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[galaxyproject/galaxy] 0b6444: Skip tool tests in test/functional/known_broken_to...
by GitHub 05 Sep '18

05 Sep '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 0b64442ed3d06bd7fdf9f0fbb53520d28e9332b9 https://github.com/galaxyproject/galaxy/commit/0b64442ed3d06bd7fdf9f0fbb535… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-25 (Sat, 25 Aug 2018) Changed paths: A test/functional/known_broken_tools.txt M test/functional/test_toolbox_pytest.py Log Message: ----------- Skip tool tests in test/functional/known_broken_tools.txt Commit: 300ab73c10332968a98eb5f77a85abc66a3f4686 https://github.com/galaxyproject/galaxy/commit/300ab73c10332968a98eb5f77a85… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-25 (Sat, 25 Aug 2018) Changed paths: M pytest.ini M test/functional/test_toolbox_pytest.py Log Message: ----------- Mark skipped tests instead of not collecting them Also marks tests as tool or data_manager, so `pytest -m <tool|data_manager>` can be used to select a subset of tests. Commit: 6f299202313c3b40d357468e9ba0e9b32f858038 https://github.com/galaxyproject/galaxy/commit/6f299202313c3b40d357468e9ba0… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-25 (Sat, 25 Aug 2018) Changed paths: M run_tests.sh Log Message: ----------- Use pytest for -framework, -installed, -data_manager, -migrated tests Commit: 546b90a6985cc6a8e4d87482778c8ac275c9903f https://github.com/galaxyproject/galaxy/commit/546b90a6985cc6a8e4d87482778c… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-25 (Sat, 25 Aug 2018) Changed paths: M run_tests.sh Log Message: ----------- Add additional test target for tools in tool_conf.xml.main Commit: e73257f8ed2556a94a6e58efff62ed1873709f42 https://github.com/galaxyproject/galaxy/commit/e73257f8ed2556a94a6e58efff62… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-25 (Sat, 25 Aug 2018) Changed paths: M test/functional/test_toolbox_pytest.py Log Message: ----------- Set conda_auto_init and conda_auto_install to true for pytest driver Commit: 7f807ce971e8d743dca0f0438e5ce078f742ec65 https://github.com/galaxyproject/galaxy/commit/7f807ce971e8d743dca0f0438e5c… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-25 (Sat, 25 Aug 2018) Changed paths: M run_tests.sh Log Message: ----------- Fix shell syntax Commit: 9099e73a3e00658082891fae7ea3de0774cce2ad https://github.com/galaxyproject/galaxy/commit/9099e73a3e00658082891fae7ea3… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-25 (Sat, 25 Aug 2018) Changed paths: M .coveragerc Log Message: ----------- Add include-ignored, otherwise spams stderr out Commit: d476fcc072dbcb8e3b19f511dc43ae731e7c97e0 https://github.com/galaxyproject/galaxy/commit/d476fcc072dbcb8e3b19f511dc43… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-25 (Sat, 25 Aug 2018) Changed paths: M lib/galaxy/jobs/runners/util/kill.py Log Message: ----------- Fix LocalShell on python3 Commit: 1c64cdd674fcbfc0f077f5d31947dd9b6c6e9149 https://github.com/galaxyproject/galaxy/commit/1c64cdd674fcbfc0f077f5d31947… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-25 (Sat, 25 Aug 2018) Changed paths: M pytest.ini M run_tests.sh M tox.ini Log Message: ----------- Use pytest to run unit and doctests Commit: 1152a19fd2cd5d6589becde3c7ebdd6435a33cff https://github.com/galaxyproject/galaxy/commit/1152a19fd2cd5d6589becde3c7eb… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-25 (Sat, 25 Aug 2018) Changed paths: M run_tests.sh Log Message: ----------- Use pytest-cov for testing coverage Commit: 66c64ccfe46cfd91bcffabaf2b4bddd7b86cef91 https://github.com/galaxyproject/galaxy/commit/66c64ccfe46cfd91bcffabaf2b4b… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-25 (Sat, 25 Aug 2018) Changed paths: M test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py Log Message: ----------- Adapt dynamic_tool_destination unit tests to pytest as driver The log capturing seems to be a bit different Commit: d9a2c5a970aafabe101842991a34074701f8854c https://github.com/galaxyproject/galaxy/commit/d9a2c5a970aafabe101842991a34… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-25 (Sat, 25 Aug 2018) Changed paths: M run_tests.sh Log Message: ----------- Don't test tools in tool_conf.xml.sample as part of -framework This replicates what the FrameworkToolsGalaxyTestDriver does. Commit: aa0becad0be33ee7fe1d430c64f1d89f475ca6e2 https://github.com/galaxyproject/galaxy/commit/aa0becad0be33ee7fe1d430c64f1… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-25 (Sat, 25 Aug 2018) Changed paths: M run_tests.sh Log Message: ----------- Simplify tool_conf selection in run_tests.sh Drops -with_framework_test_tools altogether. Thanks @nsoranzo. Commit: 8148bd91deb4d4f9b621b6e3097ae0f01ba81abd https://github.com/galaxyproject/galaxy/commit/8148bd91deb4d4f9b621b6e3097a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-09-05 (Wed, 05 Sep 2018) Changed paths: M .coveragerc M lib/galaxy/jobs/runners/util/kill.py M pytest.ini M run_tests.sh A test/functional/known_broken_tools.txt M test/functional/test_toolbox_pytest.py M test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py M tox.ini Log Message: ----------- Merge pull request #6638 from mvdbeek/move_tests_to_pytest_setup Move tests to pytest setup Compare: https://github.com/galaxyproject/galaxy/compare/bc1526ab2dd5...8148bd91deb4 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 73b6e8: Eliminate more queries in history.add_dataset(s) b...
