galaxy-commits May 2017

galaxy-commits@lists.galaxyproject.org

1 participants
135 discussions

[galaxyproject/usegalaxy-playbook] dc7efc: Fix walltime exception for align families running ...
by GitHub 30 May '17

30 May '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: dc7efc2de746b58812b8e318ed6bad54c175e515 https://github.com/galaxyproject/usegalaxy-playbook/commit/dc7efc2de746b588… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-05-30 (Tue, 30 May 2017) Changed paths: M files/galaxy/common/dynamic_rules/multi_dynamic_walltime.py M files/galaxy/usegalaxy.org/var/integrated_tool_panel.xml M files/galaxy/usegalaxy.org/var/shed_data_manager_conf.xml M files/galaxy/usegalaxy.org/var/shed_tool_data_table_conf.xml M production/galaxy_version.yml Log Message: ----------- Fix walltime exception for align families running on local cluster and update Main

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[galaxyproject/usegalaxy-playbook]
by GitHub 30 May '17

30 May '17

Branch: refs/heads/martenson-patch-1 Home: https://github.com/galaxyproject/usegalaxy-playbook

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[galaxyproject/usegalaxy-playbook] 1283e7: give salmon 16gb and rna_Star 64
by GitHub 30 May '17

30 May '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 1283e77813b20b31ee19271f289e01a149dc94cd https://github.com/galaxyproject/usegalaxy-playbook/commit/1283e77813b20b31… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-05-25 (Thu, 25 May 2017) Changed paths: M templates/galaxy/usegalaxy.org/config/job_conf.xml.j2 Log Message: ----------- give salmon 16gb and rna_Star 64 Commit: 4de1718bc260a36bc13be6d3c049a83231077e75 https://github.com/galaxyproject/usegalaxy-playbook/commit/4de1718bc260a36b… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-05-30 (Tue, 30 May 2017) Changed paths: M templates/galaxy/usegalaxy.org/config/job_conf.xml.j2 Log Message: ----------- Merge pull request #28 from galaxyproject/martenson-patch-1 give salmon 16gb and rna_Star 64 Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/07c13f0094d2...…

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[galaxyproject/galaxy] fd2e8f: Replacing configure_menu mako by JavaScript
by GitHub 30 May '17

