galaxy-commits June 2018

galaxy-commits@lists.galaxyproject.org

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170 discussions

[galaxyproject/usegalaxy-playbook] 703b5c: Install Bowtie2 2.3.4.2 and Diffbind 2.6.6.4 on Te...
by GitHub 08 Jun '18

08 Jun '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 703b5c1fd336456ac03643671dca27b2b9e8d5dc https://github.com/galaxyproject/usegalaxy-playbook/commit/703b5c1fd336456a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-06-07 (Thu, 07 Jun 2018) Changed paths: M env/main/files/galaxy/var/integrated_tool_panel.xml M env/main/files/galaxy/var/shed_tool_conf.xml M env/main/files/galaxy/var/shed_tool_data_table_conf.xml M env/test/files/galaxy/var/integrated_tool_panel.xml M env/test/files/galaxy/var/shed_tool_conf.xml M env/test/files/galaxy/var/shed_tool_data_table_conf.xml Log Message: ----------- Install Bowtie2 2.3.4.2 and Diffbind 2.6.6.4 on Test and Main. Remove Diffbind 2.6.6.3 from Main **NOTE:** This service 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] 17d7c0: Consolidate use of get_repo_for_repository()
by GitHub 08 Jun '18

08 Jun '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 17d7c0fb1f43a8cf377a76ea9484630d1c7be7f1 https://github.com/galaxyproject/galaxy/commit/17d7c0fb1f43a8cf377a76ea9484… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-06-05 (Tue, 05 Jun 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/api/repository_revisions.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/webapps/tool_shed/controllers/repository_review.py M lib/galaxy/webapps/tool_shed/controllers/upload.py M lib/galaxy/webapps/tool_shed/model/__init__.py M lib/tool_shed/capsule/capsule_manager.py M lib/tool_shed/dependencies/attribute_handlers.py M lib/tool_shed/dependencies/repository/relation_builder.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/grids/repository_grids.py M lib/tool_shed/grids/repository_review_grids.py M lib/tool_shed/grids/util.py M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/metadata/repository_metadata_manager.py M lib/tool_shed/repository_registry.py M lib/tool_shed/repository_types/metadata.py M lib/tool_shed/repository_types/repository_suite_definition.py M lib/tool_shed/repository_types/tool_dependency_definition.py M lib/tool_shed/tools/tool_validator.py M lib/tool_shed/tools/tool_version_manager.py M lib/tool_shed/util/commit_util.py M lib/tool_shed/util/hg_util.py M lib/tool_shed/util/metadata_util.py M lib/tool_shed/util/readme_util.py M lib/tool_shed/util/repository_content_util.py M lib/tool_shed/util/repository_util.py M lib/tool_shed/util/review_util.py M lib/tool_shed/util/shed_util_common.py Log Message: ----------- Consolidate use of get_repo_for_repository() Commit: a777c39b1eee65179bc1ae2e817ef269f22f2cd4 https://github.com/galaxyproject/galaxy/commit/a777c39b1eee65179bc1ae2e817e… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-06-05 (Tue, 05 Jun 2018) Changed paths: M lib/galaxy/webapps/tool_shed/controllers/upload.py M lib/tool_shed/util/hg_util.py Log Message: ----------- Consolidate use of clone_repository() Commit: db5dc5580c6e62d98207cfef6db78929d5c02a88 https://github.com/galaxyproject/galaxy/commit/db5dc5580c6e62d98207cfef6db7… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-06-07 (Thu, 07 Jun 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/api/repository_revisions.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/webapps/tool_shed/controllers/repository_review.py M lib/galaxy/webapps/tool_shed/controllers/upload.py M lib/galaxy/webapps/tool_shed/model/__init__.py M lib/tool_shed/capsule/capsule_manager.py M lib/tool_shed/dependencies/attribute_handlers.py M lib/tool_shed/dependencies/repository/relation_builder.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/grids/repository_grids.py M lib/tool_shed/grids/repository_review_grids.py M lib/tool_shed/grids/util.py M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/metadata/repository_metadata_manager.py M lib/tool_shed/repository_registry.py M lib/tool_shed/repository_types/metadata.py M lib/tool_shed/repository_types/repository_suite_definition.py M lib/tool_shed/repository_types/tool_dependency_definition.py M lib/tool_shed/tools/tool_validator.py M lib/tool_shed/tools/tool_version_manager.py M lib/tool_shed/util/commit_util.py M lib/tool_shed/util/hg_util.py M lib/tool_shed/util/metadata_util.py M lib/tool_shed/util/readme_util.py M lib/tool_shed/util/repository_content_util.py M lib/tool_shed/util/repository_util.py M lib/tool_shed/util/review_util.py M lib/tool_shed/util/shed_util_common.py Log Message: ----------- Merge pull request #6277 from nsoranzo/mercurial_api_removal2 Consolidate use of get_repo_for_repository() and clone_repository() Compare: https://github.com/galaxyproject/galaxy/compare/0dcca1a727cf...db5dc5580c6e **NOTE:** This service 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] 060d3f: Test list collection mapping over multidata input
by GitHub 08 Jun '18