by GitHub 04 Sep '18

04 Sep '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 73b6e81a0ab2f646de7d3709bcbf9e4284a1c439 https://github.com/galaxyproject/galaxy/commit/73b6e81a0ab2f646de7d3709bcbf… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-28 (Tue, 28 Aug 2018) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py Log Message: ----------- Eliminate more queries in history.add_dataset(s) by using cached IDs. Commit: 74bb5434a0e9020673f1d4acaab98a6bd9865268 https://github.com/galaxyproject/galaxy/commit/74bb5434a0e9020673f1d4acaab9… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-28 (Tue, 28 Aug 2018) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Eliminate old and invalid tool optimization comment. Commit: b2fe48a6be69bd5c05357ae0a8a7fe07f8d314db https://github.com/galaxyproject/galaxy/commit/b2fe48a6be69bd5c05357ae0a8a7… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-28 (Tue, 28 Aug 2018) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Allow history_id to be specified instead of history in check_elements. Commit: bc1526ab2dd5044f3ea274c176fcb43b490b0c63 https://github.com/galaxyproject/galaxy/commit/bc1526ab2dd5044f3ea274c176fc… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-09-04 (Tue, 04 Sep 2018) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Merge pull request #6644 from jmchilton/add_datasets Small Optimizations to Adding Datasets to History Compare: https://github.com/galaxyproject/galaxy/compare/3ca449fa73fc...bc1526ab2dd5 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 3c5991: Allow group tag selection also for multiple="true"...
by GitHub 04 Sep '18

04 Sep '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 3c5991632246d5fd404b269507642f819abf7d68 https://github.com/galaxyproject/galaxy/commit/3c5991632246d5fd404b26950764… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-03 (Mon, 03 Sep 2018) Changed paths: M lib/galaxy/tools/wrappers.py Log Message: ----------- Allow group tag selection also for multiple="true" inputs Commit: 3ca449fa73fcc18389876756814fdaa5bb6e2aed https://github.com/galaxyproject/galaxy/commit/3ca449fa73fcc18389876756814f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-09-04 (Tue, 04 Sep 2018) Changed paths: M lib/galaxy/tools/wrappers.py Log Message: ----------- Merge pull request #6661 from mvdbeek/group_tags_for_multiple_true_inputs Allow group tag selection also for multiple="true" inputs Compare: https://github.com/galaxyproject/galaxy/compare/b9d07aed22c5...3ca449fa73fc **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 77706a: Update application documentation
by GitHub 03 Sep '18

03 Sep '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 77706a8e62f6c7ffafc923b9f94f3359089e8ee9 https://github.com/galaxyproject/galaxy/commit/77706a8e62f6c7ffafc923b9f94f… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2018-09-03 (Mon, 03 Sep 2018) Changed paths: M doc/source/lib/galaxy.actions.rst M doc/source/lib/galaxy.auth.rst A doc/source/lib/galaxy.authnz.rst M doc/source/lib/galaxy.containers.rst M doc/source/lib/galaxy.datatypes.converters.rst M doc/source/lib/galaxy.datatypes.rst R doc/source/lib/galaxy.external_services.result_handlers.rst R doc/source/lib/galaxy.external_services.rst R doc/source/lib/galaxy.jobs.deferred.rst M doc/source/lib/galaxy.jobs.metrics.instrumenters.rst M doc/source/lib/galaxy.jobs.rst R doc/source/lib/galaxy.jobs.runners.util.drmaa.rst M doc/source/lib/galaxy.jobs.runners.util.rst M doc/source/lib/galaxy.managers.rst M doc/source/lib/galaxy.objectstore.rst M doc/source/lib/galaxy.rst R doc/source/lib/galaxy.sample_tracking.rst M doc/source/lib/galaxy.tools.cwl.rst M doc/source/lib/galaxy.tools.deps.resolvers.rst M doc/source/lib/galaxy.tools.deps.rst A doc/source/lib/galaxy.tools.error_reports.plugins.rst A doc/source/lib/galaxy.tools.error_reports.rst M doc/source/lib/galaxy.tools.parser.rst M doc/source/lib/galaxy.tools.rst M doc/source/lib/galaxy.tools.toolbox.lineages.rst M doc/source/lib/galaxy.tools.toolbox.rst M doc/source/lib/galaxy.tools.verify.rst R doc/source/lib/galaxy.util.backports.rst R doc/source/lib/galaxy.util.log.rst A doc/source/lib/galaxy.util.logging.rst A doc/source/lib/galaxy.util.path.rst M doc/source/lib/galaxy.util.rst M doc/source/lib/galaxy.visualization.plugins.rst R doc/source/lib/galaxy.web.base.controllers.rst