Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 17a1683a383d7f375b77371548ff7d349a561a96 https://github.com/galaxyproject/galaxy/commit/17a1683a383d7f375b77371548ff7... Author: John Chilton <jmchilton@gmail.com> Date: 2016-02-01 (Mon, 01 Feb 2016) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Warn on optional select test parameter. Commit: ccdb027d38428a38d79b4272fadb076b7f428825 https://github.com/galaxyproject/galaxy/commit/ccdb027d38428a38d79b4272fadb0... Author: guerler <aysam.guerler@gmail.com> Date: 2016-02-01 (Mon, 01 Feb 2016) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Prevent optional test parameters in conditionals Commit: 6fa7f1e1edda25ec36f2373148af223493924803 https://github.com/galaxyproject/galaxy/commit/6fa7f1e1edda25ec36f2373148af2... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2016-02-01 (Mon, 01 Feb 2016) Changed paths: M lib/galaxy/dependencies/conda-environment.txt M lib/galaxy/dependencies/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt Log Message: ----------- Bump pysam to new 0.8.4+gx1. Commit: 508ebea63f2376b5a3b452148e4a6d3c18366b3b https://github.com/galaxyproject/galaxy/commit/508ebea63f2376b5a3b452148e4a6... Author: Aysam Guerler <aysam.guerler@gmail.com> Date: 2016-02-01 (Mon, 01 Feb 2016) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge pull request #8 from jmchilton/fix_optional_001 Warn on optional select test parameter. Commit: ba9ad97c40bd994e0dc51888ef235cf3b434168a https://github.com/galaxyproject/galaxy/commit/ba9ad97c40bd994e0dc51888ef235... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2016-02-02 (Tue, 02 Feb 2016) Changed paths: M test-data/3.bam Log Message: ----------- Fix 3.bam @PG header to use : instead of = as a key:value separator. See commentary in https://github.com/galaxyproject/galaxy/pull/1638 for more details. Commit: 39eb262219beca9ec6b849b49c0430d834cfd2ae https://github.com/galaxyproject/galaxy/commit/39eb262219beca9ec6b849b49c043... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2016-02-02 (Tue, 02 Feb 2016) Changed paths: M test-data/3.bam Log Message: ----------- More fixes to 3.bam to make it valid stripped out secondary HD header and duplicated sequences chr10-16 Commit: 66f20e7df91074e07cbade57b20deb68cb840a55 https://github.com/galaxyproject/galaxy/commit/66f20e7df91074e07cbade57b20de... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2016-02-02 (Tue, 02 Feb 2016) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Fix method signature of bam.set_meta to include a positional argument which is now required. Commit: d6325c5039f28062a2cf49d00c091d83a92865c3 https://github.com/galaxyproject/galaxy/commit/d6325c5039f28062a2cf49d00c091... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2016-02-02 (Tue, 02 Feb 2016) Changed paths: M lib/galaxy/visualization/data_providers/genome.py Log Message: ----------- Update data providers pysam.AlignmentFile usage Commit: a95827751f463f35c67e76f84127f850972244c5 https://github.com/galaxyproject/galaxy/commit/a95827751f463f35c67e76f84127f... Author: John Chilton <jmchilton@gmail.com> Date: 2016-02-02 (Tue, 02 Feb 2016) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge pull request #1637 from guerler/fix_optional_001 [16.01] Prevent optional test parameters in conditionals Commit: 45f523f9229f6d943e3a65042b8cad0276a0a7d7 https://github.com/galaxyproject/galaxy/commit/45f523f9229f6d943e3a65042b8ca... Author: Bjoern Gruening <bjoern.gruening@gmail.com> Date: 2016-02-03 (Wed, 03 Feb 2016) Changed paths: M client/galaxy/scripts/layout/page.js M static/maps/layout/page.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/page.js Log Message: ----------- fix show_welcome_with_login = True Commit: b5d1c7721ee2f8ad1095e52d4e710b998f92945d https://github.com/galaxyproject/galaxy/commit/b5d1c7721ee2f8ad1095e52d4e710... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-02-03 (Wed, 03 Feb 2016) Changed paths: M client/galaxy/scripts/layout/page.js M static/maps/layout/page.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/page.js Log Message: ----------- Merge pull request #1664 from bgruening/release_16.01 fix `show_welcome_with_login = True` Commit: cd3f3b330db34e294e78374e8e8b32300c66f36e https://github.com/galaxyproject/galaxy/commit/cd3f3b330db34e294e78374e8e8b3... Author: Nate Coraor <nate@bx.psu.edu> Date: 2016-02-03 (Wed, 03 Feb 2016) Changed paths: M lib/galaxy/datatypes/binary.py M lib/galaxy/dependencies/conda-environment.txt M lib/galaxy/dependencies/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt M lib/galaxy/visualization/data_providers/genome.py M test-data/3.bam Log Message: ----------- Merge pull request #1638 from dannon/pysam_84_update Pysam 84 update [16.01] Commit: 246870c459cffd48a0fe7b4963e674638298e620 https://github.com/galaxyproject/galaxy/commit/246870c459cffd48a0fe7b4963e67... Author: Nate Coraor <nate@bx.psu.edu> Date: 2016-02-03 (Wed, 03 Feb 2016) Changed paths: M client/galaxy/scripts/layout/page.js M lib/galaxy/datatypes/binary.py M lib/galaxy/dependencies/conda-environment.txt M lib/galaxy/dependencies/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt M lib/galaxy/tools/__init__.py M lib/galaxy/visualization/data_providers/genome.py M static/maps/layout/page.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/page.js M test-data/3.bam Log Message: ----------- Merge branch 'release_16.01' into dev Commit: d97e8bbbbce862eb6b4f8f5732cd0baa029e9e20 https://github.com/galaxyproject/galaxy/commit/d97e8bbbbce862eb6b4f8f5732cd0... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2016-02-03 (Wed, 03 Feb 2016) Changed paths: M client/galaxy/scripts/layout/page.js M lib/galaxy/datatypes/binary.py M lib/galaxy/dependencies/conda-environment.txt M lib/galaxy/dependencies/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt M lib/galaxy/tools/__init__.py M lib/galaxy/visualization/data_providers/genome.py M static/maps/layout/page.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/page.js M test-data/3.bam Log Message: ----------- Merge pull request #1667 from natefoo/dev Merge release_16.01 to dev Compare: https://github.com/galaxyproject/galaxy/compare/b82efd937504...d97e8bbbbce8