Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy 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: 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: 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]

Compare: https://github.com/galaxyproject/galaxy/compare/b5d1c7721ee2...cd3f3b330db3