galaxy-commits December 2018

galaxy-commits@lists.galaxyproject.org

1 participants
76 discussions

[galaxyproject/usegalaxy-playbook] dbcc6f: Update test toolshed.
by GitHub 21 Dec '18

21 Dec '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: dbcc6f4f189fc5e801b35b20989ee5e577cf9a7e https://github.com/galaxyproject/usegalaxy-playbook/commit/dbcc6f4f189fc5e8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-12-21 (Fri, 21 Dec 2018) Changed paths: M env/testtoolshed/group_vars/toolshedservers/vars.yml Log Message: ----------- Update test toolshed. **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.

1 0

[galaxyproject/galaxy] 4fbaa1: Add simple stub for mash sketch files
by GitHub 20 Dec '18

20 Dec '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4fbaa161232f1b8e12b23788e258def10e6aa156 https://github.com/galaxyproject/galaxy/commit/4fbaa161232f1b8e12b23788e258… Author: Dan Fornika <dfornika(a)gmail.com> Date: 2018-12-07 (Fri, 07 Dec 2018) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py Log Message: ----------- Add simple stub for mash sketch files Commit: 7d5a006b01ccd37ad65156be95f5e606dc4ea985 https://github.com/galaxyproject/galaxy/commit/7d5a006b01ccd37ad65156be95f5… Author: Dan Fornika <dfornika(a)gmail.com> Date: 2018-12-07 (Fri, 07 Dec 2018) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Removed extra whitespace to appease linter Commit: 27dc7c42c97db9230657a7db86567ac8b253d6b5 https://github.com/galaxyproject/galaxy/commit/27dc7c42c97db9230657a7db8656… Author: Dan Fornika <dfornika(a)gmail.com> Date: 2018-12-07 (Fri, 07 Dec 2018) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Removed extra whitespace to appease linter Commit: 288453d4d017425f1f6121552e132fe8030624aa https://github.com/galaxyproject/galaxy/commit/288453d4d017425f1f6121552e13… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-12-20 (Thu, 20 Dec 2018) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py Log Message: ----------- Merge pull request #7087 from dfornika/mash-sketch-datatype Add datatype for Mash Sketch files. Compare: https://github.com/galaxyproject/galaxy/compare/7eca9baf5ae5...288453d4d017 **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.

1 0

[galaxyproject/galaxy] 6f669d: 7132 Updated singleton to address cors issue in to...
by GitHub 20 Dec '18

20 Dec '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 6f669dd79b3ed7ad51658ef4f9b56fad834c2390 https://github.com/galaxyproject/galaxy/commit/6f669dd79b3ed7ad51658ef4f9b5… Author: Mason <nerdinacan(a)gmail.com> Date: 2018-12-19 (Wed, 19 Dec 2018) Changed paths: M client/galaxy/scripts/app/singleton.js M client/galaxy/scripts/layout/panel.js Log Message: ----------- 7132 Updated singleton to address cors issue in toolshed frames Commit: 60146ec89be41aec9a8d6216e96908b9095e6054 https://github.com/galaxyproject/galaxy/commit/60146ec89be41aec9a8d6216e969… Author: Mason <nerdinacan(a)gmail.com> Date: 2018-12-19 (Wed, 19 Dec 2018) Changed paths: M client/galaxy/scripts/layout/panel.js Log Message: ----------- Replaced test code with real code Commit: cf7f1b0745482c5e7cd75fa9d8e91e95124fcfac https://github.com/galaxyproject/galaxy/commit/cf7f1b0745482c5e7cd75fa9d8e9… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-12-20 (Thu, 20 Dec 2018) Changed paths: M client/galaxy/scripts/layout/panel.js Log Message: ----------- Client formatting. Commit: 7eca9baf5ae5c2a43e54d9dd9e76797fe2406568 https://github.com/galaxyproject/galaxy/commit/7eca9baf5ae5c2a43e54d9dd9e76… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-12-20 (Thu, 20 Dec 2018) Changed paths: M client/galaxy/scripts/app/singleton.js M client/galaxy/scripts/layout/panel.js Log Message: ----------- Merge branch '7132_fix_cors_singleton_storage' into dev Compare: https://github.com/galaxyproject/galaxy/compare/6a0a6ec1d1ee...7eca9baf5ae5 **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.

