Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 876b460178bfb52936dc9f1d6c22149fea1f2513
https://github.com/galaxyproject/galaxy/commit/876b460178bfb52936dc9f1d6c22…
Author: M Bernt <m.bernt(a)ufz.de>
Date: 2018-11-14 (Wed, 14 Nov 2018)
Changed paths:
M lib/galaxy/jobs/runners/__init__.py
M test/unit/jobs/test_runner_local.py
Log Message:
-----------
reclaim ownership for failed jobs
Commit: 06184df405c5afa534e358664cfbad2b815b124f
https://github.com/galaxyproject/galaxy/commit/06184df405c5afa534e358664cfb…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-12-12 (Wed, 12 Dec 2018)
Changed paths:
M .travis.yml
A client/galaxy/scripts/components/GalaxyLoader.vue
M client/galaxy/scripts/components/HistoryImport.vue
M client/galaxy/scripts/components/PluginList.vue
M client/galaxy/scripts/components/WorkflowImport.vue
M client/galaxy/scripts/layout/menu.js
M client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js
M client/galaxy/scripts/mvc/history/history-item-li.js
M client/galaxy/scripts/mvc/history/options-menu.js
M client/galaxy/scripts/mvc/tool/tool-form.js
M client/galaxy/scripts/mvc/ui/ui-select-default.js
M client/galaxy/scripts/mvc/user/user-preferences.js
M client/galaxy/scripts/utils/utils.js
M client/galaxy/style/scss/trackster.scss
M config/galaxy.yml.sample
M config/job_conf.xml.sample_advanced
M config/job_resource_params_conf.xml.sample
M config/workflow_resource_params_conf.xml.sample
M doc/source/admin/framework_dependencies.rst
M doc/source/admin/galaxy_options.rst
M lib/galaxy/config.py
M lib/galaxy/containers/__init__.py
M lib/galaxy/dependencies/__init__.py
M lib/galaxy/dependencies/pipfiles/default/Pipfile
M lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt
M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt
M lib/galaxy/dependencies/pipfiles/update.sh
M lib/galaxy/jobs/__init__.py
M lib/galaxy/jobs/handler.py
M lib/galaxy/jobs/mapper.py
M lib/galaxy/jobs/runners/__init__.py
M lib/galaxy/jobs/runners/chronos.py
M lib/galaxy/jobs/runners/cli.py
M lib/galaxy/jobs/runners/condor.py
M lib/galaxy/jobs/runners/drmaa.py
M lib/galaxy/jobs/runners/godocker.py
M lib/galaxy/jobs/runners/kubernetes.py
M lib/galaxy/jobs/runners/local.py
M lib/galaxy/jobs/runners/pbs.py
M lib/galaxy/jobs/runners/pulsar.py
M lib/galaxy/jobs/runners/state_handler_factory.py
M lib/galaxy/jobs/runners/state_handlers/resubmit.py
M lib/galaxy/jobs/runners/tasks.py
A lib/galaxy/jobs/runners/univa.py
M lib/galaxy/jobs/runners/util/cli/job/lsf.py
M lib/galaxy/jobs/runners/util/job_script/MEMORY_STATEMENT.sh
M lib/galaxy/managers/configuration.py
M lib/galaxy/managers/workflows.py
M lib/galaxy/model/__init__.py
M lib/galaxy/model/mapping.py
M lib/galaxy/model/migrate/versions/0006_change_qual_datatype.py
M lib/galaxy/model/migrate/versions/0136_collection_and_workflow_state.py
A lib/galaxy/model/migrate/versions/0145_add_workflow_step_input.py
A lib/galaxy/model/migrate/versions/0146_workflow_paths.py
M lib/galaxy/queue_worker.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/deps/container_resolvers/__init__.py
M lib/galaxy/tools/deps/container_resolvers/mulled.py
M lib/galaxy/tools/deps/mulled/mulled_build.py
M lib/galaxy/tools/lint.py
M lib/galaxy/tools/parameters/meta.py
M lib/galaxy/tools/parameters/output_collect.py
M lib/galaxy/tools/parameters/validation.py
M lib/galaxy/tools/parser/xml.py
M lib/galaxy/tools/wrappers.py
M lib/galaxy/tools/xsd/galaxy.xsd
M lib/galaxy/util/__init__.py
M lib/galaxy/util/plugin_config.py
M lib/galaxy/util/submodules.py
M lib/galaxy/web/base/controller.py
M lib/galaxy/webapps/galaxy/api/workflows.py
M lib/galaxy/webapps/galaxy/config_schema.yml
M lib/galaxy/webapps/galaxy/config_watchers.py
M lib/galaxy/webapps/galaxy/controllers/dataset.py
M lib/galaxy/webapps/galaxy/controllers/history.py
