- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 975c8b: Fix activation of ``_galaxy_`` conda env
by GitHub 15 Dec '18

15 Dec '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 975c8b605fffb968106ec0d3e04569d8d8c70f44 https://github.com/galaxyproject/galaxy/commit/975c8b605fffb968106ec0d3e045… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-12-14 (Fri, 14 Dec 2018) Changed paths: M scripts/common_startup.sh M scripts/common_startup_functions.sh Log Message: ----------- Fix activation of ``_galaxy_`` conda env - Use `conda_activate`, which works also under dash - Run `conda_activate` also when `$GALAXY_CONDA_ENV` already exists - Run `virtualenv` when the conda env is active but `$GALAXY_VIRTUAL_ENV` does not exist - Update the default for `GALAXY_CONDA_ENV` in scripts/common_startup_functions.sh Follow-up on https://github.com/galaxyproject/galaxy/pull/6975 . Commit: 9dcb002505a1e2c38604ea8889fef40f41531fdd https://github.com/galaxyproject/galaxy/commit/9dcb002505a1e2c38604ea8889fe… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-12-15 (Sat, 15 Dec 2018) Changed paths: M scripts/common_startup.sh M scripts/common_startup_functions.sh Log Message: ----------- Merge pull request #7116 from nsoranzo/followup_on_6975 Fix activation of ``_galaxy_`` conda env Compare: https://github.com/galaxyproject/galaxy/compare/1caf7f4bab42...9dcb002505a1 **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.

1 0

[galaxyproject/galaxy] 876b46: reclaim ownership for failed jobs
by GitHub 14 Dec '18

14 Dec '18

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.

1 0

[galaxyproject/usegalaxy-playbook] f207ad: Add collection operations to test.
by GitHub 14 Dec '18

14 Dec '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: f207add6cb2c0484607560a8ace0bfd121360b6b https://github.com/galaxyproject/usegalaxy-playbook/commit/f207add6cb2c0484… Author: Dave B <dave(a)bx.psu.edu> Date: 2018-12-14 (Fri, 14 Dec 2018) Changed paths: M env/test/files/galaxy/config/tool_conf.xml Log Message: ----------- Add collection operations to test. **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.

1 0

[galaxyproject/usegalaxy-playbook] 61e73c: Updated slide rotation. Dropped a bunch of old ima...
by GitHub 14 Dec '18

14 Dec '18

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.

1 0

[galaxyproject/galaxy] baa7d7: Increase timeout on flakey unit test.
by GitHub 14 Dec '18

14 Dec '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: baa7d7ea8effb41bb04d73e1545e8259630eb9b0 https://github.com/galaxyproject/galaxy/commit/baa7d7ea8effb41bb04d73e1545e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-12-14 (Fri, 14 Dec 2018) Changed paths: M test/unit/tools/test_toolbox.py Log Message: ----------- Increase timeout on flakey unit test. Commit: e7c333a211b45909734ccb2c03105975937254f1 https://github.com/galaxyproject/galaxy/commit/e7c333a211b45909734ccb2c0310… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2018-12-14 (Fri, 14 Dec 2018) Changed paths: M test/unit/tools/test_toolbox.py Log Message: ----------- Merge pull request #7120 from jmchilton/unit_test_fix Increase timeout on flakey unit test. Compare: https://github.com/galaxyproject/galaxy/compare/40acf08a3cd0...e7c333a211b4 **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.

1 0

[galaxyproject/galaxy] 260fa8: Properly escape history names in scratchbook title...
by GitHub 14 Dec '18

14 Dec '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 260fa8b6d73f27ed97ebb273b6dfd17134fb8285 https://github.com/galaxyproject/galaxy/commit/260fa8b6d73f27ed97ebb273b6df… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-12-13 (Thu, 13 Dec 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-frames.js Log Message: ----------- Properly escape history names in scratchbook titles Commit: 40acf08a3cd0eda156fe17498ec5a2182a53fa8a https://github.com/galaxyproject/galaxy/commit/40acf08a3cd0eda156fe17498ec5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-12-14 (Fri, 14 Dec 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-frames.js Log Message: ----------- Merge pull request #7114 from guerler/escape_scratchbook_title Properly escape history names in scratchbook titles Compare: https://github.com/galaxyproject/galaxy/compare/7c2a0761de71...40acf08a3cd0 **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.

