/galaxyproject/galaxy/commit/9928a74c6c1cb57edbfba4068616… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-03-09 (Thu, 09 Mar 2017) Changed paths: M lib/galaxy/config.py Log Message: ----------- Merge ConfiguresGalaxyMixin.reload_toolbox() in _configure_toolbox() It's called only once from there when app is initialised, real toolbox reloads are performed by executing reload_toolbox() from lib/galaxy/queue_worker.py . Commit: a89954c8928f0997aa9a5781a39d18339914b387 https://github.com/galaxyproject/galaxy/commit/a89954c8928f0997aa9a5781a39d… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-03-09 (Thu, 09 Mar 2017) Changed paths: M lib/galaxy/queue_worker.py Log Message: ----------- Fix 2 typos Commit: bcc4e025c36c3ee394c73cee06a8031cec6e9354 https://github.com/galaxyproject/galaxy/commit/bcc4e025c36c3ee394c73cee06a8… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-03-09 (Thu, 09 Mar 2017) Changed paths: M lib/galaxy/config.py M lib/galaxy/queue_worker.py Log Message: ----------- Merge pull request #3732 from nsoranzo/reload_toolbox_merge Merge ConfiguresGalaxyMixin.reload_toolbox() in _configure_toolbox() Compare: https://github.com/galaxyproject/galaxy/compare/704e6a6676c2...bcc4e025c36c

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[galaxyproject/galaxy] 845e43: Avoid autoconversion of boolean values when callin...
by GitHub 08 Mar '17

08 Mar '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 845e43c1e537f66c8208165a82583b4ca814b1f0 https://github.com/galaxyproject/galaxy/commit/845e43c1e537f66c8208165a8258… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-03-03 (Fri, 03 Mar 2017) Changed paths: M lib/galaxy/tools/parameters/basic.py M lib/galaxy/util/json.py Log Message: ----------- Avoid autoconversion of boolean values when calling json loads Remove unused import Fix Commit: cb27f921c7e82f09c675e1e472417ad47d65bfab https://github.com/galaxyproject/galaxy/commit/cb27f921c7e82f09c675e1e47241… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-03-03 (Fri, 03 Mar 2017) Changed paths: M lib/galaxy/util/json.py Log Message: ----------- Fix comment Commit: 704e6a6676c2aa6aafe4a283f50dcfd8a646682e https://github.com/galaxyproject/galaxy/commit/704e6a6676c2aa6aafe4a283f50d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-08 (Wed, 08 Mar 2017) Changed paths: M lib/galaxy/tools/parameters/basic.py M lib/galaxy/util/json.py Log Message: ----------- Merge pull request #3702 from guerler/fix_boolean_handling Properly handle boolean values when parsed to a string-based/default tool parameter Compare: https://github.com/galaxyproject/galaxy/compare/0118c57af3ea...704e6a6676c2

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[galaxyproject/galaxy] aa0af3: Add a simple UI to manage tool dependencies
by GitHub 08 Mar '17

