Branch: refs/heads/master
Home: https://github.com/galaxyproject/usegalaxy-playbook
Commit: 7f263c2773615da2c8a60045b1ec739d228bdc16
https://github.com/galaxyproject/usegalaxy-playbook/commit/7f263c2773615da2…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2017-03-27 (Mon, 27 Mar 2017)
Changed paths:
M files/galaxy/common/dynamic_rules/bridges_select.py
M files/pulsar/common/config/bridges_dependency_resolvers_conf.xml
M stage/group_vars/pulsarservers.yml
M templates/galaxy/test.galaxyproject.org/config/job_conf.xml.j2
Log Message:
-----------
Update Pulsar on Test, resolve dependencies on Bridges using conda (after
modules) and run rnaSPAdes on Bridges
Commit: 49a1769f06256411fcbf0c92a2f4625746bcd26e
https://github.com/galaxyproject/usegalaxy-playbook/commit/49a1769f06256411…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2017-03-27 (Mon, 27 Mar 2017)
Changed paths:
M roles/galaxyprojectdotorg.interactive_environments/meta/.galaxy_install_info
M roles/galaxyprojectdotorg.interactive_environments/tasks/extract_component.yml
M roles/galaxyprojectdotorg.interactive_environments/tasks/webserver_conf.yml
A roles/galaxyprojectdotorg.interactive_environments/templates/generic_apache.conf.j2
A roles/galaxyprojectdotorg.interactive_environments/templates/generic_nginx.conf.j2
M roles/galaxyprojectdotorg.interactive_environments/templates/jupyter_apache.conf.j2
M roles/galaxyprojectdotorg.interactive_environments/templates/jupyter_nginx.conf.j2
M stage/files/interactive_environments/plugins/.ansible_ie_role_current_version
M stage/files/interactive_environments/plugins/bam_iobio/config/bam_iobio.ini.sample
M stage/files/interactive_environments/plugins/bam_iobio/static/js/bam_iobio.js
M stage/files/interactive_environments/plugins/bam_iobio/templates/bam_iobio.mako
M stage/files/interactive_environments/plugins/common/templates/ie.mako
A stage/files/interactive_environments/plugins/ethercalc/config/ethercalc.ini.sample
A stage/files/interactive_environments/plugins/ethercalc/config/ethercalc.xml
A stage/files/interactive_environments/plugins/ethercalc/static/js/ethercalc.js
A stage/files/interactive_environments/plugins/ethercalc/templates/ethercalc.mako
A stage/files/interactive_environments/plugins/jupyter/config/allowed_images.yml.sample
M stage/files/interactive_environments/plugins/jupyter/config/jupyter.ini.sample
M stage/files/interactive_environments/plugins/jupyter/config/jupyter.xml
M stage/files/interactive_environments/plugins/jupyter/static/js/jupyter.js
M stage/files/interactive_environments/plugins/jupyter/templates/jupyter.mako
A stage/files/interactive_environments/plugins/neo/config/allowed_images.yml.sample
A stage/files/interactive_environments/plugins/neo/config/neo.ini.sample
A stage/files/interactive_environments/plugins/neo/config/neo.xml
A stage/files/interactive_environments/plugins/neo/static/js/neo.js
A stage/files/interactive_environments/plugins/neo/templates/neo.mako
M stage/files/interactive_environments/plugins/phinch/config/phinch.ini.sample
M stage/files/interactive_environments/plugins/phinch/static/js/phinch.js
M stage/files/interactive_environments/plugins/phinch/templates/phinch.mako
A stage/files/interactive_environments/plugins/rstudio/config/allowed_images.yml.sample
M stage/files/interactive_environments/plugins/rstudio/config/rstudio.ini.sample
M stage/files/interactive_environments/plugins/rstudio/config/rstudio.xml
M stage/files/interactive_environments/plugins/rstudio/static/js/rstudio.js
M stage/files/interactive_environments/plugins/rstudio/templates/rstudio.mako
M stage/files/interactive_environments/proxy/.ansible_ie_role_current_version
M stage/files/interactive_environments/proxy/Dockerfile
M stage/files/interactive_environments/proxy/lib/main.js
M stage/files/interactive_environments/proxy/lib/mapper.js
M stage/files/interactive_environments/proxy/lib/proxy.js
M stage/files/interactive_environments/proxy/package.json
M stage/galaxy_version.yml
M stage/group_vars/galaxyservers.yml
Log Message:
-----------
Update galaxyprojectdotorg.interactive_environments and enable the ethercalc GIE on Test
Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/4324d0b90e77...…
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 024e296ea8fa6dc7c3b3da3e74ac9e520e8daf73
https://github.com/galaxyproject/galaxy/commit/024e296ea8fa6dc7c3b3da3e74ac…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-03-20 (Mon, 20 Mar 2017)
Changed paths:
M lib/galaxy/managers/datasets.py
Log Message:
-----------
Re-use job.finish abstraction in dataset manager stop_creating_job.