1 0

[galaxyproject/galaxy] 43a19a: Client watch referred to an old gulp task that is ...
by GitHub 13 Dec '18

13 Dec '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 43a19a05e3efbadca41a0aa38f06973157ce4563 https://github.com/galaxyproject/galaxy/commit/43a19a05e3efbadca41a0aa38f06… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-12-13 (Thu, 13 Dec 2018) Changed paths: M client/package.json Log Message: ----------- Client watch referred to an old gulp task that is no longer necessary. Commit: 7c2a0761de7128fe67258c0d2b842bfec4ced533 https://github.com/galaxyproject/galaxy/commit/7c2a0761de7128fe67258c0d2b84… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-12-13 (Thu, 13 Dec 2018) Changed paths: M client/package.json Log Message: ----------- Merge pull request #7113 from dannon/client-watch-fix Fix `make client-watch` extra error message. Compare: https://github.com/galaxyproject/galaxy/compare/c6355dfe1004...7c2a0761de71 **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.

1 0

[galaxyproject/galaxy] 48436d: Don't write outputs to object store twice.
by GitHub 13 Dec '18

13 Dec '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 48436d8efc50a1b7e7424fcc6cdd2a97775e0e01 https://github.com/galaxyproject/galaxy/commit/48436d8efc50a1b7e7424fcc6cdd… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-12-13 (Thu, 13 Dec 2018) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Don't write outputs to object store twice. Broken (?) in 009e2cbf5e9592fd8af782b2cde36d8d1687c003 by that moron @jmchilton Commit: c6355dfe10040fb0f02e08ed78373b216c7028fb https://github.com/galaxyproject/galaxy/commit/c6355dfe10040fb0f02e08ed7837… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-12-13 (Thu, 13 Dec 2018) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Merge pull request #7111 from jmchilton/seems_bad_but_okay Don't write outputs to object store twice. Compare: https://github.com/galaxyproject/galaxy/compare/1cb21fb55bac...c6355dfe1004 **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.

1 0

[galaxyproject/galaxy] 4b1d9d: Replace `credentials` with `authz_id`
by GitHub 12 Dec '18

12 Dec '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4b1d9df4d677a0db7a11f39490671567e95c45be https://github.com/galaxyproject/galaxy/commit/4b1d9df4d677a0db7a11f3949067… Author: Vahid <VJalili(a)users.noreply.github.com> Date: 2018-12-07 (Fri, 07 Dec 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/cloud.py Log Message: ----------- Replace `credentials` with `authz_id` on cloud storage get api doc string. Commit: 8ccad94bfa87dc4f6260010ac1cce5ce54a321e3 https://github.com/galaxyproject/galaxy/commit/8ccad94bfa87dc4f6260010ac1cc… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-12-12 (Wed, 12 Dec 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/cloud.py Log Message: ----------- Merge pull request #7088 from VJalili/patch-5 Replace `credentials` with `authz_id` Compare: https://github.com/galaxyproject/galaxy/compare/476be87f9220...8ccad94bfa87 **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.

1 0

[galaxyproject/galaxy] 53c378: drmaa: soft catch of external runner fails
by GitHub 12 Dec '18