08 Mar '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: aa0af352cdd034872d24b3a5f497a04204c9c017 https://github.com/galaxyproject/galaxy/commit/aa0af352cdd034872d24b3a5f497… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-03-08 (Wed, 08 Mar 2017) Changed paths: M lib/galaxy/web/base/controllers/admin.py M templates/webapps/galaxy/admin/index.mako A templates/webapps/galaxy/admin/manage_dependencies.mako M templates/webapps/tool_shed/repository/common.mako Log Message: ----------- Add a simple UI to manage tool dependencies This page simply lists all loaded tools and their dependency status. On the left are checkboxes to select multiple tools, and at the bottom is a button to install the selected tool dependencies. Commit: 818c10832a1429b79e65906d106b6fda0ed28a35 https://github.com/galaxyproject/galaxy/commit/818c10832a1429b79e65906d106b… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-03-08 (Wed, 08 Mar 2017) Changed paths: M lib/galaxy/web/base/controllers/admin.py M templates/webapps/galaxy/admin/manage_dependencies.mako Log Message: ----------- Build the dependency status more efficiently: Pass a dictionary with ToolRequirements object as key and requirements status as value Commit: f882a14886de65b0079d5eea72a7bea044ab4a02 https://github.com/galaxyproject/galaxy/commit/f882a14886de65b0079d5eea72a7… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-03-08 (Wed, 08 Mar 2017) Changed paths: M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/web/base/controllers/admin.py M templates/webapps/galaxy/admin/manage_dependencies.mako Log Message: ----------- Add new view that primarily manages dependencies Commit: f1bb5a6a7114f1aa4dc331622183432604e9dbc7 https://github.com/galaxyproject/galaxy/commit/f1bb5a6a7114f1aa4dc331622183… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-03-08 (Wed, 08 Mar 2017) Changed paths: M templates/webapps/galaxy/admin/manage_dependencies.mako Log Message: ----------- close opened div Commit: 96ae2893b3610e28101445f58966cffd61f873eb https://github.com/galaxyproject/galaxy/commit/96ae2893b3610e28101445f58966… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-03-08 (Wed, 08 Mar 2017) Changed paths: M templates/webapps/galaxy/admin/manage_dependencies.mako Log Message: ----------- improve the markup and UX a bit Commit: 5dc73b7966d3c9e90e0a58823e34bc26663d5d71 https://github.com/galaxyproject/galaxy/commit/5dc73b7966d3c9e90e0a58823e34… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-03-08 (Wed, 08 Mar 2017) Changed paths: M templates/webapps/galaxy/admin/manage_dependencies.mako Log Message: ----------- Add title and explanation for Manage Tool Dependencies page. Commit: 0118c57af3ea2bae8b5c8c72fa45f431afb4aa8f https://github.com/galaxyproject/galaxy/commit/0118c57af3ea2bae8b5c8c72fa45… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-03-08 (Wed, 08 Mar 2017) Changed paths: M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/web/base/controllers/admin.py M templates/webapps/galaxy/admin/index.mako A templates/webapps/galaxy/admin/manage_dependencies.mako M templates/webapps/tool_shed/repository/common.mako Log Message: ----------- Merge pull request #3479 from mvdbeek/manage_tool_dependencies Add a simple UI to manage tool dependencies Compare: https://github.com/galaxyproject/galaxy/compare/07490e428dc0...0118c57af3ea

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[galaxyproject/galaxy] ba8d03: Adding overlay search feature to webhooks
by GitHub 08 Mar '17