M doc/source/lib/galaxy.web.base.rst M doc/source/lib/galaxy.web.framework.helpers.rst M doc/source/lib/galaxy.web.framework.middleware.rst M doc/source/lib/galaxy.web.framework.rst M doc/source/lib/galaxy.web.stack.rst M doc/source/lib/galaxy.webapps.galaxy.api.rst M doc/source/lib/galaxy.webapps.galaxy.controllers.rst M doc/source/lib/galaxy.webapps.reports.controllers.rst A doc/source/lib/galaxy.webapps.reports.framework.rst M doc/source/lib/galaxy.webapps.reports.rst M doc/source/lib/galaxy.webapps.rst A doc/source/lib/galaxy.workflow.resources.rst M doc/source/lib/galaxy.workflow.rst M doc/source/lib/tool_shed.util.rst Log Message: ----------- Update application documentation With ``` make -C doc/ updaterst ``` Commit: ad02c53154a3d3046a814b838cffdf0a79ac9a13 https://github.com/galaxyproject/galaxy/commit/ad02c53154a3d3046a814b838cff… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2018-09-03 (Mon, 03 Sep 2018) Changed paths: M config/error_report.yml.sample M config/galaxy.yml.sample M config/job_conf.xml.sample_advanced M config/tool_shed.yml.sample M doc/source/admin/cluster.md M doc/source/admin/conda_faq.rst M doc/source/admin/config.rst M doc/source/admin/dependency_resolvers.rst M doc/source/admin/framework_dependencies.rst M doc/source/admin/galaxy_options.rst M doc/source/admin/jobs.md M doc/source/admin/production.md M doc/source/admin/scaling.md M doc/source/admin/special_topics/performance_tracking.rst M doc/source/api_doc.rst M doc/source/conf.py M doc/source/releases/16.04_announce.rst M doc/source/releases/16.10.rst M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/model/search.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/webapps/config_manage.py M lib/galaxy/webapps/galaxy/config_schema.yml M lib/galaxy/webapps/tool_shed/buildapp.py M lib/galaxy/webapps/tool_shed/config_schema.yml M lib/galaxy/webapps/uwsgi_schema.yml M run_tests.sh M scripts/api/README M scripts/slideshow/example.md M templates/admin/tool_shed_repository/select_tool_panel_section.mako M test/base/workflows_format_2/interface.py Log Message: ----------- Fix many links Commit: 59c1ed2266504a2bd03e80e9f4ec72664148524f https://github.com/galaxyproject/galaxy/commit/59c1ed2266504a2bd03e80e9f4ec… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-09-03 (Mon, 03 Sep 2018) Changed paths: M config/galaxy.yml.sample M doc/parse_gx_xsd.py M doc/schema_template.md M doc/source/admin/galaxy_options.rst M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/runners/chronos.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- Various doc fixes Commit: b9d07aed22c59c2aeb92e30d18953bc6fecea0a6 https://github.com/galaxyproject/galaxy/commit/b9d07aed22c59c2aeb92e30d1895… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-09-03 (Mon, 03 Sep 2018) Changed paths: M config/error_report.yml.sample M config/galaxy.yml.sample M config/job_conf.xml.sample_advanced M config/tool_shed.yml.sample M doc/parse_gx_xsd.py M doc/schema_template.md M doc/source/admin/cluster.md M doc/source/admin/conda_faq.rst M doc/source/admin/config.rst M doc/source/admin/dependency_resolvers.rst M doc/source/admin/framework_dependencies.rst M doc/source/admin/galaxy_options.rst M doc/source/admin/jobs.md M doc/source/admin/production.md M doc/source/admin/scaling.md M doc/source/admin/special_topics/performance_tracking.rst M doc/source/api_doc.rst M doc/source/conf.py M doc/source/lib/galaxy.actions.rst M doc/source/lib/galaxy.auth.rst A doc/source/lib/galaxy.authnz.rst M doc/source/lib/galaxy.containers.rst M doc/source/lib/galaxy.datatypes.converters.rst M doc/source/lib/galaxy.datatypes.rst R doc/source/lib/galaxy.external_services.result_handlers.rst R doc/source/lib/galaxy.external_services.rst R doc/source/lib/galaxy.jobs.deferred.rst M doc/source/lib/galaxy.jobs.metrics.instrumenters.rst M doc/source/lib/galaxy.jobs.rst R doc/source/lib/galaxy.jobs.runners.util.drmaa.rst M doc/source/lib/galaxy.jobs.runners.util.rst M doc/source/lib/galaxy.managers.rst M doc/source/lib/galaxy.objectstore.rst M doc/source/lib/galaxy.rst R doc/source/lib/galaxy.sample_tracking.rst M doc/source/lib/galaxy.tools.cwl.rst M doc/source/lib/galaxy.tools.deps.resolvers.rst M doc/source/lib/galaxy.tools.deps.rst A doc/source/lib/galaxy.tools.error_reports.plugins.rst A doc/source/lib/galaxy.tools.error_reports.rst