12 Dec '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 53c3785986f68b5d65ec037381568a1092adbccb https://github.com/galaxyproject/galaxy/commit/53c3785986f68b5d65ec03738156… Author: M Bernt <m.bernt(a)ufz.de> Date: 2018-11-14 (Wed, 14 Nov 2018) Changed paths: M lib/galaxy/jobs/runners/drmaa.py Log Message: ----------- drmaa: soft catch of external runner fails Commit: b0bc14a90524a01a162f803b5604cbb361dac386 https://github.com/galaxyproject/galaxy/commit/b0bc14a90524a01a162f803b5604… Author: M Bernt <m.bernt(a)ufz.de> Date: 2018-11-16 (Fri, 16 Nov 2018) Changed paths: M lib/galaxy/jobs/runners/drmaa.py Log Message: ----------- drmaa: make external_runjob return stripped stdio Commit: 476be87f9220e63db4aefa5933444c44d608974b https://github.com/galaxyproject/galaxy/commit/476be87f9220e63db4aefa593344… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-12-12 (Wed, 12 Dec 2018) Changed paths: M lib/galaxy/jobs/runners/drmaa.py Log Message: ----------- Merge pull request #6997 from bernt-matthias/topic/drmaa-soft-external-runner drmaa: soft catch of external runner fails Compare: https://github.com/galaxyproject/galaxy/compare/7bed9f031808...476be87f9220 **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.

1 0

[galaxyproject/galaxy] 355b48: Make handler assignment configurable in preparatio...
by GitHub 12 Dec '18

12 Dec '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 355b48c361e68a7d9fbe9fe86de7aa2313e5d608 https://github.com/galaxyproject/galaxy/commit/355b48c361e68a7d9fbe9fe86de7… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-12-10 (Mon, 10 Dec 2018) Changed paths: M lib/galaxy/app.py M lib/galaxy/config.py M lib/galaxy/exceptions/__init__.py M lib/galaxy/exceptions/error_codes.json M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/handler.py M lib/galaxy/jobs/manager.py M lib/galaxy/managers/datasets.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/actions/history_imp_exp.py M lib/galaxy/tools/actions/metadata.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/util/handlers.py M lib/galaxy/web/stack/__init__.py M lib/galaxy/web/stack/transport.py M lib/galaxy/webapps/galaxy/api/jobs.py M lib/galaxy/webapps/galaxy/config_schema.yml M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/workflow/scheduling_manager.py M test/unit/jobs/test_job_configuration.py M test/unit/tools/test_actions.py M test/unit/unittest_utils/galaxy_mock.py Log Message: ----------- Make handler assignment configurable in preparation for new assignment methods. Commit: 10c45705bca081c336214b08fcc84d209b19b345 https://github.com/galaxyproject/galaxy/commit/10c45705bca081c336214b08fcc8… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-12-10 (Mon, 10 Dec 2018) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/util/facts.py M lib/galaxy/util/handlers.py M lib/galaxy/web/stack/__init__.py M lib/galaxy/workflow/scheduling_manager.py A test/unit/jobs/handler_template_job_conf.xml M test/unit/jobs/test_job_configuration.py Log Message: ----------- Unit tests and fixes for bugs discovered while testing. Commit: 1fb8203a0c1f6f941e0b13fa6357ec04ea677ffb https://github.com/galaxyproject/galaxy/commit/1fb8203a0c1f6f941e0b13fa6357… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-12-10 (Mon, 10 Dec 2018) Changed paths: M config/galaxy.yml.sample M config/job_conf.xml.sample_advanced M config/workflow_schedulers_conf.xml.sample M doc/source/admin/galaxy_options.rst M doc/source/admin/jobs.md M doc/source/admin/scaling.md M lib/galaxy/jobs/manager.py M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- Handler assignment documentation. Commit: 40f776afde460759b5d682c19ef698fefd2d4388 https://github.com/galaxyproject/galaxy/commit/40f776afde460759b5d682c19ef6… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-12-11 (Tue, 11 Dec 2018) Changed paths: M lib/galaxy/jobs/manager.py M lib/galaxy/util/handlers.py M test/unit/jobs/handler_template_job_conf.xml M test/unit/jobs/test_job_configuration.py Log Message: ----------- Fix tests broken with changes to job_conf.xml.sample_advanced, fix the broken direct handler assignment method, document the new handler assignment methods for future method authors. Ensure that enqueue does its best to return a handler (if known). Commit: 4a006335ac4ac84a69b5cb1f851e3e63400443ae https://github.com/galaxyproject/galaxy/commit/4a006335ac4ac84a69b5cb1f851e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-12-11 (Tue, 11 Dec 2018) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Fix default job config (no job_conf.xml). Commit: e9aec176fac8bb3681ea533be6178ffd43c3bf4d https://github.com/galaxyproject/galaxy/commit/e9aec176fac8bb3681ea533be617… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-12-11 (Tue, 11 Dec 2018) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/workflow/scheduling_manager.py Log Message: ----------- Fixes for workflow scheduling tests. Commit: 7bed9f03180826f7c7f99b12b08bcb265867217b https://github.com/galaxyproject/galaxy/commit/7bed9f03180826f7c7f99b12b08b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-12-12 (Wed, 12 Dec 2018) Changed paths: M config/galaxy.yml.sample M config/job_conf.xml.sample_advanced M config/workflow_schedulers_conf.xml.sample M doc/source/admin/galaxy_options.rst M doc/source/admin/jobs.md M doc/source/admin/scaling.md M lib/galaxy/app.py M lib/galaxy/config.py M lib/galaxy/exceptions/__init__.py M lib/galaxy/exceptions/error_codes.json M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/handler.py M lib/galaxy/jobs/manager.py M lib/galaxy/managers/datasets.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/actions/history_imp_exp.py M lib/galaxy/tools/actions/metadata.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/util/facts.py M lib/galaxy/util/handlers.py M lib/galaxy/web/stack/__init__.py M lib/galaxy/web/stack/transport.py M lib/galaxy/webapps/galaxy/api/jobs.py M lib/galaxy/webapps/galaxy/config_schema.yml M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/workflow/scheduling_manager.py A test/unit/jobs/handler_template_job_conf.xml M test/unit/jobs/test_job_configuration.py M test/unit/tools/test_actions.py M test/unit/unittest_utils/galaxy_mock.py Log Message: ----------- Merge pull request #7091 from natefoo/handler-assignment-fixes Configurable job/workflow handler assignment methods Compare: https://github.com/galaxyproject/galaxy/compare/1fd3fccb216b...7bed9f031808 **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.