08 Mar '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ba8d03624cad0b0d78d11f07ee9b05446977e6a0 https://github.com/galaxyproject/galaxy/commit/ba8d03624cad0b0d78d11f07ee9b… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-01-08 (Sun, 08 Jan 2017) Changed paths: M client/galaxy/scripts/onload.js 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 M static/maps/onload.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/onload.js Log Message: ----------- Adding overlay search feature to webhooks Commit: d66e2f912964fdc05c239b52f2dab440313513b5 https://github.com/galaxyproject/galaxy/commit/d66e2f912964fdc05c239b52f2da… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-01-09 (Mon, 09 Jan 2017) Changed paths: M config/plugins/webhooks/demo/search/config/searchover.yaml Log Message: ----------- Updating the logic to pull search plugin static code Commit: f6e0d65efcb517634540d5392d7d0c44e4f25bc2 https://github.com/galaxyproject/galaxy/commit/f6e0d65efcb517634540d5392d7d… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-01-10 (Tue, 10 Jan 2017) Changed paths: M config/plugins/webhooks/demo/search/static/script.js M config/plugins/webhooks/demo/search/static/styles.css Log Message: ----------- Adding items to the favorites when pinned and filter is home Commit: 07d9b63d09f2e3918a96b6be6f4778ac97a747d2 https://github.com/galaxyproject/galaxy/commit/07d9b63d09f2e3918a96b6be6f47… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-01-10 (Tue, 10 Jan 2017) Changed paths: M config/plugins/webhooks/demo/search/config/searchover.yaml M config/plugins/webhooks/demo/search/static/script.js Log Message: ----------- Synchronising pin/ unpin actions in the favorites section Commit: 839c9091dd39056243f6d75ea4a0797749882ee3 https://github.com/galaxyproject/galaxy/commit/839c9091dd39056243f6d75ea4a0… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-01-10 (Tue, 10 Jan 2017) Changed paths: M config/plugins/webhooks/demo/search/static/styles.css Log Message: ----------- Updating styles for tiles Commit: 5ad2e5ce66a36644eead2c50f51f971363b210e1 https://github.com/galaxyproject/galaxy/commit/5ad2e5ce66a36644eead2c50f51f… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-01-11 (Wed, 11 Jan 2017) Changed paths: M config/plugins/webhooks/demo/search/static/script.js M config/plugins/webhooks/demo/search/static/styles.css Log Message: ----------- Synchronising the deletion of item in favourites with pinned item in search results if any Commit: 3b6ddb992f1c0824e688ed7c9ab913d68826eda3 https://github.com/galaxyproject/galaxy/commit/3b6ddb992f1c0824e688ed7c9ab9… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-01-13 (Fri, 13 Jan 2017) Changed paths: M config/plugins/webhooks/demo/search/static/script.js Log Message: ----------- Fixing bug with aligning items in tools section Commit: 9dc814e81171f873fce15a63210138bc239f8063 https://github.com/galaxyproject/galaxy/commit/9dc814e81171f873fce15a632101… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-01-13 (Fri, 13 Jan 2017) Changed paths: M config/plugins/webhooks/demo/search/static/styles.css Log Message: ----------- Adding hover styles for tiles Commit: 78f29eab856220bd0fe44566cba7f850a91f6e41 https://github.com/galaxyproject/galaxy/commit/78f29eab856220bd0fe44566cba7… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-01-14 (Sat, 14 Jan 2017) Changed paths: M config/plugins/webhooks/demo/search/static/styles.css Log Message: ----------- Moving the pin icon to the left of tiles Commit: 34be05339915df8554a619a086214974f98e5bcb https://github.com/galaxyproject/galaxy/commit/34be05339915df8554a619a08621… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-01-21 (Sat, 21 Jan 2017) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/jenkins/selenium/run_galaxy.bash M .ci/py3_sources.txt M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/ui/ui-misc.js M config/datatypes_conf.xml.sample M config/plugins/interactive_environments/rstudio/templates/rstudio.mako 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 M config/plugins/webhooks/demo/phdcomics/helper/__init__.py M config/plugins/webhooks/demo/phdcomics/static/script.js M doc/schema_template.md M doc/source/admin/webhooks.rst M doc/source/api/guidelines.rst M lib/galaxy/datatypes/binary.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/data.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py A lib/galaxy/datatypes/test/diamond_db.dmnd M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/actions/post.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.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/mulled.py M lib/galaxy/tools/deps/requirements.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/deps/resolvers/resolver_mixins.py M lib/galaxy/tools/deps/views.py M lib/galaxy/tools/errors.py M lib/galaxy/tools/evaluation.py 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/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/search/__init__.py M lib/galaxy/tools/util/galaxyops/__init__.py M lib/galaxy/tools/util/maf_utilities.py M lib/galaxy/tools/verify/asserts/__init__.py M lib/galaxy/tools/verify/test_data.py M lib/galaxy/tools/wrappers.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/util/object_wrapper.py M lib/galaxy/web/framework/middleware/remoteuser.py M lib/galaxy/webapps/galaxy/api/configuration.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/util/shed_util_common.py M run_tests.sh A static/maps/libs/showdown.js.map M static/maps/mvc/form/form-view.js.map M static/maps/mvc/ui/ui-misc.