M doc/source/lib/galaxy.tools.parser.rst M doc/source/lib/galaxy.tools.rst M doc/source/lib/galaxy.tools.toolbox.lineages.rst M doc/source/lib/galaxy.tools.toolbox.rst M doc/source/lib/galaxy.tools.verify.rst R doc/source/lib/galaxy.util.backports.rst R doc/source/lib/galaxy.util.log.rst A doc/source/lib/galaxy.util.logging.rst A doc/source/lib/galaxy.util.path.rst M doc/source/lib/galaxy.util.rst M doc/source/lib/galaxy.visualization.plugins.rst R doc/source/lib/galaxy.web.base.controllers.rst M doc/source/lib/galaxy.web.base.rst M doc/source/lib/galaxy.web.framework.helpers.rst M doc/source/lib/galaxy.web.framework.middleware.rst M doc/source/lib/galaxy.web.framework.rst M doc/source/lib/galaxy.web.stack.rst M doc/source/lib/galaxy.webapps.galaxy.api.rst M doc/source/lib/galaxy.webapps.galaxy.controllers.rst M doc/source/lib/galaxy.webapps.reports.controllers.rst A doc/source/lib/galaxy.webapps.reports.framework.rst M doc/source/lib/galaxy.webapps.reports.rst M doc/source/lib/galaxy.webapps.rst A doc/source/lib/galaxy.workflow.resources.rst M doc/source/lib/galaxy.workflow.rst M doc/source/lib/tool_shed.util.rst M doc/source/releases/16.04_announce.rst M doc/source/releases/16.10.rst M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/runners/chronos.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/model/search.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/webapps/config_manage.py M lib/galaxy/webapps/galaxy/config_schema.yml M lib/galaxy/webapps/tool_shed/buildapp.py M lib/galaxy/webapps/tool_shed/config_schema.yml M lib/galaxy/webapps/uwsgi_schema.yml M run_tests.sh M scripts/api/README M scripts/slideshow/example.md M templates/admin/tool_shed_repository/select_tool_panel_section.mako M test/base/workflows_format_2/interface.py Log Message: ----------- Merge pull request #6662 from nsoranzo/doc_fixes2 Various link and documentation fixes Compare: https://github.com/galaxyproject/galaxy/compare/76d89d020f56...b9d07aed22c5 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] ea34aa: adding 4 new GROMACS datatypes: cpt, xtc, top, and...
by GitHub 03 Sep '18

03 Sep '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ea34aa84be9be03489e541b928ea57adfb087e80 https://github.com/galaxyproject/galaxy/commit/ea34aa84be9be03489e541b928ea… Author: simonbray <sbray1371(a)gmail.com> Date: 2018-09-03 (Mon, 03 Sep 2018) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/tabular.py R lib/galaxy/datatypes/test/em.trr A lib/galaxy/datatypes/test/md.cpt A lib/galaxy/datatypes/test/md.trr A lib/galaxy/datatypes/test/md.xtc M lib/galaxy/datatypes/text.py Log Message: ----------- adding 4 new GROMACS datatypes: cpt, xtc, top, and gro shrinking test files Commit: 6a730bc5821c94d25411cb51a7033ab56064617b https://github.com/galaxyproject/galaxy/commit/6a730bc5821c94d25411cb51a703… Author: simonbray <sbray1371(a)gmail.com> Date: 2018-09-03 (Mon, 03 Sep 2018) Changed paths: M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/text.py Log Message: ----------- linting Commit: 3c7d7d9d49d49781f822a36c3bdbd860ddc0e8f0 https://github.com/galaxyproject/galaxy/commit/3c7d7d9d49d49781f822a36c3bdb… Author: simonbray <sbray1371(a)gmail.com> Date: 2018-09-03 (Mon, 03 Sep 2018) Changed paths: M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/text.py Log Message: ----------- tightening up the sniffer functions Commit: 0d97c55cc7256ccff7285d57dd5ed3ec64616887 https://github.com/galaxyproject/galaxy/commit/0d97c55cc7256ccff7285d57dd5e… Author: sb635 <sb635(a)bmd6.physik.privat> Date: 2018-09-03 (Mon, 03 Sep 2018) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- add refs for trr/xtc/cpt binary magic numbers Commit: 56d55399ebe2ecd614a7ba5a146739f58e917541 https://github.com/galaxyproject/galaxy/commit/56d55399ebe2ecd614a7ba5a1467… Author: sb635 <sb635(a)bmd6.physik.privat> Date: 2018-09-03 (Mon, 03 Sep 2018) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/text.py Log Message: ----------- removing top and gro sniffers, at least for now Commit: e59219deabe89cbf3a98f984bf54d314157d6599 https://github.com/galaxyproject/galaxy/commit/e59219deabe89cbf3a98f984bf54… Author: simonbray <sbray1371(a)gmail.com> Date: 2018-09-03 (Mon, 03 Sep 2018) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- created new GmxBinary class from which xtc, trr, cpt inherit Commit: 