galaxy-commits April 2017

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[galaxyproject/galaxy] 5b46c4: Fix certain aspects of dataset reductions in condi...
by GitHub 03 Apr '17

03 Apr '17

Branch: refs/heads/release_17.01 Home: https://github.com/galaxyproject/galaxy Commit: 5b46c431b416e619a7ac5467527ab30743eabd33 https://github.com/galaxyproject/galaxy/commit/5b46c431b416e619a7ac5467527a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-04-03 (Mon, 03 Apr 2017) Changed paths: M lib/galaxy/tools/actions/__init__.py M test/api/test_tools.py A test/functional/tools/identifier_multiple_in_conditional.xml A test/functional/tools/identifier_multiple_in_repeat.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Fix certain aspects of dataset reductions in conditionals/repeats. For instance, fixes #3859 restoring the correct ``element_identifier`` for reduces collections in conditionals. Add tests for combinations of repeats and conditionals. Commit: 3c080cae96aadccd824aa7cf6fda9c4b5bf7471a https://github.com/galaxyproject/galaxy/commit/3c080cae96aadccd824aa7cf6fda… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-04-03 (Mon, 03 Apr 2017) Changed paths: M lib/galaxy/tools/actions/__init__.py M test/api/test_tools.py A test/functional/tools/identifier_multiple_in_conditional.xml A test/functional/tools/identifier_multiple_in_repeat.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #3864 from jmchilton/fix_identifiers_in_conditionals [17.01] Fix certain aspects of collection reductions in conditionals/repeats. Compare: https://github.com/galaxyproject/galaxy/compare/268aac29526b...3c080cae96aa

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[galaxyproject/usegalaxy-playbook] 883f97: Forgot to commit updated GIE versions
by GitHub 03 Apr '17

03 Apr '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 883f977bf56f25af1aec54f81a19efb46e5e70e1 https://github.com/galaxyproject/usegalaxy-playbook/commit/883f977bf56f25af… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-04-03 (Mon, 03 Apr 2017) Changed paths: M production/files/interactive_environments/plugins/.ansible_ie_role_current_version M production/files/interactive_environments/proxy/.ansible_ie_role_current_version Log Message: ----------- Forgot to commit updated GIE versions

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[galaxyproject/usegalaxy-playbook] e19fdc: Update Test and Main
by GitHub 03 Apr '17

03 Apr '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: e19fdc9ee821c9dee451555fef1a12ef75f9ed93 https://github.com/galaxyproject/usegalaxy-playbook/commit/e19fdc9ee821c9de… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-04-03 (Mon, 03 Apr 2017) Changed paths: M production/galaxy_version.yml M stage/galaxy_version.yml Log Message: ----------- Update Test and Main

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[galaxyproject/galaxy] 1fbdb3: Have IGV bigWig display application make use of bu...
by GitHub 03 Apr '17

