- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 6fa0c8: add new item to the help menu
by GitHub 29 Nov '18

29 Nov '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: 6fa0c8f932831fe91db492de09a2bb4b48621738 https://github.com/galaxyproject/galaxy/commit/6fa0c8f932831fe91db492de09a2… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-11-28 (Wed, 28 Nov 2018) Changed paths: M client/galaxy/scripts/layout/menu.js M config/galaxy.yml.sample M doc/source/admin/galaxy_options.rst M lib/galaxy/config.py M lib/galaxy/managers/configuration.py M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- add new item to the help menu Commit: 72f5d1a35f0a854a242c0854f670ab82045e95a9 https://github.com/galaxyproject/galaxy/commit/72f5d1a35f0a854a242c0854f670… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2018-11-29 (Thu, 29 Nov 2018) Changed paths: M client/galaxy/scripts/layout/menu.js M config/galaxy.yml.sample M doc/source/admin/galaxy_options.rst M lib/galaxy/config.py M lib/galaxy/managers/configuration.py M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- Merge pull request #7054 from martenson/help-menu-item-rel [18.09] add new item to the help menu Compare: https://github.com/galaxyproject/galaxy/compare/2620367a5a40...72f5d1a35f0a **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/usegalaxy-playbook] 8e9e3b: Started moved from biostar to help.galaxyproject.o...
by GitHub 28 Nov '18

28 Nov '18

Branch: refs/heads/biostar-to-discourse Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 8e9e3b9ba1e1fdfda667625460ae8a772a4d1e3f https://github.com/galaxyproject/usegalaxy-playbook/commit/8e9e3b9ba1e1fdfd… Author: tnabtaf <clements(a)galaxyproject.org> Date: 2018-11-28 (Wed, 28 Nov 2018) Changed paths: R env/common/files/galaxy/static/welcome_img/GalaxyBiostar.png R env/common/files/galaxy/static/welcome_img/GalaxyBiostarHelp.png A env/common/files/galaxy/static/welcome_img/galaxy-help.png M env/common/templates/galaxy/static/welcome.html.j2 Log Message: ----------- Started moved from biostar to help.galaxyproject.org **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 58e705: changed exit code and regex parsing
by GitHub 27 Nov '18

27 Nov '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 58e705a547fc53a91e46abad12c2ab77838228c2 https://github.com/galaxyproject/galaxy/commit/58e705a547fc53a91e46abad12c2… Author: M Bernt <m.bernt(a)ufz.de> Date: 2018-11-06 (Tue, 06 Nov 2018) Changed paths: M lib/galaxy/tools/parser/xml.py Log Message: ----------- changed exit code and regex parsing - stdio are always prepended to command tag derived exit codes and regexes Commit: 2376d7f2fd57fcf9ae00264c4244ba06d63b8906 https://github.com/galaxyproject/galaxy/commit/2376d7f2fd57fcf9ae00264c4244… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-11-27 (Tue, 27 Nov 2018) Changed paths: M lib/galaxy/tools/parser/xml.py Log Message: ----------- Merge pull request #6977 from bernt-matthias/topic/stdio-add changed exit code and regex parsing Compare: https://github.com/galaxyproject/galaxy/compare/5a62a5c091a9...2376d7f2fd57 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 2299e0: Add StoredWorkflow.show_in_tool_panel function
by GitHub 27 Nov '18

27 Nov '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 2299e06a6937328f36485a8baa136c1138461144 https://github.com/galaxyproject/galaxy/commit/2299e06a6937328f36485a8baa13… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-11-15 (Thu, 15 Nov 2018) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Add StoredWorkflow.show_in_tool_panel function This is more DRY and fixes https://github.com/galaxyproject/galaxy/issues/6889#issuecomment-438991091. The bug itself was due to comparing the id of a StoredWorkflowUserShareAssociation instead of StoredWorkflow when checking if a stored workflow should be in the tool panel. Commit: b5ce8d0dcf5affd462e33902126d4dd5c5921be6 https://github.com/galaxyproject/galaxy/commit/b5ce8d0dcf5affd462e33902126d… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2018-11-15 (Thu, 15 Nov 2018) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Merge pull request #7014 from mvdbeek/fix_inability_to_remove_workflow_from_panel [18.01] Fix display_in_tool_panel status for shared workflows Commit: 1e4821c64477452f54390458dac67161467315ba https://github.com/galaxyproject/galaxy/commit/1e4821c64477452f54390458dac6… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-11-20 (Tue, 20 Nov 2018) Changed paths: M lib/galaxy/tools/wrappers.py M test/functional/tools/identifier_collection.xml Log Message: ----------- Provide element_identifier attribute in DatsetCollectionWrapper This allows accessing `$input1.element_identifier` for an `input1` of collection_type `list:pair`. Commit: 988d308a12f37ce0d6fc8c2974cdc081b3bbd6a3 https://github.com/galaxyproject/galaxy/commit/988d308a12f37ce0d6fc8c2974cd… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-11-27 (Tue, 27 Nov 2018) Changed paths: M lib/galaxy/tools/wrappers.py M test/functional/tools/identifier_collection.xml Log Message: ----------- Merge pull request #7032 from mvdbeek/backport_element_identifier_everywhere [18.01] Backport Provide element_identifier attribute in DatsetCollectionWrapper Commit: 9a6fddcdca7042e5e453bdd235ed8c5b3266fb7d https://github.com/galaxyproject/galaxy/commit/9a6fddcdca7042e5e453bdd235ed… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-11-27 (Tue, 27 Nov 2018) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/tools/wrappers.py M lib/galaxy/webapps/galaxy/api/workflows.py M test/functional/tools/identifier_collection.xml Log Message: ----------- Merge remote-tracking branch 'upstream/release_18.01' into release_18.05 Commit: 2620367a5a402274e27630817be814914ef4f90a https://github.com/galaxyproject/galaxy/commit/2620367a5a402274e27630817be8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-11-27 (Tue, 27 Nov 2018) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/tools/wrappers.py M lib/galaxy/webapps/galaxy/api/workflows.py M test/functional/tools/identifier_collection.xml Log Message: ----------- Merge remote-tracking branch 'upstream/release_18.05' into release_18.09 Commit: 5a62a5c091a9c73ffd6647af7a81e1781c59aa17 https://github.com/galaxyproject/galaxy/commit/5a62a5c091a9c73ffd6647af7a81… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-11-27 (Tue, 27 Nov 2018) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_18.09' into dev Compare: https://github.com/galaxyproject/galaxy/compare/8033f0cd6d38...5a62a5c091a9 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] a2b752: Fix resubmission on tool error detection.
by GitHub 27 Nov '18

