Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 55677f2d3db723c023540b8d640563a9f3ca04c5 https://github.com/galaxyproject/galaxy/commit/55677f2d3db723c023540b8d64056... Author: John Chilton <jmchilton@gmail.com> Date: 2016-01-13 (Wed, 13 Jan 2016) Changed paths: M config/galaxy.ini.sample 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 test/unit/jobs/test_command_factory.py Log Message: ----------- Fix to ensure integrity of tool_script.sh also. Previously the job script underwent these checks and I had assumed since that got written later it would never be the case that tool_script.sh wouldn't be synchronized by the job script was - turns out file systems are more creative and less logical than one might expected. Also increases the count for the number of syncs that will execute because 15 on rare occasion proved not to be enough as well as making both the count and sleep time configurable. Commit: 37f8038d63f8243151e817e9d564f90c58772c1f https://github.com/galaxyproject/galaxy/commit/37f8038d63f8243151e817e9d564f... Author: guerler <aysam.guerler@gmail.com> Date: 2016-01-13 (Wed, 13 Jan 2016) Changed paths: M client/galaxy/scripts/layout/menu.js M static/maps/layout/menu.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/menu.js Log Message: ----------- Undo user icon in masthead Commit: 9d91be8dd3b84a5b37b6010cbb31df7070fb6170 https://github.com/galaxyproject/galaxy/commit/9d91be8dd3b84a5b37b6010cbb31d... Author: Nate Coraor <nate@bx.psu.edu> Date: 2016-01-13 (Wed, 13 Jan 2016) Changed paths: A lib/galaxy/dependencies/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt M requirements.txt Log Message: ----------- Pin release wheel verisons. pinned-requirements.txt renamed to pinned-hashed-requirements.txt as unfortunately even Galaxy pip does not support --hash Commit: 0bcfa74ea1e0eb57927bd1850feb9331489af6bc https://github.com/galaxyproject/galaxy/commit/0bcfa74ea1e0eb57927bd1850feb9... Author: Daniel Blankenberg <dan.blankenberg@gmail.com> Date: 2016-01-13 (Wed, 13 Jan 2016) Changed paths: M lib/galaxy/datatypes/tabular.py Log Message: ----------- Set mime type when previewing tabular data that has > 50 columns, but < 1000000 bytes. Fixes the issue of losing newlines and actual spacing (i.e. do not treat as html). Commit: f78756cb79f294689227e0222c8b75f3100047b5 https://github.com/galaxyproject/galaxy/commit/f78756cb79f294689227e0222c8b7... Author: John Chilton <jmchilton@gmail.com> Date: 2016-01-13 (Wed, 13 Jan 2016) Changed paths: M lib/galaxy/tools/cwl/cwltool_deps.py M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Fix a few problems discovered through planemo. Including 'TypeError: _get_config_option() got multiple values for keyword argument 'prefix' and problem when planemo's cwltool is installed in Galaxy's virtualenv. Commit: 9d52a4a31dd9e660855bf1e12bd07d3c49b73fd9 https://github.com/galaxyproject/galaxy/commit/9d52a4a31dd9e660855bf1e12bd07... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2016-01-13 (Wed, 13 Jan 2016) Changed paths: M client/galaxy/scripts/layout/menu.js M static/maps/layout/menu.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/menu.js Log Message: ----------- Merge pull request #1493 from guerler/undo_user_000 [16.01] Undo user icon in masthead Commit: 4b5b970d7898a33faca5557b4382ddc9d3923ae6 https://github.com/galaxyproject/galaxy/commit/4b5b970d7898a33faca5557b4382d... Author: guerler <aysam.guerler@gmail.com> Date: 2016-01-13 (Wed, 13 Jan 2016) Changed paths: M client/galaxy/scripts/layout/menu.js M static/maps/layout/menu.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/menu.js M test/qunit/tests/masthead_tests.js Log Message: ----------- Fix disabled css Commit: 2e62388b2f34ad83f215bb3eff4c6ae5b1efd7b7 https://github.com/galaxyproject/galaxy/commit/2e62388b2f34ad83f215bb3eff4c6... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-01-14 (Thu, 14 Jan 2016) Changed paths: M config/galaxy.ini.sample 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 test/unit/jobs/test_command_factory.py Log Message: ----------- Merge pull request #1494 from jmchilton/tool_command_integrity [16.01] Fix to ensure integrity of tool_script.sh also. 