1 0

[galaxyproject/galaxy] 0c145b: Updated Neo4j IE to 3.1.9
by GitHub 12 Dec '18

12 Dec '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 0c145b3326f2476b05ed8ca7ee66d754099a452f https://github.com/galaxyproject/galaxy/commit/0c145b3326f2476b05ed8ca7ee66… Author: thobalose <lose.thoba(a)gmail.com> Date: 2018-10-18 (Thu, 18 Oct 2018) Changed paths: M config/plugins/interactive_environments/neo/config/allowed_images.yml.sample M config/plugins/interactive_environments/neo/config/neo.ini.sample M config/plugins/interactive_environments/neo/templates/neo.mako Log Message: ----------- Updated Neo4j IE to 3.1.9 Commit: 2da38803a3bc12a19e1fa53a1e8cc9e9448eb1b6 https://github.com/galaxyproject/galaxy/commit/2da38803a3bc12a19e1fa53a1e8c… Author: thobalose <lose.thoba(a)gmail.com> Date: 2018-10-18 (Thu, 18 Oct 2018) Changed paths: M lib/galaxy/visualization/plugins/interactive_environments.py Log Message: ----------- Catering for shlex.split(cmd_inject) behaviour Commit: 1fd3fccb216bcfab298e2cfd812f2ec3b3e45afe https://github.com/galaxyproject/galaxy/commit/1fd3fccb216bcfab298e2cfd812f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-12-12 (Wed, 12 Dec 2018) Changed paths: M config/plugins/interactive_environments/neo/config/allowed_images.yml.sample M config/plugins/interactive_environments/neo/config/neo.ini.sample M lib/galaxy/visualization/plugins/interactive_environments.py Log Message: ----------- Merge pull request #6897 from thobalose/neo4j-ie Catered for shlex.split(command_inject) and updated Neo4j IE to v3.1.9 Compare: https://github.com/galaxyproject/galaxy/compare/bf550da2afe9...1fd3fccb216b **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.