08 Jun '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 060d3f0ffdefa9903d33847346a823acfdbaa969 https://github.com/galaxyproject/galaxy/commit/060d3f0ffdefa9903d33847346a8… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-06-07 (Thu, 07 Jun 2018) Changed paths: M test/api/test_tools.py Log Message: ----------- Test list collection mapping over multidata input Commit: baa42fa8c6f867c6d2a1adcce9d8f3b946d10f0c https://github.com/galaxyproject/galaxy/commit/baa42fa8c6f867c6d2a1adcce9d8… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-06-07 (Thu, 07 Jun 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Fix mapping list over multidata input Commit: 0dcca1a727cf3678386b319bd94d5421798e6eff https://github.com/galaxyproject/galaxy/commit/0dcca1a727cf3678386b319bd94d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-06-07 (Thu, 07 Jun 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py M test/api/test_tools.py Log Message: ----------- Merge pull request #6300 from mvdbeek/multidata_list_input Make simple lists selectable again in multidata inputs Compare: https://github.com/galaxyproject/galaxy/compare/e42e0c39a7d7...0dcca1a727cf **NOTE:** This service 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]
by GitHub 07 Jun '18

07 Jun '18

Branch: refs/heads/fix_workflow_link Home: https://github.com/galaxyproject/galaxy **NOTE:** This service 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] 671c4d: fix link to workflow list
by GitHub 07 Jun '18

07 Jun '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 671c4d4f5fad7d15e6b9f70d595cf9f14ec6aeda https://github.com/galaxyproject/galaxy/commit/671c4d4f5fad7d15e6b9f70d595c… Author: Björn Grüning <bjoern.gruening(a)gmail.com> Date: 2018-06-04 (Mon, 04 Jun 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- fix link to workflow list Commit: e42e0c39a7d723ab9b99038b2d863c04848ff3e7 https://github.com/galaxyproject/galaxy/commit/e42e0c39a7d723ab9b99038b2d86… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-06-07 (Thu, 07 Jun 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Merge pull request #6270 from galaxyproject/fix_workflow_link fix link to workflow list Compare: https://github.com/galaxyproject/galaxy/compare/eb6cefc514a0...e42e0c39a7d7 **NOTE:** This service 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] 49a1be: Allow from_param to reference a child collection
by GitHub 07 Jun '18