M lib/galaxy/webapps/tool_shed/model/__init__.py
M lib/galaxy/workflow/extract.py
M lib/galaxy/workflow/modules.py
M lib/galaxy_ext/metadata/set_metadata.py
M lib/tool_shed/util/workflow_util.py
M run.sh
M run_reports.sh
M run_tool_shed.sh
M scripts/common_startup.sh
M scripts/common_startup_functions.sh
M templates/admin/tool_shed_repository/manage_repository.mako
M templates/js-app.mako
M templates/user/login.mako
M templates/user/register.mako
M templates/user/reset_password.mako
M test/api/test_workflows.py
M test/base/populators.py
M test/base/workflow_fixtures.py
A test/functional/tools/exit_code_from_env.xml
M test/functional/tools/for_workflows/head.xml
M test/functional/tools/identifier_collection.xml
M test/functional/tools/samples_tool_conf.xml
A test/integration/chained_dyndest_job_conf.xml
A test/integration/chained_dyndest_rules/__init__.py
A test/integration/chained_dyndest_rules/module1/__init__.py
A test/integration/chained_dyndest_rules/module1/rules.py
A test/integration/chained_dyndest_rules/module2/__init__.py
A test/integration/chained_dyndest_rules/module2/rules.py
A test/integration/chained_dyndest_rules/module3/__init__.py
A test/integration/chained_dyndest_rules/module3/rules.py
A test/integration/resubmission_tool_detected_always_error_job_conf.xml
A test/integration/resubmission_tool_detected_resubmit_job_conf.xml
A test/integration/test_chained_dynamic_destinations.py
M test/integration/test_dockerized_jobs.py
M test/integration/test_job_resubmission.py
A test/integration/test_workflow_sync.py
M test/unit/jobs/test_mapper.py
M test/unit/jobs/test_rules/10_site.py
A test/unit/jobs/test_rules_override/10_rule.py
A test/unit/jobs/test_rules_override/__init__.py
M test/unit/jobs/test_runner_local.py
M test/unit/test_galaxy_mapping.py
M test/unit/tools/test_parameter_parsing.py
M test/unit/tools/test_wrappers.py
M test/unit/unittest_utils/galaxy_mock.py
M test/unit/workflows/test_modules.py
M test/unit/workflows/test_render.py
M test/unit/workflows/test_workflow_progress.py
M test/unit/workflows/workflow_support.py
R tools/data_source/bed_convert.xml
M tools/data_source/genbank.xml
M tools/data_source/upload.xml
M tools/extract/liftOver_wrapper.xml
M tools/filters/CreateInterval.xml
M tools/filters/bed_to_bigbed.xml
M tools/filters/changeCase.xml
M tools/filters/fileGrep.xml
M tools/filters/fixedValueColumn.xml
M tools/filters/gff/gff_filter_by_attribute.xml
M tools/filters/gff/gff_filter_by_feature_count.xml
M tools/filters/grep.xml
M tools/filters/headWrapper.xml
M tools/filters/joiner.xml
M tools/filters/randomlines.xml
M tools/filters/remove_beginning.xml
M tools/filters/tailWrapper.xml
M tools/filters/wig_to_bigwig.xml
M tools/maf/vcf_to_maf_customtrack.xml
M tools/metag_tools/blat_wrapper.xml
M tools/metag_tools/shrimp_color_wrapper.xml
M tools/metag_tools/shrimp_wrapper.xml
M tools/plotting/bar_chart.xml
M tools/plotting/boxplot.xml
M tools/solid_tools/maq_cs_wrapper.xml
M tools/sr_mapping/PerM.xml
M tools/sr_mapping/bfast_wrapper.xml
M tools/stats/filtering.xml
M tools/stats/grouping.py
M tools/stats/grouping.xml
M tools/stats/gsummary.xml
M tools/stats/gsummary.xml.groups
Log Message:
-----------
Merge remote-tracking branch 'jmchilton/dev' into topic/reclaim_failed
Commit: 1caf7f4bab428a8c7d3d132b60e90b8ce0cb9f86
https://github.com/galaxyproject/galaxy/commit/1caf7f4bab428a8c7d3d132b60e9…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-12-14 (Fri, 14 Dec 2018)
Changed paths:
M lib/galaxy/jobs/runners/__init__.py
M test/unit/jobs/test_runner_local.py
Log Message:
-----------
Merge pull request #6996 from bernt-matthias/topic/reclaim_failed
reclaim ownership for failed jobs
Compare: https://github.com/galaxyproject/galaxy/compare/e7c333a211b4...1caf7f4bab42