27 Nov '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a2b7521140f74b443c7339cf3ef605fde4bae187 https://github.com/galaxyproject/galaxy/commit/a2b7521140f74b443c7339cf3ef6… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-11-23 (Fri, 23 Nov 2018) Changed paths: M lib/galaxy/jobs/runners/state_handlers/resubmit.py A test/functional/tools/exit_code_from_env.xml M test/functional/tools/samples_tool_conf.xml A test/integration/resubmission_tool_detected_always_error_job_conf.xml A test/integration/resubmission_tool_detected_resubmit_job_conf.xml M test/integration/test_job_resubmission.py Log Message: ----------- Fix resubmission on tool error detection. Parts of this were wired up before but pieces were missing and so it was broken. Commit: 8033f0cd6d3882b3373e31470d7fd0ae6c37c467 https://github.com/galaxyproject/galaxy/commit/8033f0cd6d3882b3373e31470d7f… Author: Helena Rasche <hxr(a)hx42.org> Date: 2018-11-27 (Tue, 27 Nov 2018) Changed paths: M lib/galaxy/jobs/runners/state_handlers/resubmit.py A test/functional/tools/exit_code_from_env.xml M test/functional/tools/samples_tool_conf.xml A test/integration/resubmission_tool_detected_always_error_job_conf.xml A test/integration/resubmission_tool_detected_resubmit_job_conf.xml M test/integration/test_job_resubmission.py Log Message: ----------- Merge pull request #7040 from jmchilton/fix_tool_detected_error_resubmission Fix resubmission on tool error detection. Compare: https://github.com/galaxyproject/galaxy/compare/015b8547ad3b...8033f0cd6d38 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 2299e0: Add StoredWorkflow.show_in_tool_panel function
by GitHub 27 Nov '18