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map A static/scripts/libs/showdown.js M static/scripts/mvc/form/form-view.js M static/scripts/mvc/ui/ui-misc.js M templates/ind_share_base.mako M templates/webapps/galaxy/history/share.mako A test-data/1.fastqsanger.bz2 A test-data/1.fastqsanger.gz M test/api/test_workflows.py M test/docker/README.md 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 A test/functional/tools/explicit_conversion.xml A test/functional/tools/implicit_conversion.xml A test/functional/tools/mulled_example_conflict.xml M test/functional/tools/sample_datatypes_conf.xml M test/functional/tools/samples_tool_conf.xml M test/galaxy_selenium/navigates_galaxy.py M test/selenium_tests/test_history_dataset_state.py M test/selenium_tests/test_history_sharing.py M test/selenium_tests/test_tool_form.py M test/selenium_tests/test_workflow_editor.py M test/selenium_tests/test_workflow_management.py Log Message: ----------- Merging with dev Commit: 823ac3cc6172db54c35fdae43553af304a6a162b https://github.com/galaxyproject/galaxy/commit/823ac3cc6172db54c35fdae43553… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2017-02-11 (Sat, 11 Feb 2017) Changed paths: M config/plugins/webhooks/demo/search/static/script.js M config/plugins/webhooks/demo/search/static/styles.css Log Message: ----------- add new Search plugin styles Commit: 4120781713cc65d3c05064bee981cf826d5c4be8 https://github.com/galaxyproject/galaxy/commit/4120781713cc65d3c05064bee981… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2017-03-05 (Sun, 05 Mar 2017) Changed paths: M config/galaxy.ini.sample M config/plugins/webhooks/demo/search/static/styles.css Log Message: ----------- increase contrast and improve readability Commit: 0bfe9fa7ca1489d744351eecc4312838a20008eb https://github.com/galaxyproject/galaxy/commit/0bfe9fa7ca1489d744351eecc431… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-03-07 (Tue, 07 Mar 2017) Changed paths: M .ci/flake8_blacklist.txt M .ci/flake8_lint_include_list.txt M .ci/jenkins/selenium/run_tests.sh M .ci/py3_sources.txt M CONTRIBUTING.md M README.rst M client/galaxy/scripts/libs/jquery/jquery.autocomplete.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-view.js M client/galaxy/scripts/mvc/history/hda-li.js M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/history/options-menu.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/ui/ui-misc.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/upload/upload-ftp.js M client/galaxy/scripts/mvc/user/user-quotameter.js M client/galaxy/scripts/mvc/workflow/workflow-canvas.js A client/galaxy/scripts/mvc/workflow/workflow-forms.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-view-node.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/scripts/ui/autocom_tagging.js M client/galaxy/scripts/viz/trackster/tracks.js M client/galaxy/style/less/base.less M client/galaxy/style/less/history.less M client/galaxy/style/less/ui.less A config/build_sites.yml.sample M config/datatypes_conf.xml.sample M config/galaxy.ini.sample A config/local_conda_mapping.yml.sample M config/plugins/interactive_environments/bam_iobio/config/bam_iobio.ini.sample 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/neo/config/neo.ini.sample M config/plugins/interactive_environments/phinch/config/phinch.ini.sample M config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample M config/plugins/tours/core.galaxy_ui.yaml M config/plugins/tours/core.history.yaml 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/ngl/viewer.js M config/plugins/visualizations/charts/static/repository/registry.json 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 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 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 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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/ui/ui-misc.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/upload/upload-ftp.js M static/scripts/mvc/user/user-quotameter.js M static/scripts/mvc/workflow/workflow-canvas.js A static/scripts/mvc/workflow/workflow-forms.js M static/scripts/mvc/workflow/workflow-manager.js M static/scripts/mvc/workflow/workflow-node.js M static/scripts/mvc/workflow/workflow-view-node.js M static/scripts/mvc/workflow/workflow-view.js M static/scripts/ui/autocom_tagging.js M static/scripts/viz/trackster/tracks.js M static/style/blue/base.css M templates/admin/reload_tool.mako M templates/grid_base.mako A templates/webapps/galaxy/user/manage_info.mako M templates/webapps/galaxy/workflow/editor.mako R 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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 M test/integration/test_resolvers.py M test/qunit/tests/form_tests.js M test/qunit/tests/workflow_editor_tests.js M test/selenium_tests/framework.py A test/selenium_tests/test_collection_builders.py M test/selenium_tests/test_stock_tours.py M test/selenium_tests/test_uploads.py M test/selenium_tests/test_workflow_editor.py M test/unit/managers/test_HDAManager.py M test/unit/managers/test_HistoryManager.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/workflows/test_modules.py M test/unit/workflows/test_workflow_progress.py M tools/data_source/upload.py M tools/evolution/add_scores.xml M tools/extract/extract_genomic_dna.xml M tools/filters/pasteWrapper.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: ----------- Merging with dev Commit: 07490e428dc0a3596d7623a7a787443494626c63 https://github.com/galaxyproject/galaxy/commit/07490e428dc0a3596d7623a7a787… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-08 (Wed, 08 Mar 2017) Changed paths: M client/galaxy/scripts/onload.js M config/galaxy.ini.sample 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 M static/maps/onload.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/onload.js Log Message: ----------- Merge pull request #3460 from bgruening/search_overlay Overlay search for tools, wf, libraries and histories Compare: https://github.com/galaxyproject/galaxy/compare/b9c1abd43a69...07490e428dc0

