Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: 3e47aa23b8426e21f5dac573f6eb96bfeac550b6 https://github.com/galaxyproject/galaxy/commit/3e47aa23b8426e21f5dac573f6eb9... Author: John Chilton <jmchilton@gmail.com> Date: 2016-01-14 (Thu, 14 Jan 2016) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh M lib/galaxy/jobs/runners/util/job_script/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py M test/unit/jobs/test_command_factory.py M test/unit/jobs/test_runner_local.py Log Message: ----------- Switch to bash as default shell (for conda resolver). I'm making more things configurable in case someday the BSD user wants to use Galaxy - the default shell for jobs can be configured at the galaxy or job destination level now. Commit: e69638277fc4e0c56347e51ed77f93c1f9261ecf https://github.com/galaxyproject/galaxy/commit/e69638277fc4e0c56347e51ed77f9... Author: John Chilton <jmchilton@gmail.com> Date: 2016-01-14 (Thu, 14 Jan 2016) Changed paths: M test/functional/tools/output_action_change_format.xml Log Message: ----------- Fix tab problem in test tool. dash will convert the literal characters \t to a tab, bash doesn't seem to do this. Use portable printf as suggested by nicola. Commit: 602dc7f6649d96086b85ed0d309eef7c4ed73a13 https://github.com/galaxyproject/galaxy/commit/602dc7f6649d96086b85ed0d309ee... Author: John Chilton <jmchilton@gmail.com> Date: 2016-01-14 (Thu, 14 Jan 2016) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/runners/util/job_script/__init__.py Log Message: ----------- Switch default job shell back to /bin/sh for 16.01. Commit: be4ddb26d4c448bee8f797b9972360c93cae33fc https://github.com/galaxyproject/galaxy/commit/be4ddb26d4c448bee8f797b997236... Author: Björn Grüning <bjoern@gruenings.eu> Date: 2016-01-14 (Thu, 14 Jan 2016) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh M lib/galaxy/jobs/runners/util/job_script/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py M test/functional/tools/output_action_change_format.xml M test/unit/jobs/test_command_factory.py M test/unit/jobs/test_runner_local.py Log Message: ----------- Merge pull request #1473 from jmchilton/job_shell [16.01] Allow override of job shell (for conda resolver). Compare: https://github.com/galaxyproject/galaxy/compare/1dac5f3bb63f...be4ddb26d4c4