27 Nov '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/galaxy Commit: 2299e06a6937328f36485a8baa136c1138461144 https://github.com/galaxyproject/galaxy/commit/2299e06a6937328f36485a8baa13… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-11-15 (Thu, 15 Nov 2018) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Add StoredWorkflow.show_in_tool_panel function This is more DRY and fixes https://github.com/galaxyproject/galaxy/issues/6889#issuecomment-438991091. The bug itself was due to comparing the id of a StoredWorkflowUserShareAssociation instead of StoredWorkflow when checking if a stored workflow should be in the tool panel. Commit: b5ce8d0dcf5affd462e33902126d4dd5c5921be6 https://github.com/galaxyproject/galaxy/commit/b5ce8d0dcf5affd462e33902126d… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2018-11-15 (Thu, 15 Nov 2018) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Merge pull request #7014 from mvdbeek/fix_inability_to_remove_workflow_from_panel [18.01] Fix display_in_tool_panel status for shared workflows Commit: 1e4821c64477452f54390458dac67161467315ba https://github.com/galaxyproject/galaxy/commit/1e4821c64477452f54390458dac6… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-11-20 (Tue, 20 Nov 2018) Changed paths: M lib/galaxy/tools/wrappers.py M test/functional/tools/identifier_collection.xml Log Message: ----------- Provide element_identifier attribute in DatsetCollectionWrapper This allows accessing `$input1.element_identifier` for an `input1` of collection_type `list:pair`. Commit: 59afe04523b8b00623b92458b4eb275f31401a19 https://github.com/galaxyproject/galaxy/commit/59afe04523b8b00623b92458b4eb… Author: Jelle Scholtalbers <j.scholtalbers(a)gmail.com> Date: 2018-11-22 (Thu, 22 Nov 2018) Changed paths: M lib/galaxy/tools/deps/mulled/mulled_build.py Log Message: ----------- fix error when building images where conda channels is passed as a string instead of a list Commit: 5255a0bf20dea411dbc4c1b9b05e757f2e554df1 https://github.com/galaxyproject/galaxy/commit/5255a0bf20dea411dbc4c1b9b05e… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-11-22 (Thu, 22 Nov 2018) Changed paths: M lib/galaxy/tools/deps/container_resolvers/__init__.py M lib/galaxy/tools/deps/container_resolvers/mulled.py Log Message: ----------- Fix ``involucro_auto_init`` default value Commit: 9aaafd8aea1930af02aeebc6b78f03164779ee7c https://github.com/galaxyproject/galaxy/commit/9aaafd8aea1930af02aeebc6b78f… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2018-11-24 (Sat, 24 Nov 2018) Changed paths: M lib/galaxy/tools/deps/container_resolvers/__init__.py M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/mulled/mulled_build.py Log Message: ----------- Merge pull request #7044 from nsoranzo/release_18.09_fix/mulled_container_default_channels [18.09] Backport #7038 Commit: 988d308a12f37ce0d6fc8c2974cdc081b3bbd6a3 https://github.com/galaxyproject/galaxy/commit/988d308a12f37ce0d6fc8c2974cd… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-11-27 (Tue, 27 Nov 2018) Changed paths: M lib/galaxy/tools/wrappers.py M test/functional/tools/identifier_collection.xml Log Message: ----------- Merge pull request #7032 from mvdbeek/backport_element_identifier_everywhere [18.01] Backport Provide element_identifier attribute in DatsetCollectionWrapper Commit: 9a6fddcdca7042e5e453bdd235ed8c5b3266fb7d https://github.com/galaxyproject/galaxy/commit/9a6fddcdca7042e5e453bdd235ed… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-11-27 (Tue, 27 Nov 2018) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/tools/wrappers.py M lib/galaxy/webapps/galaxy/api/workflows.py M test/functional/tools/identifier_collection.xml Log Message: ----------- Merge remote-tracking branch 'upstream/release_18.01' into release_18.05 Commit: 2620367a5a402274e27630817be814914ef4f90a https://github.com/galaxyproject/galaxy/commit/2620367a5a402274e27630817be8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-11-27 (Tue, 27 Nov 2018) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/tools/wrappers.py M lib/galaxy/webapps/galaxy/api/workflows.py M test/functional/tools/identifier_collection.xml Log Message: ----------- Merge remote-tracking branch 'upstream/release_18.05' into release_18.09 Commit: c228760e1f067111fff0ecf9cf69ed3b019313a2 https://github.com/galaxyproject/galaxy/commit/c228760e1f067111fff0ecf9cf69… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-11-27 (Tue, 27 Nov 2018) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/tools/deps/container_resolvers/__init__.py M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/mulled/mulled_build.py M lib/galaxy/tools/wrappers.py M lib/galaxy/webapps/galaxy/api/workflows.py M test/functional/tools/identifier_collection.xml Log Message: ----------- Merge remote-tracking branch 'upstream/release_18.09' Compare: https://github.com/galaxyproject/galaxy/compare/f2c9baf2c54b...c228760e1f06 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 2299e0: Add StoredWorkflow.show_in_tool_panel function
by GitHub 27 Nov '18

27 Nov '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: 2299e06a6937328f36485a8baa136c1138461144 https://github.com/galaxyproject/galaxy/commit/2299e06a6937328f36485a8baa13… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-11-15 (Thu, 15 Nov 2018) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Add StoredWorkflow.show_in_tool_panel function This is more DRY and fixes https://github.com/galaxyproject/galaxy/issues/6889#issuecomment-438991091. The bug itself was due to comparing the id of a StoredWorkflowUserShareAssociation instead of StoredWorkflow when checking if a stored workflow should be in the tool panel. Commit: b5ce8d0dcf5affd462e33902126d4dd5c5921be6 https://github.com/galaxyproject/galaxy/commit/b5ce8d0dcf5affd462e33902126d… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2018-11-15 (Thu, 15 Nov 2018) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Merge pull request #7014 from mvdbeek/fix_inability_to_remove_workflow_from_panel [18.01] Fix display_in_tool_panel status for shared workflows Commit: 1e4821c64477452f54390458dac67161467315ba https://github.com/galaxyproject/galaxy/commit/1e4821c64477452f54390458dac6… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-11-20 (Tue, 20 Nov 2018) Changed paths: M lib/galaxy/tools/wrappers.py M test/functional/tools/identifier_collection.xml Log Message: ----------- Provide element_identifier attribute in DatsetCollectionWrapper This allows accessing `$input1.element_identifier` for an `input1` of collection_type `list:pair`. Commit: 988d308a12f37ce0d6fc8c2974cdc081b3bbd6a3 https://github.com/galaxyproject/galaxy/commit/988d308a12f37ce0d6fc8c2974cd… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-11-27 (Tue, 27 Nov 2018) Changed paths: M lib/galaxy/tools/wrappers.py M test/functional/tools/identifier_collection.xml Log Message: ----------- Merge pull request #7032 from mvdbeek/backport_element_identifier_everywhere [18.01] Backport Provide element_identifier attribute in DatsetCollectionWrapper Commit: 9a6fddcdca7042e5e453bdd235ed8c5b3266fb7d https://github.com/galaxyproject/galaxy/commit/9a6fddcdca7042e5e453bdd235ed… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-11-27 (Tue, 27 Nov 2018) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/tools/wrappers.py M lib/galaxy/webapps/galaxy/api/workflows.py M test/functional/tools/identifier_collection.xml Log Message: ----------- Merge remote-tracking branch 'upstream/release_18.01' into release_18.05 Commit: 2620367a5a402274e27630817be814914ef4f90a https://github.com/galaxyproject/galaxy/commit/2620367a5a402274e27630817be8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-11-27 (Tue, 27 Nov 2018) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/tools/wrappers.py M lib/galaxy/webapps/galaxy/api/workflows.py M test/functional/tools/identifier_collection.xml Log Message: ----------- Merge remote-tracking branch 'upstream/release_18.05' into release_18.09 Compare: https://github.com/galaxyproject/galaxy/compare/9aaafd8aea19...2620367a5a40 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 2299e0: Add StoredWorkflow.show_in_tool_panel function
by GitHub 27 Nov '18