5d15063f7de0b7b07f7bad5d7dbbb31f5e872855 https://github.com/galaxyproject/galaxy/commit/5d15063f7de0b7b07f7bad5d7dbb… Author: simonbray <sbray1371(a)gmail.com> Date: 2018-09-03 (Mon, 03 Sep 2018) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- remove __init__() from GmxBinary subclasses Commit: 09d349cbfff5623a52f23ccd480b4975759f8d8b https://github.com/galaxyproject/galaxy/commit/09d349cbfff5623a52f23ccd480b… Author: Simon Bray <32272674+simonbray(a)users.noreply.github.com> Date: 2018-09-03 (Mon, 03 Sep 2018) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- default for magic_number None not 0 Commit: ed641aceb9d117aee7a83de9bbcd7a7876d20703 https://github.com/galaxyproject/galaxy/commit/ed641aceb9d117aee7a83de9bbcd… Author: simonbray <sbray1371(a)gmail.com> Date: 2018-09-03 (Mon, 03 Sep 2018) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- remove __init__ from GmxBinary Commit: 76d89d020f56e202939a26b06972e3bce489dd3b https://github.com/galaxyproject/galaxy/commit/76d89d020f56e202939a26b06972… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-09-03 (Mon, 03 Sep 2018) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py R lib/galaxy/datatypes/test/em.trr A lib/galaxy/datatypes/test/md.cpt A lib/galaxy/datatypes/test/md.trr A lib/galaxy/datatypes/test/md.xtc Log Message: ----------- Merge pull request #6655 from simonbray/dev Adding 4 new GROMACS datatypes: cpt, xtc, top, and gro Compare: https://github.com/galaxyproject/galaxy/compare/410ec1927c34...76d89d020f56 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] dd0a68: Fixes...
by GitHub 31 Aug '18

31 Aug '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: dd0a6884ba7b20788fdec5b38e3715596b2ac177 https://github.com/galaxyproject/galaxy/commit/dd0a6884ba7b20788fdec5b38e37… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-29 (Wed, 29 Aug 2018) Changed paths: M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/collection/pair-collection-creator.js M client/galaxy/scripts/mvc/history/history-contents.js M lib/galaxy/managers/collections.py M test/selenium_tests/test_collection_builders.py Log Message: ----------- Fixes... Commit: 5d22d73f303298fdef98c5ab8c8e8e91bae65bb3 https://github.com/galaxyproject/galaxy/commit/5d22d73f303298fdef98c5ab8c8e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-29 (Wed, 29 Aug 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/rules/rule-definitions.js M client/galaxy/scripts/mvc/upload/upload-view.js Log Message: ----------- client-format Commit: 410ec1927c34fbb4a61969e1fe188babd9a8f82b https://github.com/galaxyproject/galaxy/commit/410ec1927c34fbb4a61969e1fe18… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-31 (Fri, 31 Aug 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/collection/pair-collection-creator.js M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/rules/rule-definitions.js M client/galaxy/scripts/mvc/upload/upload-view.js M lib/galaxy/managers/collections.py M test/selenium_tests/test_collection_builders.py Log Message: ----------- Merge pull request #6656 from jmchilton/collect_builder_fixes Assorted fixes for #6572 Compare: https://github.com/galaxyproject/galaxy/compare/3a77b64aeb71...410ec1927c34 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 25ae4e: Fix get_fileobj() call in Eland.set_meta()
by GitHub 31 Aug '18

31 Aug '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 25ae4e6e26a27696fa47ea656fa36889f435e2f2 https://github.com/galaxyproject/galaxy/commit/25ae4e6e26a27696fa47ea656fa3… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-08-30 (Thu, 30 Aug 2018) Changed paths: M lib/galaxy/datatypes/tabular.py Log Message: ----------- Fix get_fileobj() call in Eland.set_meta() Broken in commit 59f44cf2be48abd4bed0f7c6ddf7cc0aee5ad1f5 . Commit: 3a77b64aeb71c027d8f8d7ca56574b63ff83afb3 https://github.com/galaxyproject/galaxy/commit/3a77b64aeb71c027d8f8d7ca5657… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-08-31 (Fri, 31 Aug 2018) Changed paths: M lib/galaxy/datatypes/tabular.py Log Message: ----------- Merge pull request #6659 from nsoranzo/fix_Eland_set_meta Fix get_fileobj() call in Eland.set_meta() Compare: https://github.com/galaxyproject/galaxy/compare/bb9545288272...3a77b64aeb71 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] feaaec: Strip API keys option from admin panel left side -...