**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.
Branch: refs/heads/biostar-to-discourse
Home: https://github.com/galaxyproject/usegalaxy-playbook
Commit: 61e73cb8800e5b722eb6eb81e5cb41eccb482d15
https://github.com/galaxyproject/usegalaxy-playbook/commit/61e73cb8800e5b72…
Author: tnabtaf <clements(a)galaxyproject.org>
Date: 2018-12-14 (Fri, 14 Dec 2018)
Changed paths:
R env/common/files/galaxy/static/welcome_img/201511_France.png
R env/common/files/galaxy/static/welcome_img/50PlusPublic.png
R env/common/files/galaxy/static/welcome_img/60PlusOdometer1.png
R env/common/files/galaxy/static/welcome_img/70PlusOdometer.png
R env/common/files/galaxy/static/welcome_img/80PlusOdometer.png
R env/common/files/galaxy/static/welcome_img/Ballaxy.png
R env/common/files/galaxy/static/welcome_img/Barcelona_2015.png
R env/common/files/galaxy/static/welcome_img/CARTGalaxy.png
R env/common/files/galaxy/static/welcome_img/CPTGalaxy.png
R env/common/files/galaxy/static/welcome_img/CoSSci.png
R env/common/files/galaxy/static/welcome_img/EDGW2017.jpg
R env/common/files/galaxy/static/welcome_img/ErasmusGalaxy.png
R env/common/files/galaxy/static/welcome_img/EuropeFall2014.png
R env/common/files/galaxy/static/welcome_img/EuropeFall2014_2.png
R env/common/files/galaxy/static/welcome_img/FROGGalaxy.png
R env/common/files/galaxy/static/welcome_img/G3_2014_v2.png
R env/common/files/galaxy/static/welcome_img/GAMe2017.png
R env/common/files/galaxy/static/welcome_img/GAMe2017RegisterNow.png
R env/common/files/galaxy/static/welcome_img/GAMe2017TalkAbstracts.png
R env/common/files/galaxy/static/welcome_img/GAT2016EarlyReg.png
R env/common/files/galaxy/static/welcome_img/GAT2016OntimeReg.png
R env/common/files/galaxy/static/welcome_img/GCC2014.png
R env/common/files/galaxy/static/welcome_img/GCC2014AvoidLate.png
R env/common/files/galaxy/static/welcome_img/GCC2014Flag.png
R env/common/files/galaxy/static/welcome_img/GCC2014RegisterNow.png
R env/common/files/galaxy/static/welcome_img/GCC2015.png
R env/common/files/galaxy/static/welcome_img/GCC2015AbstractsOpen.png
R env/common/files/galaxy/static/welcome_img/GCC2015EarlyReg.png
R env/common/files/galaxy/static/welcome_img/GCC2015PostersDue.png
R env/common/files/galaxy/static/welcome_img/GCC2015SaveTheseDates.png
R env/common/files/galaxy/static/welcome_img/GCC2015Scholarships.png
R env/common/files/galaxy/static/welcome_img/GCC2015TrainingDayVote.png
R env/common/files/galaxy/static/welcome_img/GCC2016.png
R env/common/files/galaxy/static/welcome_img/GCC2016CUBloominton.png
R env/common/files/galaxy/static/welcome_img/GCC2016June4Deadlines.png
R env/common/files/galaxy/static/welcome_img/GCC2016May20Deadlines.png
R env/common/files/galaxy/static/welcome_img/GCC2016OralAbstracts.png
R env/common/files/galaxy/static/welcome_img/GCC2016OralAbstractsDueApril8.png