03 Apr '17

Branch: refs/heads/usegalaxy Home: https://github.com/galaxyproject/galaxy Commit: 1fbdb35d6edb84a3700ea1392dcf32f1a42f8225 https://github.com/galaxyproject/galaxy/commit/1fbdb35d6edb84a3700ea1392dcf… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2017-03-27 (Mon, 27 Mar 2017) Changed paths: M display_applications/igv/bigwig.xml Log Message: ----------- Have IGV bigWig display application make use of build_sites/ site_type config instead of direct filename. Commit: a2b5c41de00505179c7ce5a5f28ac0d9f0f1dee7 https://github.com/galaxyproject/galaxy/commit/a2b5c41de00505179c7ce5a5f28a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-03-28 (Tue, 28 Mar 2017) Changed paths: M display_applications/igv/bigwig.xml Log Message: ----------- Merge pull request #3828 from blankenberg/17.01_bigwig_igv [17.01] Have IGV bigWig display application make use of build_sites/ site_typ… Commit: 5d3250fac03b32f4d14213cd6039aac884a1307e https://github.com/galaxyproject/galaxy/commit/5d3250fac03b32f4d14213cd6039… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-03-28 (Tue, 28 Mar 2017) Changed paths: M lib/galaxy/model/__init__.py M test/api/test_workflows.py Log Message: ----------- [17.01] Order processing evaluation of workflow invocations when scheduling. xref https://github.com/galaxyproject/galaxy/pull/3820#issuecomment-289725795 Also optimize the query to just pull out workflow invocation IDs per the suggestion of @nsoranzo [here](https://github.com/galaxyproject/galaxy/pull/3830#pullrequestreview-2…. Commit: 4beb98e973000e0bd51b06ad35301ddb8b905ec1 https://github.com/galaxyproject/galaxy/commit/4beb98e973000e0bd51b06ad3530… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-03-29 (Wed, 29 Mar 2017) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/model/__init__.py M lib/galaxy/workflow/run.py M test/api/test_workflows.py M test/api/test_workflows_from_yaml.py M test/base/data/test_workflow_pause.ga M test/base/populators.py A test/integration/test_maximum_worklfow_invocation_duration.py Log Message: ----------- [17.01] By default, do not allow workflow invocations to schedule indefinitely. Give up after a month but allow admins to reduce this amount as well. Commit: aba31bc0d484f3729b46a10b2b357b92fa826fae https://github.com/galaxyproject/galaxy/commit/aba31bc0d484f3729b46a10b2b35… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-03-29 (Wed, 29 Mar 2017) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/jobs/__init__.py M lib/galaxy/workflow/scheduling_manager.py A test/integration/test_workflow_handler_configuration.py A test/integration/workflow_handler_configuration_job_conf.xml Log Message: ----------- [17.01] Restrict workflow scheduling within a history to a fixed, random handler. Lets revisit the problem that background scheduling workflows (as is the default UI behavior as of 16.10) makes it easier for histories to contain datasets interleaved from different workflow invocations under certain reasonable conditions (https://github.com/galaxyproject/galaxy/issues/3474). Considering only a four year old workflow and tool feature set (no collection operations, no dynamic dataset discovery, only tool and input workflow modules), all workflows can and will fully schedule on the first scheduling iteration. Under those circumstances, this solution is functionally equivalent to history_local_serial_workflow_scheduling introduced #3520 - but should be more performant because all such workflows fully schedule in the first iteration and the double loop introduced here https://github.com/galaxyproject/galaxy/pull/3520/files#diff-d7e80a366f3965… is avoided for each workflow invocation for each iteration. This addresses both concerns I outlined [here](https://github.com/galaxyproject/galaxy/issues/3816#issuecomment-2893…. For workflows that use certain classes of newer tools or newer workflow features - I'd argue this approach will not degrade as harshly as enabling history_local_serial_workflow_scheduling. For instance, imagine a workflow with a dynamic dataset collection output step (such as used by IUC tools Deseq2, Trinity, Stacks, and various Mothur tools) half way through that takes 24 hour of queue time to reach. Now imagine a user running 5 such workflows at once. - Without this and without history_local_serial_workflow_scheduling, the 5 workflows will each run as fast as possible and the UI will show as much of each workflow as can be scheduled but the order of the datsets may be shuffled. The workflows will be complete for the users in 48 hours. - With history_local_serial_workflow_scheduling enabled, only 1 workflow will be scheduled only half way for the first 24 hours and the user will be given no visual indication for why the other workflows are not running for 1 day. The final workflow output will take nearly a week to be complete for the users. - With this enabled - the new default in this commit - each workflow will be scheduled in two chunks but these chunks will be contingious and it should be fairly clear to the user what tool caused the discontinuity of the datasets in the history. So things are still mostly ordered, but the draw backs of history_local_serial_workflow_scheduling are avoided entirely. Namely, the other four workflows aren't hidden from the user without a UI indication and the workflows will still only take 48 hours to be complete and outputs ready for the user. The only drawback of this