by GitHub 29 Aug '18

29 Aug '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: feaaecf2199f78e42668418ab4eb5c8f68ff0e8d https://github.com/galaxyproject/galaxy/commit/feaaecf2199f78e42668418ab4eb… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-08-29 (Wed, 29 Aug 2018) Changed paths: M client/galaxy/scripts/apps/panels/admin-panel.js Log Message: ----------- Strip API keys option from admin panel left side -- this is all in the user management grid now. I don't know if this got added back in a bad merge or if it was erroneously left in. Commit: 223c3988083c5397626bd33908376bc007bc28bc https://github.com/galaxyproject/galaxy/commit/223c3988083c5397626bd3390837… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-08-29 (Wed, 29 Aug 2018) Changed paths: M test/galaxy_selenium/navigation.yml Log Message: ----------- drop admin api keys navigator from selenium configs (which may break other tests, we should wait to see) Commit: bb95452882726e4f6c3f26c76abfe7b22bafadb4 https://github.com/galaxyproject/galaxy/commit/bb95452882726e4f6c3f26c76abf… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-08-29 (Wed, 29 Aug 2018) Changed paths: M client/galaxy/scripts/apps/panels/admin-panel.js M test/galaxy_selenium/navigation.yml Log Message: ----------- Merge pull request #6651 from dannon/admin_apikeys_fixup Strip API keys option from admin panel left side Compare: https://github.com/galaxyproject/galaxy/compare/2adae6c4ca77...bb9545288272 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 85751e: Add tag and group tag rule to history level rule b...
by GitHub 28 Aug '18

28 Aug '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 85751ebb163eb5474d6ba18b7bf9d75097d53e15 https://github.com/galaxyproject/galaxy/commit/85751ebb163eb5474d6ba18b7bf9… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-08-26 (Sun, 26 Aug 2018) Changed paths: M client/galaxy/scripts/mvc/rules/rule-definitions.js Log Message: ----------- Add tag and group tag rule to history level rule builder Commit: 1e7ce13b4773ffeaea169b03963a2a252187dfee https://github.com/galaxyproject/galaxy/commit/1e7ce13b4773ffeaea169b03963a… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-26 (Sun, 26 Aug 2018) Changed paths: M lib/galaxy/managers/hdas.py M lib/galaxy/model/__init__.py Log Message: ----------- Reuse HDA copy method in HDAManager Should benefit from smarter flush strategy in HDA.copy() Commit: d1f9ab88e4637d00c6c5c3c2290f6a19dd369456 https://github.com/galaxyproject/galaxy/commit/d1f9ab88e4637d00c6c5c3c2290f… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-26 (Sun, 26 Aug 2018) Changed paths: M lib/galaxy/managers/collections.py M lib/galaxy/webapps/galaxy/api/history_contents.py Log Message: ----------- Always copy HDAs when creating a new collection from exisitng datasets, and allow setting tags Commit: 91438996df29caac56bb7a6fe8dc25e52815caf8 https://github.com/galaxyproject/galaxy/commit/91438996df29caac56bb7a6fe8dc… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-26 (Sun, 26 Aug 2018) Changed paths: M test/api/test_history_contents.py Log Message: ----------- Test creation of collection from existing dataset, with a new tag Commit: eb4b878f3f5e9a898d5048c917ce2d379d7bf20f https://github.com/galaxyproject/galaxy/commit/eb4b878f3f5e9a898d5048c917ce… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-26 (Sun, 26 Aug 2018) Changed paths: M lib/galaxy/managers/collections.py M lib/galaxy/managers/hdas.py Log Message: ----------- Simplify hda manager usage Commit: 5dd63dd6d077e9836f126d97a3c50b8a25ea66cc https://github.com/galaxyproject/galaxy/commit/5dd63dd6d077e9836f126d97a3c5… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-26 (Sun, 26 Aug 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue Log Message: ----------- Include tags in element_identifier when building collection from datasets Commit: ce892a028cb9d65aa19f8a4333626b421a184ec9 https://github.com/galaxyproject/galaxy/commit/ce892a028cb9d65aa19f8a433362… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-26 (Sun, 26 Aug 2018) Changed paths: M lib/galaxy/managers/collections.py Log Message: ----------- Restore hiding of dataset instances Commit: d4a80e61e13fbeeda43a65874910d85cfc1c8b29 https://github.com/galaxyproject/galaxy/commit/d4a80e61e13fbeeda43a65874910… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-26 (Sun, 26 Aug 2018) Changed paths: M test/unit/managers/test_CollectionManager.py M test/unit/managers/test_HistoryContentsManager.py Log Message: ----------- Adapt unit tests to copying HDAs when creating collections Commit: a9cb290754f09a1ea3073e8858df6f9a9e45b147 https://github.com/galaxyproject/galaxy/commit/a9cb290754f09a1ea3073e8858df… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-26 (Sun, 26 Aug 2018) Changed paths: M test/api/test_history_contents.py M test/api/test_tools.py M test/api/test_workflows.py Log Message: ----------- Adjust API tests to copying HDAs when creating collection Commit: 711016ab9aac78c96fa65cd04f9421fbb6473b49 https://github.com/galaxyproject/galaxy/commit/711016ab9aac78c96fa65cd04f94… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-26 (Sun, 26 Aug 2018) Changed paths: M lib/galaxy/managers/collections.py M lib/galaxy/webapps/galaxy/api/history_contents.py Log Message: ----------- Treat LDDA as HDA when creating collection This avoids copying the LDDA to HDA and then copying the HDA again. Commit: 34cfdcac6a583c84c8641ac8e26243769d09598d https://github.com/galaxyproject/galaxy/commit/34cfdcac6a583c84c8641ac8e262… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-26 (Sun, 26 Aug 2018) Changed paths: M test/api/test_history_contents.py Log Message: ----------- Test for proper 403 response Coincidentally fixed by e013f2fbd1596b103ef195afcba8cbd787c49b33. Commit: c00ae9f81b953df7909aa591e411ebd6298a6f7c https://github.com/galaxyproject/galaxy/commit/c00ae9f81b953df7909aa591e411… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-26 (Sun, 26 Aug 2018) Changed paths: M lib/galaxy/managers/collections.py M lib/galaxy/managers/collections_util.py M lib/galaxy/webapps/galaxy/api/history_contents.py Log Message: ----------- Default to not copying source HDAs when creating new collections via API Commit: 9409322a730d431344d4438e379e61559632812d https://github.com/galaxyproject/galaxy/commit/9409322a730d431344d4438e379e… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-26 (Sun, 26 Aug 2018) Changed paths: M test/unit/managers/test_CollectionManager.py M test/unit/managers/test_HistoryContentsManager.py Log Message: ----------- Revert "Adapt unit tests to copying HDAs when creating collections" This reverts commit 408a003f171be73e4b347579ee6f662a18fc1990. Commit: b13cce0a1340a5f9b7a77ab7eda1ceb0930ed161 https://github.com/galaxyproject/galaxy/commit/b13cce0a1340a5f9b7a77ab7eda1… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-26 (Sun, 26 Aug 2018) Changed paths: M test/api/test_history_contents.py M test/api/test_tools.py M test/api/test_workflows.py Log Message: ----------- Revert "Adjust API tests to copying HDAs when creating collection" This reverts commit f120390a63700ff0ec6c09185aad26b91ad8f842. Commit: cfd8379917703ce03b631fd48b5a2bcecc30bbea https://github.com/galaxyproject/galaxy/commit/cfd8379917703ce03b631fd48b5a… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-26 (Sun, 26 Aug 2018) Changed paths: M test/api/test_history_contents.py Log Message: ----------- Send copy_elements=True in new create collection test Commit: 43ee13a0ce43ae5b29ffa1e317df1db645cb93a8 https://github.com/galaxyproject/galaxy/commit/43ee13a0ce43ae5b29ffa1e317df… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-26 (Sun, 26 Aug 2018) Changed paths: M client/galaxy/scripts/mvc/history/history-contents.js Log Message: ----------- Default to copying HDAs when creating collections via the UI Commit: 50a524496a4ed52184967ede53094e5c8243d93d https://github.com/galaxyproject/galaxy/commit/50a524496a4ed52184967ede5309… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-26 (Sun, 26 Aug 2018) Changed paths: M test/unit/managers/test_HistoryContentsManager.py Log Message: ----------- Add unit test for copy_element option Commit: ddb0c74b9bd9f534691a93911f10903da3609927 https://github.com/galaxyproject/galaxy/commit/ddb0c74b9bd9f534691a93911f10… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-26 (Sun, 26 Aug 2018) Changed paths: M lib/galaxy/managers/collections.py Log Message: ----------- Original HDA must be owned by user if hiding source elements Commit: 366701cfb23d8de31eac3c4312c6accca2e74ef1 https://github.com/galaxyproject/galaxy/commit/366701cfb23d8de31eac3c4312c6… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-26 (Sun, 26 Aug 2018) Changed paths: M lib/galaxy/managers/tags.py M lib/galaxy/util/__init__.py A test/unit/managers/test_TagManager.py Log Message: ----------- Strip unicode control characters from tags Leaving them in can trip up postgresql: ``` Traceback (most recent call last): File "lib/galaxy/web/framework/decorators.py", line 283, in decorator rval = func(self, trans, *args, **kwargs) File "lib/galaxy/webapps/galaxy/api/history_contents.py", line 396, in create return self.