30 May '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: fd2e8fe517608f506d57b2a131b520c7c720da82 https://github.com/galaxyproject/galaxy/commit/fd2e8fe517608f506d57b2a131b5… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-05-15 (Mon, 15 May 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/mvc/workflow/workflow.js M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/workflow.py 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.map M static/scripts/mvc/workflow/workflow.js Log Message: ----------- Replacing configure_menu mako by JavaScript Commit: 5d48e62eeae3dd7e55a0b51d64f9b71f90e50582 https://github.com/galaxyproject/galaxy/commit/5d48e62eeae3dd7e55a0b51d64f9… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-05-15 (Mon, 15 May 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow.js 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.map M static/scripts/mvc/workflow/workflow.js Log Message: ----------- Removing unused code Commit: 91d08cc746a28cc19ced4d1cdb03f54b27691d47 https://github.com/galaxyproject/galaxy/commit/91d08cc746a28cc19ced4d1cdb03… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-05-15 (Mon, 15 May 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js A client/galaxy/scripts/mvc/workflow/workflow-configure-menu.js M client/galaxy/scripts/mvc/workflow/workflow.js A static/maps/mvc/workflow/workflow-configure-menu.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 A static/scripts/mvc/workflow/workflow-configure-menu.js M static/scripts/mvc/workflow/workflow.js Log Message: ----------- New file for configure workflow menu and adding check and uncheck all buttons Commit: 64312c4331abb4b75b3b55e8366e7c1f351dca0c https://github.com/galaxyproject/galaxy/commit/64312c4331abb4b75b3b55e8366e… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-05-19 (Fri, 19 May 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-configure-menu.js M client/galaxy/style/less/base.less M static/maps/mvc/workflow/workflow-configure-menu.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/workflow/workflow-configure-menu.js M static/style/blue/base.css Log Message: ----------- Adding styling and back button to configure workflow menu page Commit: f0d28992a4bf47d4a3bf338696c202144e8463cb https://github.com/galaxyproject/galaxy/commit/f0d28992a4bf47d4a3bf338696c2… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-05-19 (Fri, 19 May 2017) Changed paths: 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/layout/menu.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/layout/panel.js M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/grid/grid-template.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/upload/collection/collection-view.js M client/galaxy/scripts/nls/fr/locale.js M client/galaxy/scripts/nls/locale.js M client/galaxy/style/less/history.less M client/galaxy/style/less/ui.less M client/webpack.config.js M config/galaxy.ini.sample M config/job_conf.xml.sample_advanced M config/plugins/tours/core.history.yaml M config/plugins/webhooks/demo/search/config/searchover.yaml M config/plugins/webhooks/demo/tool_list/config/tool_list.yml M doc/source/admin/special_topics/webhooks.rst M lib/galaxy/config.py M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/jobs/rule_helper.py M lib/galaxy/jobs/runners/__init__.py A lib/galaxy/jobs/runners/chronos.py M lib/galaxy/managers/configuration.py M lib/galaxy/managers/datasets.py M lib/galaxy/objectstore/s3.py M lib/galaxy/tools/__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/installable.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/util/plugin_config.py M lib/galaxy/web/base/controller.py M lib/galaxy/web/base/controllers/admin.py M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py A lib/galaxy/webapps/galaxy/api/toolshed.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/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/buildapp.py M lib/tool_shed/util/repository_util.py A static/maps/admin.toolshed.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/mvc/dataset/dataset-li.js.map M static/maps/mvc/grid/grid-template.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/upload/collection/collection-view.js.map M static/maps/nls/fr/locale.js.map M static/maps/nls/locale.js.map A static/scripts/admin.toolshed.js 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/layout/page.js M static/scripts/layout/panel.js M static/scripts/mvc/dataset/dataset-li.js M static/scripts/mvc/grid/grid-template.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/upload/collection/collection-view.js M static/scripts/nls/fr/locale.js M static/scripts/nls/locale.js M static/style/blue/base.css R templates/admin/tool_shed_repository/browse_toolsheds.mako M templates/show_params.mako R templates/webapps/galaxy/admin/index.mako A test/functional/tools/collection_creates_dynamic_nested_fail.xml A test/functional/tools/collection_creates_list_fail.xml M test/functional/tools/samples_tool_conf.xml M test/functional/webhooks/trans_object/config/trans_object.yaml M test/qunit/tests/page_tests.js Log Message: ----------- Merging with dev Commit: b9b45870730f9cdab6b9dca343aaf86072063161 https://github.com/galaxyproject/galaxy/commit/b9b45870730f9cdab6b9dca343aa… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-05-19 (Fri, 19 May 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: ----------- Replacing the centerPanel by this.page in analysis.js Commit: 091195fa23c58fc84e51155fa2fb9dfd446a9280 https://github.com/galaxyproject/galaxy/commit/091195fa23c58fc84e51155fa2fb… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-05-19 (Fri, 19 May 2017) Changed paths: R templates/webapps/galaxy/workflow/configure_menu.mako Log Message: ----------- Removing configure_menu.mako file Commit: 35ec338d5dc039a81bc470ad3c6736ea9b84887e https://github.com/galaxyproject/galaxy/commit/35ec338d5dc039a81bc470ad3c67… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-05-20 (Sat, 20 May 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Fixing build failure comments and removing commented out lines Commit: 358ce8013fe61901efbe6e296ae9e29f422b675c https://github.com/galaxyproject/galaxy/commit/358ce8013fe61901efbe6e296ae9… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-05-22 (Mon, 22 May 2017) Changed paths: M .gitignore M CONTRIBUTORS.md M lib/galaxy/jobs/runners/kubernetes.py M lib/galaxy/webapps/tool_shed/api/repositories.py A static/scripts/bundled/admin.bundled.js A static/scripts/bundled/admin.bundled.js.map M test/galaxy_selenium/navigates_galaxy.py Log Message: ----------- Merging with dev Commit: a95a78a6c5c5aea880c1dde49e652372c11e902e https://github.com/galaxyproject/galaxy/commit/a95a78a6c5c5aea880c1dde49e65… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-05-22 (Mon, 22 May 2017) Log Message: ----------- Merge branch 'dev' of https://github.com/bgruening/galaxy into workflowexport_mako Commit: 60cb6b4d3185233237284eed5daa01c06ea4d9ed https://github.com/galaxyproject/galaxy/commit/60cb6b4d3185233237284eed5daa… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-05-22 (Mon, 22 May 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-configure-menu.js M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/buildapp.py M static/maps/mvc/workflow/workflow-configure-menu.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/workflow/workflow-configure-menu.js Log Message: ----------- Fixing PR review comment to split api calls into two Commit: 8975327cfd5c2e26675dc70ad5f8425a8b085ef0 https://github.com/galaxyproject/galaxy/commit/8975327cfd5c2e26675dc70ad5f8… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-05-22 (Mon, 22 May 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Adjusting indentation Commit: 56fcd293b5095dfa87cce8864def490d05cc0143 https://github.com/galaxyproject/galaxy/commit/56fcd293b5095dfa87cce8864def… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-05-22 (Mon, 22 May 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-configure-menu.js M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/buildapp.py M static/maps/mvc/workflow/workflow-configure-menu.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/workflow/workflow-configure-menu.js Log Message: ----------- Fixing PR review comments Commit: 852aa51225238d2150441063932564b5562b9e35 https://github.com/galaxyproject/galaxy/commit/852aa51225238d21504410639325… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-05-23 (Tue, 23 May 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-configure-menu.js M lib/galaxy/webapps/galaxy/buildapp.py M static/maps/mvc/workflow/workflow-configure-menu.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/workflow/workflow-configure-menu.js Log Message: ----------- Making one api url for getting and setting workflows menu Commit: 53037f6006ec4d4306234dd05642f3a80746f49b https://github.com/galaxyproject/galaxy/commit/53037f6006ec4d4306234dd05642… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-05-23 (Tue, 23 May 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Updating url in the comments of workflow api Commit: 4dcc145dbf8c0122b88afa3e38b33781a71d8b06 https://github.com/galaxyproject/galaxy/commit/4dcc145dbf8c0122b88afa3e38b3… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-05-23 (Tue, 23 May 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Remove composite api function and duplicate resource connector Commit: 9896fc0e9f478ea47378a514e9a1fc9ef65f54e4 https://github.com/galaxyproject/galaxy/commit/9896fc0e9f478ea47378a514e9a1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-05-30 (Tue, 30 May 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js A client/galaxy/scripts/mvc/workflow/workflow-configure-menu.js M client/galaxy/style/less/base.less M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/workflow.py A static/maps/mvc/workflow/workflow-configure-menu.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/workflow/workflow-configure-menu.js M static/style/blue/base.css R templates/webapps/galaxy/workflow/configure_menu.mako Log Message: ----------- Merge pull request #4092 from bgruening/workflowexport_mako New Configure Workflow Menu UI Compare: https://github.com/galaxyproject/galaxy/compare/aa7d701cbc76...9896fc0e9f47