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: f2c3eaaf64041021abb39ea4595e3619658554e1 https://github.com/galaxyproject/galaxy/commit/f2c3eaaf64041021abb39ea4595e3... Author: John Chilton <jmchilton@gmail.com> Date: 2016-01-14 (Thu, 14 Jan 2016) Changed paths: M client/galaxy/scripts/layout/menu.js M lib/galaxy/tools/cwl/cwltool_deps.py M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py M static/maps/layout/menu.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/menu.js Log Message: ----------- Merge branch 'release_16.01' into dev_merge_0 Conflicts: static/scripts/bundled/analysis.bundled.js.map static/scripts/bundled/libs.bundled.js static/scripts/bundled/libs.bundled.js.map Commit: 0902c23f3491b4840b649a203315939d0c7caa8c https://github.com/galaxyproject/galaxy/commit/0902c23f3491b4840b649a2033159... Author: John Chilton <jmchilton@gmail.com> Date: 2016-01-14 (Thu, 14 Jan 2016) Changed paths: M client/galaxy/scripts/layout/menu.js M static/maps/layout/menu.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/menu.js M test/qunit/tests/masthead_tests.js Log Message: ----------- Merge pull request #1501 from guerler/fix_disabled_000 [16.01] Fix disabled css Commit: eb3fc642fc1bddaeb5aaec3d4dbba8efd0ab398d https://github.com/galaxyproject/galaxy/commit/eb3fc642fc1bddaeb5aaec3d4dbba... Author: John Chilton <jmchilton@gmail.com> Date: 2016-01-14 (Thu, 14 Jan 2016) Changed paths: M lib/galaxy/datatypes/tabular.py Log Message: ----------- Merge pull request #1498 from blankenberg/tab_mime [16.01] Set mime type when previewing tabular data that has > 50 columns, but < 1000000 bytes. Commit: 7de3bcdd7e4ecfbe4202bff1ad69a0d8b6b716cc https://github.com/galaxyproject/galaxy/commit/7de3bcdd7e4ecfbe4202bff1ad69a... Author: John Chilton <jmchilton@gmail.com> Date: 2016-01-14 (Thu, 14 Jan 2016) Changed paths: A lib/galaxy/dependencies/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt M requirements.txt Log Message: ----------- Merge pull request #1495 from natefoo/pin-release-wheels [16.01] Pin release wheel versions Commit: 1dac5f3bb63f7b34e7a84ae79d3eb60089712d0b https://github.com/galaxyproject/galaxy/commit/1dac5f3bb63f7b34e7a84ae79d3eb... Author: Björn Grüning <bjoern@gruenings.eu> Date: 2016-01-14 (Thu, 14 Jan 2016) Changed paths: M lib/galaxy/tools/cwl/cwltool_deps.py M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Merge pull request #1502 from jmchilton/planemo_fix [16.01] Fix a few problems discovered through planemo. 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). Commit: 793fbdbedc3e59140ece9aa2caed11d69815069b https://github.com/galaxyproject/galaxy/commit/793fbdbedc3e59140ece9aa2caed1... Author: John Chilton <jmchilton@gmail.com> Date: 2016-01-14 (Thu, 14 Jan 2016) Changed paths: M client/galaxy/scripts/layout/menu.js M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/datatypes/tabular.py A lib/galaxy/dependencies/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt 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 requirements.txt M static/maps/layout/menu.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/menu.js M test/functional/tools/output_action_change_format.xml M test/qunit/tests/masthead_tests.js M test/unit/jobs/test_command_factory.py M test/unit/jobs/test_runner_local.py Log Message: ----------- Merge remote-tracking branch 'jmchilton/release_16.01' into dev_merge_0 Conflicts: static/scripts/bundled/libs.bundled.js static/scripts/bundled/libs.bundled.js.map Commit: aeafcb1d6d389401e9c24267da75fa297375a2e4 https://github.com/galaxyproject/galaxy/commit/aeafcb1d6d389401e9c24267da75f... Author: John Chilton <jmchilton@gmail.com> Date: 2016-01-14 (Thu, 14 Jan 2016) Changed paths: M client/galaxy/scripts/layout/menu.js M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/datatypes/tabular.py A lib/galaxy/dependencies/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt 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/cwl/cwltool_deps.py M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py M requirements.txt M static/maps/layout/menu.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/menu.js M test/functional/tools/output_action_change_format.xml M test/qunit/tests/masthead_tests.js M test/unit/jobs/test_command_factory.py M test/unit/jobs/test_runner_local.py Log Message: ----------- Merge pull request #1504 from jmchilton/dev_merge_0 Merge release 16.01 into dev. Compare: https://github.com/galaxyproject/galaxy/compare/33a3ae4562ce...aeafcb1d6d38