27 Nov '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: 2299e06a6937328f36485a8baa136c1138461144 https://github.com/galaxyproject/galaxy/commit/2299e06a6937328f36485a8baa13… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-11-15 (Thu, 15 Nov 2018) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Add StoredWorkflow.show_in_tool_panel function This is more DRY and fixes https://github.com/galaxyproject/galaxy/issues/6889#issuecomment-438991091. The bug itself was due to comparing the id of a StoredWorkflowUserShareAssociation instead of StoredWorkflow when checking if a stored workflow should be in the tool panel. Commit: b5ce8d0dcf5affd462e33902126d4dd5c5921be6 https://github.com/galaxyproject/galaxy/commit/b5ce8d0dcf5affd462e33902126d… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2018-11-15 (Thu, 15 Nov 2018) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Merge pull request #7014 from mvdbeek/fix_inability_to_remove_workflow_from_panel [18.01] Fix display_in_tool_panel status for shared workflows Commit: 1e4821c64477452f54390458dac67161467315ba https://github.com/galaxyproject/galaxy/commit/1e4821c64477452f54390458dac6… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-11-20 (Tue, 20 Nov 2018) Changed paths: M lib/galaxy/tools/wrappers.py M test/functional/tools/identifier_collection.xml Log Message: ----------- Provide element_identifier attribute in DatsetCollectionWrapper This allows accessing `$input1.element_identifier` for an `input1` of collection_type `list:pair`. Commit: 988d308a12f37ce0d6fc8c2974cdc081b3bbd6a3 https://github.com/galaxyproject/galaxy/commit/988d308a12f37ce0d6fc8c2974cd… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-11-27 (Tue, 27 Nov 2018) Changed paths: M lib/galaxy/tools/wrappers.py M test/functional/tools/identifier_collection.xml Log Message: ----------- Merge pull request #7032 from mvdbeek/backport_element_identifier_everywhere [18.01] Backport Provide element_identifier attribute in DatsetCollectionWrapper Commit: 9a6fddcdca7042e5e453bdd235ed8c5b3266fb7d https://github.com/galaxyproject/galaxy/commit/9a6fddcdca7042e5e453bdd235ed… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-11-27 (Tue, 27 Nov 2018) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/tools/wrappers.py M lib/galaxy/webapps/galaxy/api/workflows.py M test/functional/tools/identifier_collection.xml Log Message: ----------- Merge remote-tracking branch 'upstream/release_18.01' into release_18.05 Compare: https://github.com/galaxyproject/galaxy/compare/45e475e19aa1...9a6fddcdca70 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 1e4821: Provide element_identifier attribute in DatsetColl...
by GitHub 27 Nov '18

27 Nov '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: 1e4821c64477452f54390458dac67161467315ba https://github.com/galaxyproject/galaxy/commit/1e4821c64477452f54390458dac6… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-11-20 (Tue, 20 Nov 2018) Changed paths: M lib/galaxy/tools/wrappers.py M test/functional/tools/identifier_collection.xml Log Message: ----------- Provide element_identifier attribute in DatsetCollectionWrapper This allows accessing `$input1.element_identifier` for an `input1` of collection_type `list:pair`. Commit: 988d308a12f37ce0d6fc8c2974cdc081b3bbd6a3 https://github.com/galaxyproject/galaxy/commit/988d308a12f37ce0d6fc8c2974cd… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-11-27 (Tue, 27 Nov 2018) Changed paths: M lib/galaxy/tools/wrappers.py M test/functional/tools/identifier_collection.xml Log Message: ----------- Merge pull request #7032 from mvdbeek/backport_element_identifier_everywhere [18.01] Backport Provide element_identifier attribute in DatsetCollectionWrapper Compare: https://github.com/galaxyproject/galaxy/compare/b5ce8d0dcf5a...988d308a12f3 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/ansible-galaxy] 0133c0: Add 'become: yes' statement to sample playbook cod...
by GitHub 27 Nov '18