1 0

[galaxyproject/galaxy] 1edb74: Drop tools without installable dependencies
by GitHub 20 Dec '18

20 Dec '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1edb7489a16775ef2e3810e675c8182762d92540 https://github.com/galaxyproject/galaxy/commit/1edb7489a16775ef2e3810e675c8… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-12-20 (Thu, 20 Dec 2018) Changed paths: M config/tool_conf.xml.sample Log Message: ----------- Drop tools without installable dependencies These seem to be beyond legacy, and since their not installable let's drop them from the default config. I left them in tool_conf.xml.main, since they appear to be installed on main. Commit: 6a0a6ec1d1ee638731eb456da7abdee8b5582853 https://github.com/galaxyproject/galaxy/commit/6a0a6ec1d1ee638731eb456da7ab… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-12-20 (Thu, 20 Dec 2018) Changed paths: M config/tool_conf.xml.sample Log Message: ----------- Merge pull request #7136 from mvdbeek/remove_tools_without_deps Drop tools without installable dependencies Compare: https://github.com/galaxyproject/galaxy/compare/1854c934cb23...6a0a6ec1d1ee **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.

1 0

[galaxyproject/galaxy] fe2b7e: Enable tagging+annotation of jobs regardless of st...
by GitHub 19 Dec '18

19 Dec '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: fe2b7eb1e690239932b2c49ac9350ee56fe1c5a6 https://github.com/galaxyproject/galaxy/commit/fe2b7eb1e690239932b2c49ac935… Author: Sergey Golitsynskiy <sgolitsynskiy(a)gmail.com> Date: 2018-12-13 (Thu, 13 Dec 2018) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js Log Message: ----------- Enable tagging+annotation of jobs regardless of state See issue #6330 Commit: a3d1c6872b558d470b1a2f2667e6abffd920d856 https://github.com/galaxyproject/galaxy/commit/a3d1c6872b558d470b1a2f2667e6… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-12-18 (Tue, 18 Dec 2018) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js Log Message: ----------- Minor formatting; tabstop=4 Commit: 5a666eb656093cd3df5332ca78c617cb3d547b8c https://github.com/galaxyproject/galaxy/commit/5a666eb656093cd3df5332ca78c6… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-12-18 (Tue, 18 Dec 2018) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js Log Message: ----------- Avoid using underscore where there's a vanilla alternative. Commit: 1854c934cb23131662dfb5a903ad5cae98a93662 https://github.com/galaxyproject/galaxy/commit/1854c934cb23131662dfb5a903ad… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-12-19 (Wed, 19 Dec 2018) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js Log Message: ----------- Merge pull request #7115 from ic4f/feature_i6330 [WIP] Enable tagging+annotation of jobs regardless of state Compare: https://github.com/galaxyproject/galaxy/compare/e31274b7f58d...1854c934cb23 **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.

1 0

[galaxyproject/galaxy] e1e32c: Test for 'metadata' in newer style discovered prim...
by GitHub 18 Dec '18

18 Dec '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e1e32cdcc6e3a300f5534ca961d2459634142367 https://github.com/galaxyproject/galaxy/commit/e1e32cdcc6e3a300f5534ca961d2… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-12-18 (Tue, 18 Dec 2018) Changed paths: M test/functional/tools/samples_tool_conf.xml A test/functional/tools/tool_provided_metadata_10.xml Log Message: ----------- Test for 'metadata' in newer style discovered primary datasets. Commit: 62a7c40ba4f29293bc921e81bd90ea59a570319b https://github.com/galaxyproject/galaxy/commit/62a7c40ba4f29293bc921e81bd90… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-12-18 (Tue, 18 Dec 2018) Changed paths: M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/verify/__init__.py Log Message: ----------- Fix for testing extra files in tool tests. Wouldn't be testing if primary file didn't specify a filename to test against. Commit: 953730d61ca81e79f898312b526ab8fa0680c9e0 https://github.com/galaxyproject/galaxy/commit/953730d61ca81e79f898312b526a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-12-18 (Tue, 18 Dec 2018) Changed paths: M test/functional/tools/samples_tool_conf.xml A test/functional/tools/tool_provided_metadata_11.xml A test/functional/tools/tool_provided_metadata_12.xml Log Message: ----------- Tests for tool provided metadata specifing extra files. Commit: e31274b7f58dec15c45874acebdf82ae35e39999 https://github.com/galaxyproject/galaxy/commit/e31274b7f58dec15c45874acebdf… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-12-18 (Tue, 18 Dec 2018) Changed paths: M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/verify/__init__.py M test/functional/tools/samples_tool_conf.xml A test/functional/tools/tool_provided_metadata_10.xml A test/functional/tools/tool_provided_metadata_11.xml A test/functional/tools/tool_provided_metadata_12.xml Log Message: ----------- Merge pull request #7131 from jmchilton/extra_files_3 Fixes and tests for collecting extra files for discovered datasets. Compare: https://github.com/galaxyproject/galaxy/compare/b7bb1df769e6...e31274b7f58d **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.