07 Jun '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 49a1be4f1de3cfe48bbfd0b709bc8a158f7d36e6 https://github.com/galaxyproject/galaxy/commit/49a1be4f1de3cfe48bbfd0b709bc… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-06-04 (Mon, 04 Jun 2018) Changed paths: M lib/galaxy/tools/parser/output_actions.py Log Message: ----------- Allow from_param to reference a child collection This is necessary when mapping over a collection over an input that is referenced in the output section, like so: ``` ... <when value="paired_collection"> <action type="format"> <option type="from_param" name="library.input_1" param_attribute="reverse.ext" /> </action> </when> ... ``` Commit: bc8254faecf9b9f9bbd000d9ba7601ce9fe472a5 https://github.com/galaxyproject/galaxy/commit/bc8254faecf9b9f9bbd000d9ba76… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-06-04 (Mon, 04 Jun 2018) Changed paths: M lib/galaxy/dataset_collections/subcollections.py Log Message: ----------- Do not adapt target collection to child collection type Otherwise mapping over list:list:pair to a pair input breaks at https://github.com/galaxyproject/galaxy/blob/21b44bf348ae10d170ab96a3b6f30b…. This and the previous commit should fix https://github.com/galaxyproject/tools-iuc/issues/1563. Commit: 3e22b0b11b600a4e957557d3cece03665bdc7de5 https://github.com/galaxyproject/galaxy/commit/3e22b0b11b600a4e957557d3cece… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-06-04 (Mon, 04 Jun 2018) Changed paths: M test/api/test_tools.py A test/functional/tools/output_action_change_format_paired.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Test case for mapping over inputs with output ftype determined via input extension Commit: 7b741a32cddb94442c7663f94c6c3b29e91e4158 https://github.com/galaxyproject/galaxy/commit/7b741a32cddb94442c7663f94c6c… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-06-06 (Wed, 06 Jun 2018) Changed paths: M run.sh Log Message: ----------- Fix `GALAXY_RUN_ALL=1 ./run.sh --daemon` Broken in commit 0ea8107191ea1a3bc8b4b57623c981c06f38092e . Reported by @lparsons in https://github.com/galaxyproject/galaxy/pull/6262#issuecomment-395113621 Commit: a2fe4b0c76fa9cfff9e974b76e4d5ea34679a881 https://github.com/galaxyproject/galaxy/commit/a2fe4b0c76fa9cfff9e974b76e4d… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-06-06 (Wed, 06 Jun 2018) Changed paths: M run.sh Log Message: ----------- Merge pull request #6295 from nsoranzo/release_18.01_followup_on_6262 [18.01] Fix `GALAXY_RUN_ALL=1 ./run.sh --daemon` Commit: 3007c93d7c5bf6ccb7c6b8d5df95ebdf60ac4a8b https://github.com/galaxyproject/galaxy/commit/3007c93d7c5bf6ccb7c6b8d5df95… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-06-06 (Wed, 06 Jun 2018) Changed paths: M lib/galaxy/dataset_collections/subcollections.py M lib/galaxy/tools/parser/output_actions.py M test/api/test_tools.py A test/functional/tools/output_action_change_format_paired.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #6266 from jmchilton/from_param_fixes_backport [18.01] Backport fixes for collection output actions. Commit: 711070dc4c18af7a2da2a2a8bcafb4112efb0daf https://github.com/galaxyproject/galaxy/commit/711070dc4c18af7a2da2a2a8bcaf… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-06-07 (Thu, 07 Jun 2018) Changed paths: M lib/galaxy/dataset_collections/subcollections.py M lib/galaxy/tools/parser/output_actions.py M run.sh M test/api/test_tools.py A test/functional/tools/output_action_change_format_paired.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge branch 'release_18.01' into release_18.05 Commit: eb6cefc514a0ec96fbbb820e14712782653210c7 https://github.com/galaxyproject/galaxy/commit/eb6cefc514a0ec96fbbb820e1471… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-06-07 (Thu, 07 Jun 2018) Changed paths: M run.sh Log Message: ----------- Merge branch 'release_18.05' into dev Compare: https://github.com/galaxyproject/galaxy/compare/fae66e65f40b...eb6cefc514a0 **NOTE:** This service 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] 49a1be: Allow from_param to reference a child collection
by GitHub 07 Jun '18