It is used in purge a bit above and it is the better abstraction.
Commit: f153400e95ff3888fab1b6c0fb7be5686a882532
https://github.com/galaxyproject/galaxy/commit/f153400e95ff3888fab1b6c0fb7b…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-03-20 (Mon, 20 Mar 2017)
Changed paths:
M test/api/test_jobs.py
Log Message:
-----------
Rework jobs API to not use deprecated TestsDatasets mixin.
Commit: 009e2cbf5e9592fd8af782b2cde36d8d1687c003
https://github.com/galaxyproject/galaxy/commit/009e2cbf5e9592fd8af782b2cde3…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-03-20 (Mon, 20 Mar 2017)
Changed paths:
M lib/galaxy/jobs/__init__.py
M lib/galaxy/managers/datasets.py
M test/api/test_jobs.py
M test/base/api_asserts.py
M test/base/driver_util.py
M test/base/populators.py
M test/functional/tools/create_10.xml
A test/functional/tools/create_2.xml
M test/functional/tools/samples_tool_conf.xml
Log Message:
-----------
Improve interaction between job state and purged datasets.
There are two basic behavior changes here and bunch of testing to verify the new behaviors.
1) Previously purging a dataset would cause a creating job to be cancelled but all outputs would need to be "deleted" in order to cause the creating job to be cancelled. After this change the behavior is the same for both deletion and purging - the job will run until all outputs are deleted or purged.
2) Previously Galaxy jobs wouldn't attempt to cleanup purged datasets that were created by a running tool - this cleanup now occurs.
These are tackled as a pair because I assume the difference in the behaviors between deletion and purging was a hack around tools populating datasets that had been purged while running. Cancelling the job wasn't a sure fix - but it would reduce the likelihood of such problems. I think the new approach is a bit more robust and explicit.
Commit: 967d0b6c0aef6fe331c4e9c92bc1b902363e660a
https://github.com/galaxyproject/galaxy/commit/967d0b6c0aef6fe331c4e9c92bc1…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-03-27 (Mon, 27 Mar 2017)
Changed paths:
M lib/galaxy/jobs/__init__.py
M lib/galaxy/managers/datasets.py
M test/api/test_jobs.py
M test/base/api_asserts.py
M test/base/driver_util.py
M test/base/populators.py
M test/functional/tools/create_10.xml
A test/functional/tools/create_2.xml
M test/functional/tools/samples_tool_conf.xml
Log Message:
-----------
Merge pull request #3619 from jmchilton/purge_jobs_rework
Improve interaction between job state and purged datasets.
Compare: https://github.com/galaxyproject/galaxy/compare/1c716eb9da35...967d0b6c0aef
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: ca36c0dbfd438708e35e18d06c603f2cc2ce7047
https://github.com/galaxyproject/galaxy/commit/ca36c0dbfd438708e35e18d06c60…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-03-23 (Thu, 23 Mar 2017)
Changed paths:
M client/galaxy/scripts/mvc/tool/tools.js
M static/maps/mvc/tool/tools.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/tool/tools.js
Log Message:
-----------
Have tool-search listen to change as well as keyup
Commit: 1c716eb9da355864bd0116ce2579be3f03482e7c
https://github.com/galaxyproject/galaxy/commit/1c716eb9da355864bd0116ce2579…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-03-27 (Mon, 27 Mar 2017)
Changed paths:
M client/galaxy/scripts/mvc/tool/tools.js
M static/maps/mvc/tool/tools.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/tool/tools.js
Log Message:
-----------
Merge pull request #3808 from dannon/trigger-search-input
Have tool-search listen to change as well as keyup
Compare: https://github.com/galaxyproject/galaxy/compare/a6240c4b8c74...1c716eb9da35
Branch: refs/heads/usegalaxy
Home: https://github.com/galaxyproject/galaxy
Commit: 15aa0bd615726ed46fa7beec9a364bb3c11df9f2
https://github.com/galaxyproject/galaxy/commit/15aa0bd615726ed46fa7beec9a36…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-03-22 (Wed, 22 Mar 2017)
Changed paths:
M lib/galaxy/jobs/runners/__init__.py
Log Message:
-----------
Fix problem with cleaning up jobs in local runner.
Fixes #3801 (broken in b78287f as part of #3291).