1 0

[galaxyproject/galaxy] 952fda: Remove unused and broken tool
by GitHub 12 Dec '18

12 Dec '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 952fdac419e9b4123c158fd088f90a9a09bc7fd3 https://github.com/galaxyproject/galaxy/commit/952fdac419e9b4123c158fd088f9… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-09-10 (Mon, 10 Sep 2018) Changed paths: R tools/data_source/bed_convert.xml Log Message: ----------- Remove unused and broken tool Commit: f865e8359fa6c8d599011edcea61a2a728afb9ea https://github.com/galaxyproject/galaxy/commit/f865e8359fa6c8d599011edcea61… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-09-10 (Mon, 10 Sep 2018) Changed paths: M config/job_resource_params_conf.xml.sample M config/workflow_resource_params_conf.xml.sample M lib/galaxy/tools/parameters/validation.py M lib/galaxy/tools/xsd/galaxy.xsd M test/functional/tools/for_workflows/head.xml M test/unit/tools/test_wrappers.py 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/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/gsummary.xml M tools/stats/gsummary.xml.groups Log Message: ----------- Deprecate `size` attribute of `<param/>` and remove it from tools Also: - dos2unix test/functional/tools/for_workflows/head.xml - Single-quote text and data params in `<command/>` - Remove deprecated `interpreter` attribute of `<command />` Commit: bf550da2afe94ad53aae71e3d930a49cb98558a4 https://github.com/galaxyproject/galaxy/commit/bf550da2afe94ad53aae71e3d930… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-12-12 (Wed, 12 Dec 2018) Changed paths: M config/job_resource_params_conf.xml.sample M config/workflow_resource_params_conf.xml.sample M lib/galaxy/tools/parameters/validation.py M lib/galaxy/tools/xsd/galaxy.xsd M test/functional/tools/for_workflows/head.xml M test/unit/tools/test_wrappers.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/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/gsummary.xml M tools/stats/gsummary.xml.groups Log Message: ----------- Merge pull request #6684 from nsoranzo/deprecate_param_size Deprecate `size` attribute of `<param/>` and remove it from tools Compare: https://github.com/galaxyproject/galaxy/compare/d06718ef2420...bf550da2afe9 **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.

1 0

[galaxyproject/galaxy] 7b027d: improved grouping
by GitHub 12 Dec '18

12 Dec '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 7b027d8a1fbed0b5471f774fe3d3a3cab123093f https://github.com/galaxyproject/galaxy/commit/7b027d8a1fbed0b5471f774fe3d3… Author: M Bernt <m.bernt(a)ufz.de> Date: 2018-09-10 (Mon, 10 Sep 2018) Changed paths: M tools/stats/grouping.py M tools/stats/grouping.xml Log Message: ----------- improved grouping - replaces non 'floatable' values to a user supplied default value - do not strip lines because this removes empty cells at the ends - added some comments to python code Commit: d06718ef24202d2fcaf3d6e8bfaa9a862044f90f https://github.com/galaxyproject/galaxy/commit/d06718ef24202d2fcaf3d6e8bfaa… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-12-12 (Wed, 12 Dec 2018) Changed paths: M tools/stats/grouping.py M tools/stats/grouping.xml Log Message: ----------- Merge pull request #6577 from bernt-matthias/topic/grouping-wreplace improved grouping tool Compare: https://github.com/galaxyproject/galaxy/compare/c6fc4dc83a6a...d06718ef2420 **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.

1 0

[galaxyproject/galaxy] e5c9d9: Fix ``size_to_bytes`` for some float values
by GitHub 12 Dec '18

12 Dec '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e5c9d9673d6d92291b7911f4255cbbafebceed0e https://github.com/galaxyproject/galaxy/commit/e5c9d9673d6d92291b7911f4255c… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-12-12 (Wed, 12 Dec 2018) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Fix ``size_to_bytes`` for some float values Values like `.01` and `1.` were broken in commit 26a6b1c83381d1c75131f330d8b8f4c23680f1dd . The new regexp allows also scientific notation like `1.2E2` . Commit: c6fc4dc83a6ac46244ff05d560864cba1de8bf55 https://github.com/galaxyproject/galaxy/commit/c6fc4dc83a6ac46244ff05d56086… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-12-12 (Wed, 12 Dec 2018) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Merge pull request #7096 from nsoranzo/followup_on_7067 Fix ``size_to_bytes`` for some float values Compare: https://github.com/galaxyproject/galaxy/compare/0b0c0084198d...c6fc4dc83a6a **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.