R env/common/files/galaxy/static/welcome_img/GCC2016ScholarshipsDomestic.png
R env/common/files/galaxy/static/welcome_img/GCC2016ScholarshipsInternational.png
R env/common/files/galaxy/static/welcome_img/GCC2016TrNom.png
R env/common/files/galaxy/static/welcome_img/GCC2016TrVote.png
R env/common/files/galaxy/static/welcome_img/GCC2017.png
R env/common/files/galaxy/static/welcome_img/GCC2017EarlyReg.png
R env/common/files/galaxy/static/welcome_img/GCUKisLive.png
R env/common/files/galaxy/static/welcome_img/GTN.png
R env/common/files/galaxy/static/welcome_img/GalaxEast.png
R env/common/files/galaxy/static/welcome_img/GalaxyAdmins201502.png
R env/common/files/galaxy/static/welcome_img/GalaxyCast1.png
R env/common/files/galaxy/static/welcome_img/GalaxyIFBDay2014.png
R env/common/files/galaxy/static/welcome_img/GalaxyQuest1.png
R env/common/files/galaxy/static/welcome_img/ISMB2014.png
R env/common/files/galaxy/static/welcome_img/ISMBECCB2017Tutorial.png
R env/common/files/galaxy/static/welcome_img/ImmPortGalaxy.png
R env/common/files/galaxy/static/welcome_img/LookingToLearn.png
R env/common/files/galaxy/static/welcome_img/MBAC.png
R env/common/files/galaxy/static/welcome_img/MPI-HLR-Galaxy.png
R env/common/files/galaxy/static/welcome_img/MississippiGalaxy.png
R env/common/files/galaxy/static/welcome_img/PAG2017.png
R env/common/files/galaxy/static/welcome_img/PIAGalaxy.png
R env/common/files/galaxy/static/welcome_img/PRABIGalaxy.png
R env/common/files/galaxy/static/welcome_img/PreSTIGEGalaxy.png
R env/common/files/galaxy/static/welcome_img/RDF2GraphGalaxy.png
R env/common/files/galaxy/static/welcome_img/RNA-Seq-Portal.png
R env/common/files/galaxy/static/welcome_img/RepeatExplorer.png
R env/common/files/galaxy/static/welcome_img/Riboseq.png
R env/common/files/galaxy/static/welcome_img/SG2016.png
R env/common/files/galaxy/static/welcome_img/SlipStreamSlide.png
R env/common/files/galaxy/static/welcome_img/SupAgro201502.png
R env/common/files/galaxy/static/welcome_img/VSU.png
R env/common/files/galaxy/static/welcome_img/VideosAreBack.png
R env/common/files/galaxy/static/welcome_img/WhaleSharkGalaxy.png
R env/common/files/galaxy/static/welcome_img/ZBIT.png
A env/common/files/galaxy/static/welcome_img/admin-training-adv-reg.png
R env/common/files/galaxy/static/welcome_img/deepTools.png
R env/common/files/galaxy/static/welcome_img/emory_logo.png
R env/common/files/galaxy/static/welcome_img/gccbosc2018.png
R env/common/files/galaxy/static/welcome_img/gccbosc2018_ext.png
R env/common/files/galaxy/static/welcome_img/kmerSVMGalaxy.png
R env/common/files/galaxy/static/welcome_img/peaks-to-genes-300.png
A env/common/files/galaxy/static/welcome_img/platform-dir.png
M env/common/templates/galaxy/static/welcome.html.j2
Log Message:
-----------
Updated slide rotation. Dropped a bunch of old images that aren't used anymore.
**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.