new default behavior is that you could potentially see some performance improvements by scheduling multiple workflow invocations within one history - but this was never a design goal in my mind when implementing background scheduling and under typical Galaxy use cases I don't think this would be worth the UI problems. So, the older behavior can be re-enabled by setting parallelize_workflow_scheduling_within_histories to True in galaxy.ini but it won't be on by default or really recommended if the Galaxy UI is being used. Commit: 8f8526bf307d083c64330859793c112a9823b5d8 https://github.com/galaxyproject/galaxy/commit/8f8526bf307d083c64330859793c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-30 (Thu, 30 Mar 2017) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/model/__init__.py M lib/galaxy/workflow/run.py M test/api/test_workflows.py M test/api/test_workflows_from_yaml.py M test/base/data/test_workflow_pause.ga M test/base/populators.py A test/integration/test_maximum_worklfow_invocation_duration.py Log Message: ----------- Merge pull request #3659 from jmchilton/1701_maximum_workflow_invocation_duration [17.01] By default, do not allow workflow invocations to schedule indefinitely. Commit: c51adf781a1a711c4e54d89fbdca7ea9d3331f08 https://github.com/galaxyproject/galaxy/commit/c51adf781a1a711c4e54d89fbdca… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-03-30 (Thu, 30 Mar 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-options.js M static/maps/mvc/ui/ui-options.js.map M static/scripts/bundled/analysis.bundled.js 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/mvc/ui/ui-options.js Log Message: ----------- Insert update caller/helper for options Commit: 07887be3a162678859e32c063dae024f0a8da25c https://github.com/galaxyproject/galaxy/commit/07887be3a162678859e32c063dae… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-31 (Fri, 31 Mar 2017) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/jobs/__init__.py M lib/galaxy/workflow/scheduling_manager.py A test/integration/test_workflow_handler_configuration.py A test/integration/workflow_handler_configuration_job_conf.xml Log Message: ----------- Merge pull request #3820 from jmchilton/fixed_history_handler [17.01] Restrict workflow scheduling within a history to a fixed, random handler. Commit: bf6b65f005965eff9d01f432bf52f5d1104294b7 https://github.com/galaxyproject/galaxy/commit/bf6b65f005965eff9d01f432bf52… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-31 (Fri, 31 Mar 2017) Changed paths: M lib/galaxy/model/__init__.py M test/api/test_workflows.py Log Message: ----------- Merge pull request #3830 from jmchilton/1701_order_collection_invocation_processing [17.01] Order processing evaluation of workflow invocations when scheduling. Commit: c8eb2c186def4b505143a5a6b0d971549b15d19a https://github.com/galaxyproject/galaxy/commit/c8eb2c186def4b505143a5a6b0d9… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-31 (Fri, 31 Mar 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-options.js M static/maps/mvc/ui/ui-options.js.map M static/scripts/bundled/analysis.bundled.js 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/mvc/ui/ui-options.js Log Message: ----------- Merge pull request #3851 from guerler/add_lost_update_caller [17.01] Fix update caller/helper for options Commit: 99c8f2c9fc6f335863f134a5b8b4055d5079cfe1 https://github.com/galaxyproject/galaxy/commit/99c8f2c9fc6f335863f134a5b8b4… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-03-31 (Fri, 31 Mar 2017) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Fix setting UUID on steps when copying steps from another workflow. It seems like the client is correctly setting the UUID to None, but the backend is treating the None as a UUID because it was (incorrectly IMO) making a distinction between ``uuid`` being absent and being set to ``None``. Fixes #3845. Commit: 268aac29526b3526a42457576e8de7867c2bfe1f https://github.com/galaxyproject/galaxy/commit/268aac29526b3526a42457576e8d… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-04-03 (Mon, 03 Apr 2017) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Merge pull request #3856 from jmchilton/1701_uuid_on_copy_fix [17.01] Fix setting UUID on steps when copying steps from another workflow. Commit: aafb8e305ace53af9aebd67626f8127b60b1219a https://github.com/galaxyproject/galaxy/commit/aafb8e305ace53af9aebd67626f8… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-04-03 (Mon, 03 Apr 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-options.js M config/galaxy.ini.sample M display_applications/igv/bigwig.xml M lib/galaxy/config.py M lib/galaxy/jobs/__init__.py M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/workflow/run.py M lib/galaxy/workflow/scheduling_manager.py M static/maps/mvc/ui/ui-options.js.map M static/scripts/bundled/analysis.bundled.js 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/mvc/ui/ui-options.js M test/api/test_workflows.py M test/api/test_workflows_from_yaml.py M test/base/data/test_workflow_pause.ga M test/base/populators.py A test/integration/test_maximum_worklfow_invocation_duration.py A test/integration/test_workflow_handler_configuration.py A test/integration/workflow_handler_configuration_job_conf.xml Log Message: ----------- Merge branch 'release_17.01' of https://github.com/galaxyproject/galaxy into usegalaxy Compare: https://github.com/galaxyproject/galaxy/compare/812b04bb3abe...aafb8e305ace