1 0

[galaxyproject/usegalaxy-playbook] 73a612: Updated cutadapt wrapper.
by GitHub 18 Dec '18

18 Dec '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 73a61205376ffddb17603600bf386867e8a22303 https://github.com/galaxyproject/usegalaxy-playbook/commit/73a61205376ffddb… Author: Dave B <dave(a)bx.psu.edu> Date: 2018-12-18 (Tue, 18 Dec 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 Log Message: ----------- Updated cutadapt wrapper. Commit: b9659ce1d7dd5d5af392a54339475544bda739b3 https://github.com/galaxyproject/usegalaxy-playbook/commit/b9659ce1d7dd5d5a… Author: Dave B <dave(a)bx.psu.edu> Date: 2018-12-18 (Tue, 18 Dec 2018) Changed paths: M env/main/files/galaxy/galaxy_version.yml 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: ----------- Merge upstream. Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/dcaa75ccda4b...… **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.

1 0

[galaxyproject/usegalaxy-playbook] dcaa75: Update main, mutables.
by GitHub 18 Dec '18

18 Dec '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: dcaa75ccda4baacd89b3a9698bec96270aa34cf9 https://github.com/galaxyproject/usegalaxy-playbook/commit/dcaa75ccda4baacd… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-12-18 (Tue, 18 Dec 2018) Changed paths: M env/main/files/galaxy/galaxy_version.yml Log Message: ----------- Update main, mutables. **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.

1 0

[galaxyproject/usegalaxy-playbook] 9494e6: Update main mutable configs for bcf tools installa...
by GitHub 18 Dec '18

18 Dec '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 9494e6e572427514f483381349126d43fdca0f07 https://github.com/galaxyproject/usegalaxy-playbook/commit/9494e6e572427514… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-12-18 (Tue, 18 Dec 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 Log Message: ----------- Update main mutable configs for bcf tools installation **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.

1 0

[galaxyproject/galaxy] 22e135: Update help text as per suggestion from CWunder
by GitHub 18 Dec '18

18 Dec '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 22e1350f7a9eeddd53ffa5b6febb492ceefb004c https://github.com/galaxyproject/galaxy/commit/22e1350f7a9eeddd53ffa5b6febb… Author: pvanheus <pvh(a)sanbi.ac.za> Date: 2018-12-18 (Tue, 18 Dec 2018) Changed paths: M lib/galaxy/tools/filter_from_file.xml Log Message: ----------- Update help text as per suggestion from CWunder This [thread](https://help.galaxyproject.org/t/clearer-documentation-for-filter-l… suggests that the help text for this tool is not clear. This PR attempts to address that weakness. Commit: b7bb1df769e683f1b5e23b04de3194f6cb1d5545 https://github.com/galaxyproject/galaxy/commit/b7bb1df769e683f1b5e23b04de31… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-12-18 (Tue, 18 Dec 2018) Changed paths: M lib/galaxy/tools/filter_from_file.xml Log Message: ----------- Merge pull request #7127 from pvanheus/patch-10 Update help text as per suggestion from CWunder Compare: https://github.com/galaxyproject/galaxy/compare/faec3dc05891...b7bb1df769e6 **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.

1 0

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

galaxy-commits December 2018