27 Nov '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/ansible-galaxy Commit: 0133c0585afcae71663052a332ca6742a27e4114 https://github.com/galaxyproject/ansible-galaxy/commit/0133c0585afcae716630… Author: Sergey Golitsynskiy <sgolitsynskiy(a)gmail.com> Date: 2018-11-13 (Tue, 13 Nov 2018) Changed paths: M README.md Log Message: ----------- Add 'become: yes' statement to sample playbook code Solves permissions issue in the advanced playbook sample code: `postgresql_conf_dir` is set to `/etc/postgresql/[version]/main` (in vars/[os-family].yml, which requires privilege escalation. Commit: 9e3ed89cbe7c6190b1f5c644ff84731bd0a220e6 https://github.com/galaxyproject/ansible-galaxy/commit/9e3ed89cbe7c6190b1f5… Author: Sergey Golitsynskiy <sgolitsynskiy(a)gmail.com> Date: 2018-11-26 (Mon, 26 Nov 2018) Changed paths: M README.md Log Message: ----------- Fix error in sample code/advanced playbook Change dictionary duplicate keys (mule) into a sequence. For details, see closed Issue #42 and closed PR #43. Commit: 2298c56b399769889a832f5d640370d8cf26bfa6 https://github.com/galaxyproject/ansible-galaxy/commit/2298c56b399769889a83… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-11-27 (Tue, 27 Nov 2018) Changed paths: M README.md Log Message: ----------- Merge pull request #44 from ic4f/master Edits to sample code/advanced playbook in README (dupl. keys + become: yes) Compare: https://github.com/galaxyproject/ansible-galaxy/compare/5506cd5d683e...2298… **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] b082da: remove sudo from travis, it will stop being suppor...
by GitHub 26 Nov '18

26 Nov '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b082daa39f2cd47d75872d9176af0bbde6b94311 https://github.com/galaxyproject/galaxy/commit/b082daa39f2cd47d75872d9176af… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-11-21 (Wed, 21 Nov 2018) Changed paths: M .travis.yml Log Message: ----------- remove sudo from travis, it will stop being supported soon https://blog.travis-ci.com/2018-11-19-required-linux-infrastructure-migrati… Commit: 81e337622580d22b8170f9a85ad4f825ea30c440 https://github.com/galaxyproject/galaxy/commit/81e337622580d22b8170f9a85ad4… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-11-26 (Mon, 26 Nov 2018) Changed paths: M .travis.yml Log Message: ----------- Add workaround for https://github.com/travis-ci/travis-ci/issues/7940 Commit: 015b8547ad3b56e32decf0bc803d1a800b35182c https://github.com/galaxyproject/galaxy/commit/015b8547ad3b56e32decf0bc803d… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-11-26 (Mon, 26 Nov 2018) Changed paths: M .travis.yml Log Message: ----------- Merge pull request #7035 from martenson/remove-sudo Remove ``sudo: false`` from .travis.yml, it will stop being supported soon Compare: https://github.com/galaxyproject/galaxy/compare/284e906df0a0...015b8547ad3b **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 536f7c: Do not replace mismatching data-reference based in...
by GitHub 26 Nov '18

26 Nov '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 536f7c9c6b24b027731cddbcced600aedc518de6 https://github.com/galaxyproject/galaxy/commit/536f7c9c6b24b027731cddbcced6… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-11-23 (Fri, 23 Nov 2018) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Do not replace mismatching data-reference based input parameters with default values Commit: 284e906df0a0cf4215483088f0120c14ca1f1b24 https://github.com/galaxyproject/galaxy/commit/284e906df0a0cf4215483088f012… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-11-26 (Mon, 26 Nov 2018) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge pull request #7043 from guerler/column_match Avoid replacing data-referenced input values with default values Compare: https://github.com/galaxyproject/galaxy/compare/03acc9857608...284e906df0a0 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 9aaafd: Merge pull request #7044 from nsoranzo/release_18....
by GitHub 25 Nov '18

25 Nov '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 9aaafd8aea1930af02aeebc6b78f03164779ee7c https://github.com/galaxyproject/galaxy/commit/9aaafd8aea1930af02aeebc6b78f… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2018-11-24 (Sat, 24 Nov 2018) Changed paths: M lib/galaxy/tools/deps/container_resolvers/__init__.py M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/mulled/mulled_build.py Log Message: ----------- Merge pull request #7044 from nsoranzo/release_18.09_fix/mulled_container_default_channels [18.09] Backport #7038 Commit: 03acc98576085039ab1363b8248369ca646a031d https://github.com/galaxyproject/galaxy/commit/03acc98576085039ab1363b82483… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-11-25 (Sun, 25 Nov 2018) Log Message: ----------- Merge branch 'release_18.09' into dev Compare: https://github.com/galaxyproject/galaxy/compare/12dbbb81a7c7...03acc9857608 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 59afe0: fix error when building images where conda channel...
by GitHub 24 Nov '18