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[galaxyproject/galaxy]
by GitHub 08 Mar '17

08 Mar '17

Branch: refs/heads/datamanager_conda_install Home: https://github.com/galaxyproject/galaxy

1 0

[galaxyproject/galaxy] b7820d: Allow display of install_resolver_checkbox when in...
by GitHub 08 Mar '17

08 Mar '17

Branch: refs/heads/datamanager_conda_install Home: https://github.com/galaxyproject/galaxy Commit: b7820d1269ca6bf7571ab6d0305504e9826a5872 https://github.com/galaxyproject/galaxy/commit/b7820d1269ca6bf7571ab6d03055… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-03-01 (Wed, 01 Mar 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M templates/admin/tool_shed_repository/select_shed_tool_panel_config.mako Log Message: ----------- Allow display of install_resolver_checkbox when installing data manager tools Commit: 2abc7b0d2b0c422a4f7c89ae7bdf767088323be2 https://github.com/galaxyproject/galaxy/commit/2abc7b0d2b0c422a4f7c89ae7bdf… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-03-08 (Wed, 08 Mar 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py R templates/admin/tool_shed_repository/select_shed_tool_panel_config.mako M templates/admin/tool_shed_repository/select_tool_panel_section.mako Log Message: ----------- Merge select_shed_tool_panel_config.mako functionality into select_tool_panel_section.mako Commit: 7d7e36e5d40c3418f5712d9f9a9e8bd4140c5bc5 https://github.com/galaxyproject/galaxy/commit/7d7e36e5d40c3418f5712d9f9a9e… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-03-08 (Wed, 08 Mar 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py Log Message: ----------- Remove checks for `includes_tools_for_display_in_tool_panel` and `includes_tools_for_display_in_tool_panel` when determining if initiate_repository_installation.mako should be posted to. It is sufficient to check that select_tool_panel_section_button has been clicked. Commit: 7372d5a339794f8eecc31afbc7f21c983c50b7a6 https://github.com/galaxyproject/galaxy/commit/7372d5a339794f8eecc31afbc7f2… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-03-08 (Wed, 08 Mar 2017) Changed paths: M test/shed_functional/functional/test_1150_datatype_converters.py Log Message: ----------- Adjust wording of datatype converter install test. Compare: https://github.com/galaxyproject/galaxy/compare/b7820d1269ca^...7372d5a33979

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[galaxyproject/galaxy] 072f99: Fix cycle detection for single node workflows.
by GitHub 08 Mar '17

08 Mar '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 072f998bbaaf74fbf4f6992d264af9a853f723ec https://github.com/galaxyproject/galaxy/commit/072f998bbaaf74fbf4f6992d264a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-27 (Tue, 27 Dec 2016) Changed paths: M lib/galaxy/workflow/steps.py Log Message: ----------- Fix cycle detection for single node workflows. Fixes #3236. Commit: b9c1abd43a69241accd54d3531442b56508efc0f https://github.com/galaxyproject/galaxy/commit/b9c1abd43a69241accd54d353144… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2017-03-07 (Tue, 07 Mar 2017) Changed paths: M lib/galaxy/workflow/steps.py Log Message: ----------- Merge pull request #3374 from jmchilton/singleton_workflow_cycles Fix cycle detection for single node workflows. Compare: https://github.com/galaxyproject/galaxy/compare/9aa911d509ac...b9c1abd43a69

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[galaxyproject/galaxy] 79945f: Do not require stored workflow id for subworkflows
by GitHub 07 Mar '17

07 Mar '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 79945f37c31d4d42be86bee352370af11b063271 https://github.com/galaxyproject/galaxy/commit/79945f37c31d4d42be86bee35237… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-03-07 (Tue, 07 Mar 2017) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Do not require stored workflow id for subworkflows Commit: 9aa911d509ac50f44ba4e6c5dca2cb9dba61ebbb https://github.com/galaxyproject/galaxy/commit/9aa911d509ac50f44ba4e6c5dca2… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-03-07 (Tue, 07 Mar 2017) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Merge pull request #3723 from guerler/fix_subworkflow_id Do not require stored workflow id for subworkflows Compare: https://github.com/galaxyproject/galaxy/compare/1b12259739e2...9aa911d509ac

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