March 2017 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/usegalaxy-playbook] 7f263c: Update Pulsar on Test, resolve dependencies on Bri...
by GitHub 27 Mar '17

27 Mar '17

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...…

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[galaxyproject/galaxy] 024e29: Re-use job.finish abstraction in dataset manager s...
by GitHub 27 Mar '17

27 Mar '17

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

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[galaxyproject/galaxy] ca36c0: Have tool-search listen to change as well as keyup
by GitHub 27 Mar '17

27 Mar '17

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

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[galaxyproject/galaxy] 15aa0b: Fix problem with cleaning up jobs in local runner.
by GitHub 27 Mar '17

27 Mar '17

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

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[galaxyproject/infrastructure-playbook] 2c6e2d: Update orval access list
by GitHub 27 Mar '17

27 Mar '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 2c6e2d24d1da0b667f97bcaf1edfd24e2dda9954 https://github.com/galaxyproject/infrastructure-playbook/commit/2c6e2d24d1d… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-03-27 (Mon, 27 Mar 2017) Changed paths: M galaxyenv/secret_host_vars/orval.galaxyproject.org.yml Log Message: ----------- Update orval access list

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[galaxyproject/infrastructure-playbook] ccef6d: Depot login for DaveC
by GitHub 27 Mar '17

27 Mar '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: ccef6dfcc0641a1fe5daf49be17675e2ec54c8d1 https://github.com/galaxyproject/infrastructure-playbook/commit/ccef6dfcc06… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-27 (Mon, 27 Mar 2017) Changed paths: M galaxyenv/secret_host_vars/orval.galaxyproject.org.yml Log Message: ----------- Depot login for DaveC

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[galaxyproject/galaxy] d8af12: Update __init__.py
by GitHub 27 Mar '17

27 Mar '17

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

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[galaxyproject/galaxy] 229c0a: Update __init__.py
by GitHub 27 Mar '17

27 Mar '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 229c0a2339b38f6481a489e5a8454018458297d2 https://github.com/galaxyproject/galaxy/commit/229c0a2339b38f6481a489e5a845… 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 using the lagacy python environemnt is also required for "CONVERTER_bed_to_fli_0" when displaying a bed file in trackster Commit: 37fd039bd5bf0ca2beda8183e298cd1454b16544 https://github.com/galaxyproject/galaxy/commit/37fd039bd5bf0ca2beda8183e298… 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: a6240c4b8c7477d2aca39ef97217139962fd5848 https://github.com/galaxyproject/galaxy/commit/a6240c4b8c7477d2aca39ef97217… 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: ----------- Merge pull request #3822 from hrhotz/patch-1 fix bedfile display in trackster Compare: https://github.com/galaxyproject/galaxy/compare/a47828bf892f...a6240c4b8c74

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[galaxyproject/galaxy] ad68b1: Make ToolConfWatcher watch ToolCache
by GitHub 25 Mar '17

25 Mar '17

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

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[galaxyproject/infrastructure-playbook] b129f6: Disable pipelining by default (for cloud stuff), u...
by GitHub 24 Mar '17

24 Mar '17

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…

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