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[galaxyproject/galaxy] 55336d: Fix legacy Python path for genome diversity tools ...
by GitHub 30 May '17

30 May '17

Branch: refs/heads/release_17.05 Home: https://github.com/galaxyproject/galaxy Commit: 55336d2c3142051f605231e6db1cb6a45639417c https://github.com/galaxyproject/galaxy/commit/55336d2c3142051f605231e6db1c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-05-28 (Sun, 28 May 2017) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Fix legacy Python path for genome diversity tools from miller lab. Fixes #4108. Commit: 96e1cf58f480549cf5b39647c8772863405f582f https://github.com/galaxyproject/galaxy/commit/96e1cf58f480549cf5b39647c877… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2017-05-29 (Mon, 29 May 2017) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge pull request #4117 from jmchilton/genome_diversity_fixes [17.01] Fix legacy Python path for genome diversity tools from miller lab. Commit: 42e274d3342720037d441222b9fb1bbcbce2d7c1 https://github.com/galaxyproject/galaxy/commit/42e274d3342720037d441222b9fb… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-05-30 (Tue, 30 May 2017) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge pull request #4122 from galaxyproject/release_17.01 [17.05] merge Release 17.01 Compare: https://github.com/galaxyproject/galaxy/compare/3d16319a15b7...42e274d33427

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[galaxyproject/galaxy] 54d6a5: Avoid locale specific string.letters for job_name
by GitHub 30 May '17

30 May '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 54d6a54367ed6a852b54a89f567d901f494e682a https://github.com/galaxyproject/galaxy/commit/54d6a54367ed6a852b54a89f567d… Author: peterjc <p.j.a.cock(a)googlemail.com> Date: 2017-05-29 (Mon, 29 May 2017) Changed paths: M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/drmaa.py Log Message: ----------- Avoid locale specific string.letters for job_name The job_name sanitation can fail if the locale specific string.letters contains unexpected characters. e.g. Saravanaraj Ayyampalayam reported getting the following under locale en_US.iso885915 Traceback (most recent call last): File /.../galaxy-dist/lib/galaxy/jobs/runners/drmaa.py, line 397, in <genexpr> job_name = ''.join( x if x in ( string.letters + string.digits + '_' ) else '_' for x in job_name ) UnicodeDecodeError: 'ascii' codec can't decode byte 0xa6 in position 52: ordinal not in range(128) See http://dev.list.galaxyproject.org/Issue-with-job-name-UnicodeDecodeError-in… or https://lists.galaxyproject.org/pipermail/galaxy-dev/2017-May/025687.html The downside of this proposed change would be to mask reasonable non ASCII letters from the job name on a well defined system with consistent locale settings for both Galaxy and the Cluster. But ASCII only seems safer. Commit: aa7d701cbc7674a13a4db30fce333e81558b2fea https://github.com/galaxyproject/galaxy/commit/aa7d701cbc7674a13a4db30fce33… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-05-29 (Mon, 29 May 2017) Changed paths: M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/drmaa.py Log Message: ----------- Merge pull request #4121 from peterjc/locales_string_letters Avoid locale specific string.letters for job_name Compare: https://github.com/galaxyproject/galaxy/compare/64d6ffd59dee...aa7d701cbc76