24 Nov '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: 59afe04523b8b00623b92458b4eb275f31401a19 https://github.com/galaxyproject/galaxy/commit/59afe04523b8b00623b92458b4eb… Author: Jelle Scholtalbers <j.scholtalbers(a)gmail.com> Date: 2018-11-22 (Thu, 22 Nov 2018) Changed paths: M lib/galaxy/tools/deps/mulled/mulled_build.py Log Message: ----------- fix error when building images where conda channels is passed as a string instead of a list Commit: 5255a0bf20dea411dbc4c1b9b05e757f2e554df1 https://github.com/galaxyproject/galaxy/commit/5255a0bf20dea411dbc4c1b9b05e… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-11-22 (Thu, 22 Nov 2018) Changed paths: M lib/galaxy/tools/deps/container_resolvers/__init__.py M lib/galaxy/tools/deps/container_resolvers/mulled.py Log Message: ----------- Fix ``involucro_auto_init`` default value Commit: 9aaafd8aea1930af02aeebc6b78f03164779ee7c https://github.com/galaxyproject/galaxy/commit/9aaafd8aea1930af02aeebc6b78f… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2018-11-24 (Sat, 24 Nov 2018) Changed paths: M lib/galaxy/tools/deps/container_resolvers/__init__.py M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/mulled/mulled_build.py Log Message: ----------- Merge pull request #7044 from nsoranzo/release_18.09_fix/mulled_container_default_channels [18.09] Backport #7038 Compare: https://github.com/galaxyproject/galaxy/compare/4ab4a190fe89...9aaafd8aea19 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 7474ee: fix error when building images where conda channel...
by GitHub 23 Nov '18

23 Nov '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 7474eeadf6375b90fd66bb7545970fd2eb05afe8 https://github.com/galaxyproject/galaxy/commit/7474eeadf6375b90fd66bb754597… Author: Jelle Scholtalbers <j.scholtalbers(a)gmail.com> Date: 2018-11-22 (Thu, 22 Nov 2018) Changed paths: M lib/galaxy/tools/deps/mulled/mulled_build.py Log Message: ----------- fix error when building images where conda channels is passed as a string instead of a list Commit: 12dbbb81a7c76b5de0d195f25f0a7b46992db9e0 https://github.com/galaxyproject/galaxy/commit/12dbbb81a7c76b5de0d195f25f0a… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-11-23 (Fri, 23 Nov 2018) Log Message: ----------- Merge pull request #7036 from scholtalbers/fix/mulled_container_default_channels Fix error when building images Compare: https://github.com/galaxyproject/galaxy/compare/dcfbedaa53dd...12dbbb81a7c7 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 59afe0: fix error when building images where conda channel...
by GitHub 23 Nov '18

23 Nov '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 59afe04523b8b00623b92458b4eb275f31401a19 https://github.com/galaxyproject/galaxy/commit/59afe04523b8b00623b92458b4eb… Author: Jelle Scholtalbers <j.scholtalbers(a)gmail.com> Date: 2018-11-22 (Thu, 22 Nov 2018) Changed paths: M lib/galaxy/tools/deps/mulled/mulled_build.py Log Message: ----------- fix error when building images where conda channels is passed as a string instead of a list Commit: 5255a0bf20dea411dbc4c1b9b05e757f2e554df1 https://github.com/galaxyproject/galaxy/commit/5255a0bf20dea411dbc4c1b9b05e… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-11-22 (Thu, 22 Nov 2018) Changed paths: M lib/galaxy/tools/deps/container_resolvers/__init__.py M lib/galaxy/tools/deps/container_resolvers/mulled.py Log Message: ----------- Fix ``involucro_auto_init`` default value Commit: dcfbedaa53ddc488b2ac74a63c8bae5a3d206abc https://github.com/galaxyproject/galaxy/commit/dcfbedaa53ddc488b2ac74a63c8b… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-11-23 (Fri, 23 Nov 2018) Changed paths: M lib/galaxy/tools/deps/container_resolvers/__init__.py M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/mulled/mulled_build.py Log Message: ----------- Merge pull request #7038 from nsoranzo/release_18.09_fix/mulled_container_default_channels [18.09] Fix error when building images Compare: https://github.com/galaxyproject/galaxy/compare/90076617651b...dcfbedaa53dd **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 992ea5: Pass through ``--daemon`` option to gunicorn
by GitHub 23 Nov '18

23 Nov '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 992ea5e4b957bb0723d7c8702f26bce8f50d5a05 https://github.com/galaxyproject/galaxy/commit/992ea5e4b957bb0723d7c8702f26… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-11-23 (Fri, 23 Nov 2018) Changed paths: M scripts/common_startup_functions.sh Log Message: ----------- Pass through ``--daemon`` option to gunicorn Documented at http://docs.gunicorn.org/en/stable/settings.html#daemon Commit: 4ab4a190fe89ecf410ccef269ecb59d985da5804 https://github.com/galaxyproject/galaxy/commit/4ab4a190fe89ecf410ccef269ecb… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2018-11-23 (Fri, 23 Nov 2018) Changed paths: M scripts/common_startup_functions.sh Log Message: ----------- Merge pull request #7042 from nsoranzo/release_18.09_gunicorn_daemon [18.09] Pass through ``--daemon`` option to gunicorn Commit: 90076617651b8159fc75bfeefff2ab5db85cab59 https://github.com/galaxyproject/galaxy/commit/90076617651b8159fc75bfeefff2… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-11-23 (Fri, 23 Nov 2018) Changed paths: M scripts/common_startup_functions.sh Log Message: ----------- Merge branch 'release_18.09' into dev Compare: https://github.com/galaxyproject/galaxy/compare/8470e9129693...90076617651b **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 992ea5: Pass through ``--daemon`` option to gunicorn
by GitHub 23 Nov '18

