Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a6cbb88ad12288eca031c0469113abc831a42d37 https://github.com/galaxyproject/galaxy/commit/a6cbb88ad12288eca031c0469113a... Author: John Chilton <jmchilton@gmail.com> Date: 2016-01-02 (Sat, 02 Jan 2016) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py Log Message: ----------- Enable tool isolation by default and fix bugs. Commit: 1084f14dd0637bc47978a33122c74d86cb617241 https://github.com/galaxyproject/galaxy/commit/1084f14dd0637bc47978a33122c74... Author: John Chilton <jmchilton@gmail.com> Date: 2016-01-02 (Sat, 02 Jan 2016) Changed paths: M test/unit/jobs/test_command_factory.py Log Message: ----------- Unit test modifications for running tool commands in isolated scripts. Commit: 7f8e37d5a1aa96c2c839acea4511e071e81eb450 https://github.com/galaxyproject/galaxy/commit/7f8e37d5a1aa96c2c839acea4511e... Author: John Chilton <jmchilton@gmail.com> Date: 2016-01-02 (Sat, 02 Jan 2016) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/command_factory.py Log Message: ----------- Attempt to fix samtools resolution for metadata when tool command externalized. Commit: acab90d63c6c96a6e609f32080f5b610b33dd549 https://github.com/galaxyproject/galaxy/commit/acab90d63c6c96a6e609f32080f5b... Author: John Chilton <jmchilton@gmail.com> Date: 2016-01-02 (Sat, 02 Jan 2016) Changed paths: M lib/galaxy/jobs/command_factory.py Log Message: ----------- Fix unicode-y problem with tool command externalization. Commit: 340aef2550d16bb987b36bc7b2df8e0ed4f6f56b https://github.com/galaxyproject/galaxy/commit/340aef2550d16bb987b36bc7b2df8... Author: John Chilton <jmchilton@gmail.com> Date: 2016-01-02 (Sat, 02 Jan 2016) Changed paths: M lib/galaxy/jobs/command_factory.py Log Message: ----------- Fix logging for tool script externalization. Commit: 7cbf41feb3dfd6eb12c99630692776565c72c579 https://github.com/galaxyproject/galaxy/commit/7cbf41feb3dfd6eb12c9963069277... Author: John Chilton <jmchilton@gmail.com> Date: 2016-01-03 (Sun, 03 Jan 2016) Changed paths: M lib/galaxy/datatypes/binary.py M lib/galaxy/tools/deps/commands.py M lib/galaxy/util/__init__.py Log Message: ----------- Better exception when samtools is required but not on PATH. Commit: 905adbac38992ae2fc889d23f000fa2541e87939 https://github.com/galaxyproject/galaxy/commit/905adbac38992ae2fc889d23f000f... Author: Björn Grüning <bjoern@gruenings.eu> Date: 2016-01-04 (Mon, 04 Jan 2016) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/datatypes/binary.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/tools/deps/commands.py M lib/galaxy/util/__init__.py M test/unit/jobs/test_command_factory.py Log Message: ----------- Merge pull request #1412 from jmchilton/isolate Isolate tool commands by default. Compare: https://github.com/galaxyproject/galaxy/compare/10677319f74f...905adbac3899