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[galaxyproject/galaxy] 99c8f2: Fix setting UUID on steps when copying steps from ...
by GitHub 03 Apr '17

03 Apr '17

Branch: refs/heads/release_17.01 Home: https://github.com/galaxyproject/galaxy Commit: 99c8f2c9fc6f335863f134a5b8b4055d5079cfe1 https://github.com/galaxyproject/galaxy/commit/99c8f2c9fc6f335863f134a5b8b4… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-03-31 (Fri, 31 Mar 2017) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Fix setting UUID on steps when copying steps from another workflow. It seems like the client is correctly setting the UUID to None, but the backend is treating the None as a UUID because it was (incorrectly IMO) making a distinction between ``uuid`` being absent and being set to ``None``. Fixes #3845. Commit: 268aac29526b3526a42457576e8de7867c2bfe1f https://github.com/galaxyproject/galaxy/commit/268aac29526b3526a42457576e8d… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-04-03 (Mon, 03 Apr 2017) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Merge pull request #3856 from jmchilton/1701_uuid_on_copy_fix [17.01] Fix setting UUID on steps when copying steps from another workflow. Compare: https://github.com/galaxyproject/galaxy/compare/c8eb2c186def...268aac29526b

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[galaxyproject/galaxy]
by GitHub 31 Mar '17

31 Mar '17

Branch: refs/heads/contrib_changes Home: https://github.com/galaxyproject/galaxy

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[galaxyproject/galaxy] b5fe42: Small changes to links and add gitter
by GitHub 31 Mar '17

31 Mar '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b5fe42c462ebcbf4fb9f0a09fd63e11c2a68fd7e https://github.com/galaxyproject/galaxy/commit/b5fe42c462ebcbf4fb9f0a09fd63… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-04-01 (Sat, 01 Apr 2017) Changed paths: M CONTRIBUTING.md Log Message: ----------- Small changes to links and add gitter Commit: ffce14e65d70441827086c1eccdae46a28819df3 https://github.com/galaxyproject/galaxy/commit/ffce14e65d70441827086c1eccda… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-03-31 (Fri, 31 Mar 2017) Changed paths: M CONTRIBUTING.md Log Message: ----------- change devteam to iuc Commit: 224a5b39004e93c7ced8a6ce317e2ac85b553b40 https://github.com/galaxyproject/galaxy/commit/224a5b39004e93c7ced8a6ce317e… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-03-31 (Fri, 31 Mar 2017) Changed paths: M CONTRIBUTING.md Log Message: ----------- fix contribute pdf link Commit: 5169fbe917c90ee6b13a345e869bf88bf51f6512 https://github.com/galaxyproject/galaxy/commit/5169fbe917c90ee6b13a345e869b… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-03-31 (Fri, 31 Mar 2017) Changed paths: M CONTRIBUTING.md Log Message: ----------- Merge pull request #3861 from galaxyproject/contrib_changes Small changes to links and add gitter Compare: https://github.com/galaxyproject/galaxy/compare/6af5334f1254...5169fbe917c9

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[galaxyproject/galaxy] 224a5b: fix contribute pdf link
by GitHub 31 Mar '17

31 Mar '17

Branch: refs/heads/contrib_changes Home: https://github.com/galaxyproject/galaxy Commit: 224a5b39004e93c7ced8a6ce317e2ac85b553b40 https://github.com/galaxyproject/galaxy/commit/224a5b39004e93c7ced8a6ce317e… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-03-31 (Fri, 31 Mar 2017) Changed paths: M CONTRIBUTING.md Log Message: ----------- fix contribute pdf link

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[galaxyproject/galaxy] ffce14: change devteam to iuc
by GitHub 31 Mar '17

31 Mar '17

Branch: refs/heads/contrib_changes Home: https://github.com/galaxyproject/galaxy Commit: ffce14e65d70441827086c1eccdae46a28819df3 https://github.com/galaxyproject/galaxy/commit/ffce14e65d70441827086c1eccda… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-03-31 (Fri, 31 Mar 2017) Changed paths: M CONTRIBUTING.md Log Message: ----------- change devteam to iuc

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[galaxyproject/galaxy] b5fe42: Small changes to links and add gitter
by GitHub 31 Mar '17

31 Mar '17

Branch: refs/heads/contrib_changes Home: https://github.com/galaxyproject/galaxy Commit: b5fe42c462ebcbf4fb9f0a09fd63e11c2a68fd7e https://github.com/galaxyproject/galaxy/commit/b5fe42c462ebcbf4fb9f0a09fd63… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-04-01 (Sat, 01 Apr 2017) Changed paths: M CONTRIBUTING.md Log Message: ----------- Small changes to links and add gitter

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galaxy-commits April 2017