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[galaxyproject/galaxy] 55336d: Fix legacy Python path for genome diversity tools ...
by GitHub 29 May '17

29 May '17

Branch: refs/heads/release_17.01 Home: https://github.com/galaxyproject/galaxy Commit: 55336d2c3142051f605231e6db1cb6a45639417c https://github.com/galaxyproject/galaxy/commit/55336d2c3142051f605231e6db1c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-05-28 (Sun, 28 May 2017) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Fix legacy Python path for genome diversity tools from miller lab. Fixes #4108. Commit: 96e1cf58f480549cf5b39647c8772863405f582f https://github.com/galaxyproject/galaxy/commit/96e1cf58f480549cf5b39647c877… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2017-05-29 (Mon, 29 May 2017) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge pull request #4117 from jmchilton/genome_diversity_fixes [17.01] Fix legacy Python path for genome diversity tools from miller lab. Compare: https://github.com/galaxyproject/galaxy/compare/b7a66f182ef8...96e1cf58f480

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[galaxyproject/galaxy] 68433b: Force uniqueness of preserved tags (so, don't allo...
by GitHub 27 May '17

27 May '17

Branch: refs/heads/release_17.05 Home: https://github.com/galaxyproject/galaxy Commit: 68433b1eff0a93704544a49f3d8f3a912d97c285 https://github.com/galaxyproject/galaxy/commit/68433b1eff0a93704544a49f3d8f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-05-25 (Thu, 25 May 2017) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Force uniqueness of preserved tags (so, don't allow many inputs with a 'name:foo' tag to add a ton of 'name:foo' tags to a dataset; just use one) Commit: b6e8d3e8acd00c1a595f15f2654c1b7809ecc831 https://github.com/galaxyproject/galaxy/commit/b6e8d3e8acd00c1a595f15f2654c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-05-26 (Fri, 26 May 2017) Changed paths: M lib/galaxy/managers/collections.py M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Slight refactoring to use a dict for unique'ing preserved tags. TODO: enhance object builtins to compare correctly so we can use a set, maybe. Not a big deal unless/until we have a second type of preserved tag though. Commit: dd06a01746f2ace048b9e1e604756e648a6ef1fd https://github.com/galaxyproject/galaxy/commit/dd06a01746f2ace048b9e1e60475… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-05-26 (Fri, 26 May 2017) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Handle *both* paths for tag appending using the now-dict correctly. Commit: 2ac04bbf095573f2621ffeea0e2fdeb59b21da53 https://github.com/galaxyproject/galaxy/commit/2ac04bbf095573f2621ffeea0e2f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-05-26 (Fri, 26 May 2017) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/history/hdca-li.js M static/maps/mvc/dataset/dataset-li.js.map M static/maps/mvc/history/hdca-li.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/dataset/dataset-li.js M static/scripts/mvc/history/hdca-li.js Log Message: ----------- Uniqueify hashtag display Commit: 3d16319a15b7ac2f947eca24c36957894ae00afe https://github.com/galaxyproject/galaxy/commit/3d16319a15b7ac2f947eca24c369… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2017-05-27 (Sat, 27 May 2017) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/history/hdca-li.js M lib/galaxy/managers/collections.py M lib/galaxy/tools/actions/__init__.py M static/maps/mvc/dataset/dataset-li.js.map M static/maps/mvc/history/hdca-li.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/dataset/dataset-li.js M static/scripts/mvc/history/hdca-li.js Log Message: ----------- Merge pull request #4114 from dannon/force_uniqueness_preserved_tags [17.05] Force uniqueness of preserved tags Compare: https://github.com/galaxyproject/galaxy/compare/18ef6a6ab0dc...3d16319a15b7

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[galaxyproject/usegalaxy-playbook] 1283e7: give salmon 16gb and rna_Star 64
by GitHub 25 May '17

25 May '17

Branch: refs/heads/martenson-patch-1 Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 1283e77813b20b31ee19271f289e01a149dc94cd https://github.com/galaxyproject/usegalaxy-playbook/commit/1283e77813b20b31… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-05-25 (Thu, 25 May 2017) Changed paths: M templates/galaxy/usegalaxy.org/config/job_conf.xml.j2 Log Message: ----------- give salmon 16gb and rna_Star 64

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[galaxyproject/usegalaxy-playbook] 07c13f: Update Main
by GitHub 25 May '17

25 May '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 07c13f0094d292a15b5c8a930304bc9914fd2062 https://github.com/galaxyproject/usegalaxy-playbook/commit/07c13f0094d292a1… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-05-25 (Thu, 25 May 2017) Changed paths: A env/main/files/galaxy/galaxy_version.yml Log Message: ----------- Update Main

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