Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 2495ceae267da873813d2dc1aae145b686d18672 https://github.com/galaxyproject/galaxy/commit/2495ceae267da873813d2dc1aae14... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-09-21 (Thu, 21 Sep 2017) Changed paths: M lib/galaxy/jobs/actions/post.py Log Message: ----------- Remove overly chatty debug statement in workflow output cleanup -- this happens pretty often and much of the time is not a problem at all. If we have to track down any new issues with workflow output cleanup, it's easy enough to temporarily add this logging. Commit: 244fc834cd4dd3980cc3edb755d22ca5a9372421 https://github.com/galaxyproject/galaxy/commit/244fc834cd4dd3980cc3edb755d22... Author: Nate Coraor <nate@bx.psu.edu> Date: 2017-09-21 (Thu, 21 Sep 2017) Changed paths: M scripts/common_startup.sh Log Message: ----------- Explicitly include PyPI as an --extra-index-url to pip so we can install from PyPI even when a package exists (but the correct version or architecture does not exist) on wheels.galaxyproject.org. Previously, PyPI was only checked after wheels.galaxyproject.org because pypiserver performs an automatic redirect to PyPI for any packages that do not exist in its index. Commit: 832da6ca66cba8fe155adccd4d327289c9e04430 https://github.com/galaxyproject/galaxy/commit/832da6ca66cba8fe155adccd4d327... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-09-21 (Thu, 21 Sep 2017) Changed paths: M scripts/common_startup.sh Log Message: ----------- Merge pull request #4674 from natefoo/use-pypi [17.09] Explicitly include PyPI as an --extra-index-url to pip Commit: 74ad0acb52031355c7efe28b00d1d9b0205174f2 https://github.com/galaxyproject/galaxy/commit/74ad0acb52031355c7efe28b00d1d... Author: Nate Coraor <nate@bx.psu.edu> Date: 2017-09-21 (Thu, 21 Sep 2017) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh Log Message: ----------- Remove repetition in Galaxy env setup in the job script and fix issues with remote metadata on Pulsar. Commit: 276af4db2ab5e81f4af8f35b7d09f48d9fed8dcd https://github.com/galaxyproject/galaxy/commit/276af4db2ab5e81f4af8f35b7d09f... Author: Nate Coraor <nate@bx.psu.edu> Date: 2017-09-21 (Thu, 21 Sep 2017) Changed paths: M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh Log Message: ----------- Job script enhancements based on feedback. Commit: 53095d688be81a36c31b9721caebf58b383cfe72 https://github.com/galaxyproject/galaxy/commit/53095d688be81a36c31b9721caebf... Author: Nate Coraor <nate@bx.psu.edu> Date: 2017-09-21 (Thu, 21 Sep 2017) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/model/metadata.py Log Message: ----------- Fix remote datatypes_conf.xml and registry.xml param rewriting with Pulsar Commit: db5185cca0bb9b5f59d8fcf218eb4c5d81cb5911 https://github.com/galaxyproject/galaxy/commit/db5185cca0bb9b5f59d8fcf218eb4... Author: Nate Coraor <nate@bx.psu.edu> Date: 2017-09-21 (Thu, 21 Sep 2017) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/jobs/runners/pulsar.py Log Message: ----------- Pulsar release was 0.8.0 not 0.7.5 Commit: 2669ab022ed2f90faac54c510014f87783efeaa0 https://github.com/galaxyproject/galaxy/commit/2669ab022ed2f90faac54c510014f... Author: Nate Coraor <nate@bx.psu.edu> Date: 2017-09-21 (Thu, 21 Sep 2017) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/runners/pulsar.py Log Message: ----------- Pass job output file unqualified names to Pulsar so that it can create them before running the job. Commit: 3344c77a188cd92ffb2e7150a4f4a2f4f7facedb https://github.com/galaxyproject/galaxy/commit/3344c77a188cd92ffb2e7150a4f4a... Author: Nate Coraor <nate@bx.psu.edu> Date: 2017-09-21 (Thu, 21 Sep 2017) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt Log Message: ----------- Bump pulsar lib version to 0.8.0 for output touch support. Commit: c7699cd3a0e16b9522af334cf2ea1a107fbe5f57 https://github.com/galaxyproject/galaxy/commit/c7699cd3a0e16b9522af334cf2ea1... Author: Nate Coraor <nate@bx.psu.edu> Date: 2017-09-21 (Thu, 21 Sep 2017) Changed paths: M lib/galaxy/jobs/runners/pulsar.py Log Message: ----------- Fix lint error Commit: 27a28e2c406d274e396cf3cb095576ebae9cd38c https://github.com/galaxyproject/galaxy/commit/27a28e2c406d274e396cf3cb09557... Author: John Chilton <jmchilton@gmail.com> Date: 2017-09-22 (Fri, 22 Sep 2017) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/runners/pulsar.py Log Message: ----------- Merge pull request #4662 from natefoo/pulsar-touch-outputs [17.09] Pass job output file unqualified names to Pulsar so that it can create them before running the job Commit: d1be9e6a8fa1a383b3f75d1ea5f1b0d486b69258 https://github.com/galaxyproject/galaxy/commit/d1be9e6a8fa1a383b3f75d1ea5f1b... Author: John Chilton <jmchilton@gmail.com> Date: 2017-09-22 (Fri, 22 Sep 2017) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh M lib/galaxy/model/metadata.py Log Message: ----------- Merge pull request #4622 from natefoo/pulsar-remote-metadata-fixes [17.09] Pulsar remote metadata fixes Commit: 7896413b2b6a55ea99958504134ab6027baefbe8 https://github.com/galaxyproject/galaxy/commit/7896413b2b6a55ea99958504134ab... Author: John Chilton <jmchilton@gmail.com> Date: 2017-09-23 (Sat, 23 Sep 2017) Changed paths: M lib/galaxy/jobs/actions/post.py Log Message: ----------- Merge pull request #4671 from dannon/remove_debug [17.09] Remove chatty debug statement Commit: 41013563e5e15745fd2bf796340578f6d758fbe8 https://github.com/galaxyproject/galaxy/commit/41013563e5e15745fd2bf79634057... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-09-24 (Sun, 24 Sep 2017) Changed paths: M CITATION Log Message: ----------- Update CITATION file with 2016 paper Commit: 3ae6318b02e61fcf997b6d2726f12851f51aa802 https://github.com/galaxyproject/galaxy/commit/3ae6318b02e61fcf997b6d2726f12... Author: Eric Rasche <hxr@hx42.org> Date: 2017-09-25 (Mon, 25 Sep 2017) Changed paths: M CITATION Log Message: ----------- Merge pull request #4686 from mvdbeek/citation_update Update CITATION file with 2016 paper Commit: 0c23d40b22b659abc3636b76a15fb7d392cbb92f https://github.com/galaxyproject/galaxy/commit/0c23d40b22b659abc3636b76a15fb... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2017-09-25 (Mon, 25 Sep 2017) Changed paths: M CITATION M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/actions/post.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh M lib/galaxy/model/metadata.py M scripts/common_startup.sh Log Message: ----------- Merge branch 'release_17.09' into dev Compare: https://github.com/galaxyproject/galaxy/compare/9e4259192dd7...0c23d40b22b6