23 Nov '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/galaxy Commit: 992ea5e4b957bb0723d7c8702f26bce8f50d5a05 https://github.com/galaxyproject/galaxy/commit/992ea5e4b957bb0723d7c8702f26… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-11-23 (Fri, 23 Nov 2018) Changed paths: M scripts/common_startup_functions.sh Log Message: ----------- Pass through ``--daemon`` option to gunicorn Documented at http://docs.gunicorn.org/en/stable/settings.html#daemon Commit: 4ab4a190fe89ecf410ccef269ecb59d985da5804 https://github.com/galaxyproject/galaxy/commit/4ab4a190fe89ecf410ccef269ecb… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2018-11-23 (Fri, 23 Nov 2018) Changed paths: M scripts/common_startup_functions.sh Log Message: ----------- Merge pull request #7042 from nsoranzo/release_18.09_gunicorn_daemon [18.09] Pass through ``--daemon`` option to gunicorn Commit: f2c9baf2c54b4f6983887149bb5a9dc01a501c1c https://github.com/galaxyproject/galaxy/commit/f2c9baf2c54b4f6983887149bb5a… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-11-23 (Fri, 23 Nov 2018) Changed paths: M scripts/common_startup_functions.sh Log Message: ----------- Merge branch 'release_18.09' Compare: https://github.com/galaxyproject/galaxy/compare/1ae8eb577db9...f2c9baf2c54b **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 992ea5: Pass through ``--daemon`` option to gunicorn
by GitHub 23 Nov '18

23 Nov '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: 992ea5e4b957bb0723d7c8702f26bce8f50d5a05 https://github.com/galaxyproject/galaxy/commit/992ea5e4b957bb0723d7c8702f26… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-11-23 (Fri, 23 Nov 2018) Changed paths: M scripts/common_startup_functions.sh Log Message: ----------- Pass through ``--daemon`` option to gunicorn Documented at http://docs.gunicorn.org/en/stable/settings.html#daemon Commit: 4ab4a190fe89ecf410ccef269ecb59d985da5804 https://github.com/galaxyproject/galaxy/commit/4ab4a190fe89ecf410ccef269ecb… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2018-11-23 (Fri, 23 Nov 2018) Changed paths: M scripts/common_startup_functions.sh Log Message: ----------- Merge pull request #7042 from nsoranzo/release_18.09_gunicorn_daemon [18.09] Pass through ``--daemon`` option to gunicorn Compare: https://github.com/galaxyproject/galaxy/compare/a1277b0e43b2...4ab4a190fe89 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/ansible-galaxy] 640012: Make safe for --check
by GitHub 23 Nov '18

23 Nov '18

Branch: refs/heads/make-check-safe Home: https://github.com/galaxyproject/ansible-galaxy Commit: 640012f0d7883e011d41e085fdbaedfdeb7d1fae https://github.com/galaxyproject/ansible-galaxy/commit/640012f0d7883e011d41… Author: Helena Rasche <hxr(a)hx42.org> Date: 2018-11-23 (Fri, 23 Nov 2018) Changed paths: M tasks/clone.yml Log Message: ----------- Make safe for --check **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] f04342: workflows api call made public
by GitHub 21 Nov '18

21 Nov '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f04342541d3b43adacf8b9f194069e72dc77ec61 https://github.com/galaxyproject/galaxy/commit/f04342541d3b43adacf8b9f19406… Author: Frederik Coppens <frederik.coppens(a)psb.vib-ugent.be> Date: 2018-11-15 (Thu, 15 Nov 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- workflows api call made public Commit: a94d22a7b3767217cbc90fda118f1e27ded1962c https://github.com/galaxyproject/galaxy/commit/a94d22a7b3767217cbc90fda118f… Author: Frederik Coppens <frederik.coppens(a)psb.vib-ugent.be> Date: 2018-11-16 (Fri, 16 Nov 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- published workflows accessible through API endpoint Commit: 983f490f9e2928a0abcdd74086952db3043ac1bf https://github.com/galaxyproject/galaxy/commit/983f490f9e2928a0abcdd7408695… Author: Frederik Coppens <frederik.coppens(a)psb.vib-ugent.be> Date: 2018-11-16 (Fri, 16 Nov 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- show_published only defaults to True when not logged in Commit: 45345533fb6495a109c49b6fe058f1a26609fe15 https://github.com/galaxyproject/galaxy/commit/45345533fb6495a109c49b6fe058… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-11-21 (Wed, 21 Nov 2018) Changed paths: M test/api/test_workflows.py Log Message: ----------- Test cases for public WF access to published workflows. Commit: 8470e91296931ea9d23f4b655a4a2be7d1d51b4c https://github.com/galaxyproject/galaxy/commit/8470e91296931ea9d23f4b655a4a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-11-21 (Wed, 21 Nov 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py M test/api/test_workflows.py Log Message: ----------- Merge pull request #7020 from frederikcoppens/public_api_wf Expose published workflows through API Compare: https://github.com/galaxyproject/galaxy/compare/c7bd5c794b3c...8470e9129693 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/usegalaxy-playbook] 63d0a4: Remove downtime banner
by GitHub 20 Nov '18