07 Jun '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: 49a1be4f1de3cfe48bbfd0b709bc8a158f7d36e6 https://github.com/galaxyproject/galaxy/commit/49a1be4f1de3cfe48bbfd0b709bc… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-06-04 (Mon, 04 Jun 2018) Changed paths: M lib/galaxy/tools/parser/output_actions.py Log Message: ----------- Allow from_param to reference a child collection This is necessary when mapping over a collection over an input that is referenced in the output section, like so: ``` ... <when value="paired_collection"> <action type="format"> <option type="from_param" name="library.input_1" param_attribute="reverse.ext" /> </action> </when> ... ``` Commit: bc8254faecf9b9f9bbd000d9ba7601ce9fe472a5 https://github.com/galaxyproject/galaxy/commit/bc8254faecf9b9f9bbd000d9ba76… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-06-04 (Mon, 04 Jun 2018) Changed paths: M lib/galaxy/dataset_collections/subcollections.py Log Message: ----------- Do not adapt target collection to child collection type Otherwise mapping over list:list:pair to a pair input breaks at https://github.com/galaxyproject/galaxy/blob/21b44bf348ae10d170ab96a3b6f30b…. This and the previous commit should fix https://github.com/galaxyproject/tools-iuc/issues/1563. Commit: 3e22b0b11b600a4e957557d3cece03665bdc7de5 https://github.com/galaxyproject/galaxy/commit/3e22b0b11b600a4e957557d3cece… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-06-04 (Mon, 04 Jun 2018) Changed paths: M test/api/test_tools.py A test/functional/tools/output_action_change_format_paired.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Test case for mapping over inputs with output ftype determined via input extension Commit: 7b741a32cddb94442c7663f94c6c3b29e91e4158 https://github.com/galaxyproject/galaxy/commit/7b741a32cddb94442c7663f94c6c… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-06-06 (Wed, 06 Jun 2018) Changed paths: M run.sh Log Message: ----------- Fix `GALAXY_RUN_ALL=1 ./run.sh --daemon` Broken in commit 0ea8107191ea1a3bc8b4b57623c981c06f38092e . Reported by @lparsons in https://github.com/galaxyproject/galaxy/pull/6262#issuecomment-395113621 Commit: a2fe4b0c76fa9cfff9e974b76e4d5ea34679a881 https://github.com/galaxyproject/galaxy/commit/a2fe4b0c76fa9cfff9e974b76e4d… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-06-06 (Wed, 06 Jun 2018) Changed paths: M run.sh Log Message: ----------- Merge pull request #6295 from nsoranzo/release_18.01_followup_on_6262 [18.01] Fix `GALAXY_RUN_ALL=1 ./run.sh --daemon` Commit: 3007c93d7c5bf6ccb7c6b8d5df95ebdf60ac4a8b https://github.com/galaxyproject/galaxy/commit/3007c93d7c5bf6ccb7c6b8d5df95… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-06-06 (Wed, 06 Jun 2018) Changed paths: M lib/galaxy/dataset_collections/subcollections.py M lib/galaxy/tools/parser/output_actions.py M test/api/test_tools.py A test/functional/tools/output_action_change_format_paired.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #6266 from jmchilton/from_param_fixes_backport [18.01] Backport fixes for collection output actions. Commit: 711070dc4c18af7a2da2a2a8bcafb4112efb0daf https://github.com/galaxyproject/galaxy/commit/711070dc4c18af7a2da2a2a8bcaf… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-06-07 (Thu, 07 Jun 2018) Changed paths: M lib/galaxy/dataset_collections/subcollections.py M lib/galaxy/tools/parser/output_actions.py M run.sh M test/api/test_tools.py A test/functional/tools/output_action_change_format_paired.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge branch 'release_18.01' into release_18.05 Compare: https://github.com/galaxyproject/galaxy/compare/acb4cdf5843a...711070dc4c18 **NOTE:** This service 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] f3dccb: Overhaul workflow execution response, including ap...
by GitHub 07 Jun '18