Commit: 65cbddee7c3bc2d772686b261aaf853f84f76235
https://github.com/galaxyproject/galaxy/commit/65cbddee7c3bc2d772686b261aaf…
Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com>
Date: 2017-03-22 (Wed, 22 Mar 2017)
Changed paths:
M lib/galaxy/jobs/runners/__init__.py
Log Message:
-----------
Merge pull request #3803 from jmchilton/1701_fixes_0
[17.01] Fix problem with cleaning up jobs in local runner.
Commit: d8af125af4d3798c32b31793c10f9b9426d7dfe2
https://github.com/galaxyproject/galaxy/commit/d8af125af4d3798c32b31793c10f…
Author: Hans-Rudolf Hotz <hrhotz(a)users.noreply.github.com>
Date: 2017-03-27 (Mon, 27 Mar 2017)
Changed paths:
M lib/galaxy/tools/__init__.py
Log Message:
-----------
Update __init__.py
Commit: 3068c9f053554c448a30388d46b91a6979e39cb7
https://github.com/galaxyproject/galaxy/commit/3068c9f053554c448a30388d46b9…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-03-27 (Mon, 27 Mar 2017)
Changed paths:
M lib/galaxy/tools/__init__.py
Log Message:
-----------
Fix CONVERTER_gff_to_fli_0 for striping Galaxy from Python environment.
Taking another stab at fixing #3499 which was broken with #3364. Last attempt at fixing converters didn't cover this (#3690) but I missed this tool and bed to fli fixed in #3822.
Commit: 70b22dffc28830b4f9fc3c9a89845d6ccf32e559
https://github.com/galaxyproject/galaxy/commit/70b22dffc28830b4f9fc3c9a8984…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-03-27 (Mon, 27 Mar 2017)
Changed paths:
M lib/galaxy/tools/__init__.py
Log Message:
-----------
Merge pull request #3824 from jmchilton/more_tool_env_fixes
[17.01] More CONVERTER fixes for restricting tools' Python environment.
Commit: 812b04bb3abec97f1f465e9e9136904bd7e4164c
https://github.com/galaxyproject/galaxy/commit/812b04bb3abec97f1f465e9e9136…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-03-27 (Mon, 27 Mar 2017)
Changed paths:
M lib/galaxy/jobs/runners/__init__.py
M lib/galaxy/tools/__init__.py
Log Message:
-----------
Merge pull request #3826 from galaxyproject/release_17.01
[usegalaxy] Merge 17.01
Compare: https://github.com/galaxyproject/galaxy/compare/f9b8e6a51a17...812b04bb3abe
Branch: refs/heads/release_17.01
Home: https://github.com/galaxyproject/galaxy
Commit: d8af125af4d3798c32b31793c10f9b9426d7dfe2
https://github.com/galaxyproject/galaxy/commit/d8af125af4d3798c32b31793c10f…
Author: Hans-Rudolf Hotz <hrhotz(a)users.noreply.github.com>
Date: 2017-03-27 (Mon, 27 Mar 2017)
Changed paths:
M lib/galaxy/tools/__init__.py
Log Message:
-----------
Update __init__.py
Commit: 3068c9f053554c448a30388d46b91a6979e39cb7
https://github.com/galaxyproject/galaxy/commit/3068c9f053554c448a30388d46b9…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-03-27 (Mon, 27 Mar 2017)
Changed paths:
M lib/galaxy/tools/__init__.py
Log Message:
-----------
Fix CONVERTER_gff_to_fli_0 for striping Galaxy from Python environment.
Taking another stab at fixing #3499 which was broken with #3364. Last attempt at fixing converters didn't cover this (#3690) but I missed this tool and bed to fli fixed in #3822.
Commit: 70b22dffc28830b4f9fc3c9a89845d6ccf32e559
https://github.com/galaxyproject/galaxy/commit/70b22dffc28830b4f9fc3c9a8984…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-03-27 (Mon, 27 Mar 2017)
Changed paths:
M lib/galaxy/tools/__init__.py
Log Message:
-----------
Merge pull request #3824 from jmchilton/more_tool_env_fixes
[17.01] More CONVERTER fixes for restricting tools' Python environment.
Compare: https://github.com/galaxyproject/galaxy/compare/65cbddee7c3b...70b22dffc288
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: ad68b154d4cbecdbc2e96e58d9d3c4153e014eeb
https://github.com/galaxyproject/galaxy/commit/ad68b154d4cbecdbc2e96e58d9d3…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-03-24 (Fri, 24 Mar 2017)
Changed paths:
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/tools/toolbox/cache.py
M lib/galaxy/tools/toolbox/watcher.py
M test/unit/tools/test_toolbox.py
Log Message:
-----------
Make ToolConfWatcher watch ToolCache
If any item in the tool cache has changed (local tool update, repository
update, tool deleted) the toolbox will be reloaded and any tool changes are
applied.