20 Nov '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 63d0a4e022ae19201fce2db1fee1699d2d51e1eb https://github.com/galaxyproject/usegalaxy-playbook/commit/63d0a4e022ae1920… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-11-20 (Tue, 20 Nov 2018) Changed paths: M env/main/group_vars/galaxyservers/vars.yml Log Message: ----------- Remove downtime banner **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 5f04db: Fix typo in import error messages
by GitHub 20 Nov '18

20 Nov '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 5f04dbd996f4034aa9db45037c6c6e43518bcd1f https://github.com/galaxyproject/galaxy/commit/5f04dbd996f4034aa9db45037c6c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-11-20 (Tue, 20 Nov 2018) Changed paths: M client/galaxy/scripts/components/HistoryImport.vue M client/galaxy/scripts/components/PluginList.vue M client/galaxy/scripts/components/WorkflowImport.vue Log Message: ----------- Fix typo in import error messages Commit: c7bd5c794b3c0f6a34fe01c7928ca5dbf43284d5 https://github.com/galaxyproject/galaxy/commit/c7bd5c794b3c0f6a34fe01c7928c… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-11-20 (Tue, 20 Nov 2018) Changed paths: M client/galaxy/scripts/components/HistoryImport.vue M client/galaxy/scripts/components/PluginList.vue M client/galaxy/scripts/components/WorkflowImport.vue Log Message: ----------- Merge pull request #7033 from guerler/import_typos Fix typos in import error messages Compare: https://github.com/galaxyproject/galaxy/compare/fe671f67ec6b...c7bd5c794b3c **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 1b5fd3: Restore jquery style for text field autocomplete o...
by GitHub 20 Nov '18

20 Nov '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1b5fd373cb2f260c9f29afd2ed7722bbc0cd6299 https://github.com/galaxyproject/galaxy/commit/1b5fd373cb2f260c9f29afd2ed77… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-11-20 (Tue, 20 Nov 2018) Changed paths: M templates/js-app.mako Log Message: ----------- Restore jquery style for text field autocomplete options Commit: fe671f67ec6ba222115bb4c5c5a3705ca868b3a6 https://github.com/galaxyproject/galaxy/commit/fe671f67ec6ba222115bb4c5c5a3… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-11-20 (Tue, 20 Nov 2018) Changed paths: M templates/js-app.mako Log Message: ----------- Merge pull request #7027 from guerler/fix_text_options Use solid background for text field autocomplete options Compare: https://github.com/galaxyproject/galaxy/compare/6778fa47ed89...fe671f67ec6b **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 306b11: Pass a ``JobWrapper`` instead of a ``Job`` to ``st...
by GitHub 20 Nov '18

20 Nov '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 306b114191a1d326afcbdca68f489b015ba07660 https://github.com/galaxyproject/galaxy/commit/306b114191a1d326afcbdca68f48… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-11-17 (Sat, 17 Nov 2018) Changed paths: M lib/galaxy/jobs/handler.py M lib/galaxy/jobs/runners/__init__.py M 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/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/tasks.py M test/unit/jobs/test_runner_local.py Log Message: ----------- Pass a ``JobWrapper`` instead of a ``Job`` to ``stop_job()`` methods Commit: 0ddc5aeba1827833991cd782a9d806fa9ccd414e https://github.com/galaxyproject/galaxy/commit/0ddc5aeba1827833991cd782a9d8… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-11-17 (Sat, 17 Nov 2018) Changed paths: M lib/galaxy/jobs/handler.py M lib/galaxy/jobs/runners/drmaa.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/model/__init__.py Log Message: ----------- Drop ``get_id()`` method Commit: 183d84e5dc8ce4530835852292f3d20318dc9980 https://github.com/galaxyproject/galaxy/commit/183d84e5dc8ce4530835852292f3… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-11-17 (Sat, 17 Nov 2018) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- 2 small simplifications in ``JobWrapper`` After commit eeb1dae5b71200ffe9f2056b2a7fd8ed560033c1, `JobWrapper.job_destination()` does not call `self._job_dataset_path_rewriter()` any more. Commit: 6778fa47ed899eefe1418139f43832f225760e0f https://github.com/galaxyproject/galaxy/commit/6778fa47ed899eefe1418139f438… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-11-20 (Tue, 20 Nov 2018) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/handler.py M lib/galaxy/jobs/runners/__init__.py M 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/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/tasks.py M lib/galaxy/model/__init__.py M test/unit/jobs/test_runner_local.py Log Message: ----------- Merge pull request #7023 from nsoranzo/stop_job_wrapper Pass a ``JobWrapper`` instead of a ``Job`` to ``stop_job()`` methods Compare: https://github.com/galaxyproject/galaxy/compare/cd0b7a9347c8...6778fa47ed89 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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