- 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 26 Nov '18

26 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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