Should fix https://github.com/galaxyproject/galaxy/issues/3813.
Commit: c91c988c852e5a30e1c7c69168b5df770933dcd5
https://github.com/galaxyproject/galaxy/commit/c91c988c852e5a30e1c7c69168b5…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-03-24 (Fri, 24 Mar 2017)
Changed paths:
M test/unit/tools/test_watcher.py
Log Message:
-----------
Fix ToolConfWatcher test: can only watch existing files
Commit: 5be7ebe780b487175563eb4661955a07df1d30cd
https://github.com/galaxyproject/galaxy/commit/5be7ebe780b487175563eb466195…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-03-24 (Fri, 24 Mar 2017)
Changed paths:
M lib/galaxy/queue_worker.py
M test/unit/tools/test_toolbox.py
Log Message:
-----------
Only call tool_cache.cleanup if tool_cache exists
Commit: 4d9cf642a80025e28ea0276f8c41fcd9d9a53903
https://github.com/galaxyproject/galaxy/commit/4d9cf642a80025e28ea0276f8c41…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-03-24 (Fri, 24 Mar 2017)
Changed paths:
M lib/galaxy/tools/toolbox/base.py
Log Message:
-----------
Fix toolshed startup by setting tool_cache to `None` (the toolshed loads an empty toolbox)
Commit: 0bf2493233fd0afbc07da6620740536938d8d059
https://github.com/galaxyproject/galaxy/commit/0bf2493233fd0afbc07da6620740…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-03-24 (Fri, 24 Mar 2017)
Changed paths:
M lib/galaxy/tools/toolbox/cache.py
Log Message:
-----------
Wrap tool_cache cleanup in try/except clause
Commit: 197aa402d72895d370307ce9724c86b892cded96
https://github.com/galaxyproject/galaxy/commit/197aa402d72895d370307ce9724c…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-03-25 (Sat, 25 Mar 2017)
Changed paths:
M lib/galaxy/tools/toolbox/cache.py
Log Message:
-----------
Improve ToolCache cleanup logic
Pull `removed_tool_ids` out of try/except, so that we can return
`removed_tool_ids` even if an exception occured. Fix a typo in the
`_should_cleanup` docstring. Many thanks for the suggestions @nsoranzo.
Commit: a47828bf892f8e1627bcb5f00ae63be56c9b6fcf
https://github.com/galaxyproject/galaxy/commit/a47828bf892f8e1627bcb5f00ae6…
Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com>
Date: 2017-03-25 (Sat, 25 Mar 2017)
Changed paths:
M lib/galaxy/queue_worker.py
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/tools/toolbox/cache.py
M lib/galaxy/tools/toolbox/watcher.py
M test/unit/tools/test_toolbox.py
M test/unit/tools/test_watcher.py
Log Message:
-----------
Merge pull request #3814 from mvdbeek/repository_updates
Awesome, thanks @mvdbeek !
Compare: https://github.com/galaxyproject/galaxy/compare/18a26c5f376b...a47828bf892f
Branch: refs/heads/master
Home: https://github.com/galaxyproject/infrastructure-playbook
Commit: b129f6c6c8eb83debd820e49099d92a50e68c0f7
https://github.com/galaxyproject/infrastructure-playbook/commit/b129f6c6c8e…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2017-03-24 (Fri, 24 Mar 2017)
Changed paths:
M ansible.cfg
Log Message:
-----------
Disable pipelining by default (for cloud stuff), unless this can be made
conditional it's just too much of a pain.
Commit: 206a8a617f317520f03452730eaa3c7725f83e54
https://github.com/galaxyproject/infrastructure-playbook/commit/206a8a617f3…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2017-03-24 (Fri, 24 Mar 2017)
Changed paths:
A jetstreamdockerenv/README.md
A jetstreamdockerenv/group_vars/all.yml
A jetstreamdockerenv/group_vars/baseinstances.yml
A jetstreamdockerenv/group_vars/imageinstances.yml
A jetstreamdockerenv/inc_clouds_yaml.yml
A jetstreamdockerenv/inc_delete.yml
A jetstreamdockerenv/inc_spawn.yml
A jetstreamdockerenv/inventory
A jetstreamdockerenv/secret_group_vars/instances.yml
A jetstreamdockerenv/snapshot_docker_base.yml
A jetstreamdockerenv/snapshot_docker_image.yml
A jetstreamdockerenv/ssh_config.jetstream_iu
A jetstreamdockerenv/ssh_config.jetstream_tacc
Log Message:
-----------
Environment for creating Jetstream server and volume images for GIE docker swarm workers
Compare: https://github.com/galaxyproject/infrastructure-playbook/compare/aedc4f2b0a…