07 Jun '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f3dccb7b6c897d44cb3fe94e6e4541f6273fe85c https://github.com/galaxyproject/galaxy/commit/f3dccb7b6c897d44cb3fe94e6e45… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-29 (Tue, 29 May 2018) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js Log Message: ----------- Overhaul workflow execution response, including appropriate text for new histories, and multiple executions. With links. Commit: 78fabab53c4e511dc5a3db4d3cc62eb71a5f097d https://github.com/galaxyproject/galaxy/commit/78fabab53c4e511dc5a3db4d3cc6… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-29 (Tue, 29 May 2018) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js Log Message: ----------- Drop debug statement Commit: 5845d64a48ad9528a45315cb2252afeaa067911b https://github.com/galaxyproject/galaxy/commit/5845d64a48ad9528a45315cb2252… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-29 (Tue, 29 May 2018) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js Log Message: ----------- Cleanup in tool-form-composite Commit: 6c9953cfe2b98f0f23a4496d3a45437029b8945c https://github.com/galaxyproject/galaxy/commit/6c9953cfe2b98f0f23a4496d3a45… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-30 (Wed, 30 May 2018) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js Log Message: ----------- Clarify/reuse new history target logic, fix links to avoid redundant slash on root Commit: fae66e65f40b6d8c03fea1236e12a420fbb2058e https://github.com/galaxyproject/galaxy/commit/fae66e65f40b6d8c03fea1236e12… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2018-06-06 (Wed, 06 Jun 2018) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js Log Message: ----------- Merge pull request #6240 from dannon/workflow_submit_text_links Workflow submit text links Compare: https://github.com/galaxyproject/galaxy/compare/ee56e570e027...fae66e65f40b **NOTE:** This service 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] 936c16: Index select2 field values
by GitHub 07 Jun '18

07 Jun '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 936c165818880bacd17416c7e848d6fba292e586 https://github.com/galaxyproject/galaxy/commit/936c165818880bacd17416c7e848… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-06-05 (Tue, 05 Jun 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-default.js Log Message: ----------- Index select2 field values Commit: ee56e570e027eb7306becc95890c68fcb415c1fb https://github.com/galaxyproject/galaxy/commit/ee56e570e027eb7306becc95890c… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-06-06 (Wed, 06 Jun 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-default.js Log Message: ----------- Merge pull request #6286 from guerler/column_performance Index select2 field values Compare: https://github.com/galaxyproject/galaxy/compare/d2723428391a...ee56e570e027 **NOTE:** This service 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] 49a1be: Allow from_param to reference a child collection
by GitHub 07 Jun '18

07 Jun '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: 49a1be4f1de3cfe48bbfd0b709bc8a158f7d36e6 https://github.com/galaxyproject/galaxy/commit/49a1be4f1de3cfe48bbfd0b709bc… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-06-04 (Mon, 04 Jun 2018) Changed paths: M lib/galaxy/tools/parser/output_actions.py Log Message: ----------- Allow from_param to reference a child collection This is necessary when mapping over a collection over an input that is referenced in the output section, like so: ``` ... <when value="paired_collection"> <action type="format"> <option type="from_param" name="library.input_1" param_attribute="reverse.ext" /> </action> </when> ... ``` Commit: bc8254faecf9b9f9bbd000d9ba7601ce9fe472a5 https://github.com/galaxyproject/galaxy/commit/bc8254faecf9b9f9bbd000d9ba76… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-06-04 (Mon, 04 Jun 2018) Changed paths: M lib/galaxy/dataset_collections/subcollections.py Log Message: ----------- Do not adapt target collection to child collection type Otherwise mapping over list:list:pair to a pair input breaks at https://github.com/galaxyproject/galaxy/blob/21b44bf348ae10d170ab96a3b6f30b…. This and the previous commit should fix https://github.com/galaxyproject/tools-iuc/issues/1563. Commit: 3e22b0b11b600a4e957557d3cece03665bdc7de5 https://github.com/galaxyproject/galaxy/commit/3e22b0b11b600a4e957557d3cece… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-06-04 (Mon, 04 Jun 2018) Changed paths: M test/api/test_tools.py A test/functional/tools/output_action_change_format_paired.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Test case for mapping over inputs with output ftype determined via input extension Commit: 3007c93d7c5bf6ccb7c6b8d5df95ebdf60ac4a8b https://github.com/galaxyproject/galaxy/commit/3007c93d7c5bf6ccb7c6b8d5df95… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-06-06 (Wed, 06 Jun 2018) Changed paths: M lib/galaxy/dataset_collections/subcollections.py M lib/galaxy/tools/parser/output_actions.py M test/api/test_tools.py A test/functional/tools/output_action_change_format_paired.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #6266 from jmchilton/from_param_fixes_backport [18.01] Backport fixes for collection output actions. Compare: https://github.com/galaxyproject/galaxy/compare/a2fe4b0c76fa...3007c93d7c5b **NOTE:** This service 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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galaxy-commits June 2018