__create_dataset_collection(trans, history, payload, **kwd) File "lib/galaxy/webapps/galaxy/api/history_contents.py", line 525, in __create_dataset_collection **create_params File "lib/galaxy/managers/collections.py", line 108, in create copy_elements=copy_elements, File "lib/galaxy/managers/collections.py", line 181, in create_dataset_collection copy_elements=copy_elements) File "lib/galaxy/managers/collections.py", line 217, in _element_identifiers_to_elements copy_elements=copy_elements) File "lib/galaxy/managers/collections.py", line 389, in __load_elements copy_elements=copy_elements) File "lib/galaxy/managers/collections.py", line 434, in __load_element self.tag_manager.apply_item_tags(user=trans.user, item=element, tags_str=tag_str) File "lib/galaxy/managers/tags.py", line 182, in apply_item_tags self.apply_item_tag(user, item, name, value) File "lib/galaxy/managers/tags.py", line 154, in apply_item_tag tag = self._get_or_create_tag(lc_name) File "lib/galaxy/managers/tags.py", line 233, in _get_or_create_tag tag = self.get_tag_by_name(scrubbed_tag_str) File "lib/galaxy/managers/tags.py", line 205, in get_tag_by_name return self.sa_session.query(galaxy.model.Tag).filter_by(name=tag_name.lower()).first() File "/bioinfo/guests/mvandenb/galaxy/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2789, in first ret = list(self[0:1]) File "/bioinfo/guests/mvandenb/galaxy/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2581, in __getitem__ return list(res) File "/bioinfo/guests/mvandenb/galaxy/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2889, in __iter__ return self._execute_and_instances(context) File "/bioinfo/guests/mvandenb/galaxy/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2912, in _execute_and_instances result = conn.execute(querycontext.statement, self._params) File "/bioinfo/guests/mvandenb/galaxy/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 948, in execute return meth(self, multiparams, params) File "/bioinfo/guests/mvandenb/galaxy/.venv/local/lib/python2.7/site-packages/sqlalchemy/sql/elements.py", line 269, in _execute_on_connection return connection._execute_clauseelement(self, multiparams, params) File "/bioinfo/guests/mvandenb/galaxy/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1060, in _execute_clauseelement compiled_sql, distilled_params File "/bioinfo/guests/mvandenb/galaxy/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1200, in _execute_context context) File "/bioinfo/guests/mvandenb/galaxy/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1416, in _handle_dbapi_exception util.reraise(*exc_info) File "/bioinfo/guests/mvandenb/galaxy/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1193, in _execute_context context) File "/bioinfo/guests/mvandenb/galaxy/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/default.py", line 507, in do_execute cursor.execute(statement, parameters) ValueError: A string literal cannot contain NUL (0x00) characters. ``` Commit: 2adae6c4ca77067f2f45f3f101218d411fec7e25 https://github.com/galaxyproject/galaxy/commit/2adae6c4ca77067f2f45f3f10121… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-28 (Tue, 28 Aug 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/rules/rule-definitions.js M lib/galaxy/managers/collections.py M lib/galaxy/managers/collections_util.py M lib/galaxy/managers/hdas.py M lib/galaxy/managers/tags.py M lib/galaxy/model/__init__.py M lib/galaxy/util/__init__.py M lib/galaxy/webapps/galaxy/api/history_contents.py M test/api/test_history_contents.py M test/unit/managers/test_HistoryContentsManager.py A test/unit/managers/test_TagManager.py Log Message: ----------- Merge pull request #6572 from mvdbeek/add_group_tags_to_history_rule_builder Add tagging rule to history level rule builder, copy HDAs when building collection Compare: https://github.com/galaxyproject/galaxy/compare/3121d9f0a468...2adae6c4ca77 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 167ab6: Fix color of workflow panel background
by GitHub 28 Aug '18

28 Aug '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 167ab6b54eb330ad44b8c7900d52514a1c90d1cb https://github.com/galaxyproject/galaxy/commit/167ab6b54eb330ad44b8c7900d52… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-08-27 (Mon, 27 Aug 2018) Changed paths: M client/galaxy/style/scss/base.scss M static/style/blue/base.css Log Message: ----------- Fix color of workflow panel background Commit: 3121d9f0a468d23f6619e3496cf46c627560d90c https://github.com/galaxyproject/galaxy/commit/3121d9f0a468d23f6619e3496cf4… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-08-28 (Tue, 28 Aug 2018) Changed paths: M client/galaxy/style/scss/base.scss M static/style/blue/base.css Log Message: ----------- Merge pull request #6643 from guerler/fix_panel_background Fix color of workflow panel background Compare: https://github.com/galaxyproject/galaxy/compare/7fa539162791...3121d9f0a468 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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