1 0

[galaxyproject/galaxy] c4ab2a: Add workaround for https://github.com/travis-ci/tr...
by GitHub 11 Dec '18

11 Dec '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c4ab2a0c6bb768fe27b48648d21ab42733133c08 https://github.com/galaxyproject/galaxy/commit/c4ab2a0c6bb768fe27b48648d21a… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-12-11 (Tue, 11 Dec 2018) Changed paths: M .travis.yml Log Message: ----------- Add workaround for https://github.com/travis-ci/travis-ci/issues/7940 Commit: 3a1bdd0ea688948db9115a500224c5947c326e99 https://github.com/galaxyproject/galaxy/commit/3a1bdd0ea688948db9115a500224… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-12-11 (Tue, 11 Dec 2018) Changed paths: M .travis.yml Log Message: ----------- Merge pull request #7092 from martenson/boto-workaround [18.09] boto cfg workaround Commit: 0b0c0084198d59e5767decb9b79580cc2a3932b2 https://github.com/galaxyproject/galaxy/commit/0b0c0084198d59e5767decb9b795… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-12-12 (Wed, 12 Dec 2018) Log Message: ----------- Merge branch 'release_18.09' into dev Compare: https://github.com/galaxyproject/galaxy/compare/10aa953a40e1...0b0c0084198d **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.

1 0

[galaxyproject/galaxy] c4ab2a: Add workaround for https://github.com/travis-ci/tr...
by GitHub 11 Dec '18

11 Dec '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: c4ab2a0c6bb768fe27b48648d21ab42733133c08 https://github.com/galaxyproject/galaxy/commit/c4ab2a0c6bb768fe27b48648d21a… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-12-11 (Tue, 11 Dec 2018) Changed paths: M .travis.yml Log Message: ----------- Add workaround for https://github.com/travis-ci/travis-ci/issues/7940 Commit: 3a1bdd0ea688948db9115a500224c5947c326e99 https://github.com/galaxyproject/galaxy/commit/3a1bdd0ea688948db9115a500224… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-12-11 (Tue, 11 Dec 2018) Changed paths: M .travis.yml Log Message: ----------- Merge pull request #7092 from martenson/boto-workaround [18.09] boto cfg workaround Compare: https://github.com/galaxyproject/galaxy/compare/57459954de18...3a1bdd0ea688 **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.

1 0

[galaxyproject/usegalaxy-playbook] 55bd75: Update TTS
by GitHub 11 Dec '18

11 Dec '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 55bd75a7ce10d1088e75a799b5ec6e025c9a67df https://github.com/galaxyproject/usegalaxy-playbook/commit/55bd75a7ce10d108… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-12-11 (Tue, 11 Dec 2018) Changed paths: M env/testtoolshed/group_vars/toolshedservers/vars.yml Log Message: ----------- Update TTS **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.

1 0

[galaxyproject/galaxy] 2de4a0: Remove legacy job handling hacks.
by GitHub 11 Dec '18

11 Dec '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 2de4a0f72e5d51661318e1abeb727fdaa10f7444 https://github.com/galaxyproject/galaxy/commit/2de4a0f72e5d51661318e1abeb72… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-12-07 (Fri, 07 Dec 2018) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy_ext/metadata/set_metadata.py Log Message: ----------- Remove legacy job handling hacks. These were left in to let Galaxy jobs complete after version upgrades, but the plan was always to remove them eventually. Commit: 10aa953a40e171246bdd1804c74e8019da8e8200 https://github.com/galaxyproject/galaxy/commit/10aa953a40e171246bdd1804c74e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-12-11 (Tue, 11 Dec 2018) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy_ext/metadata/set_metadata.py Log Message: ----------- Merge pull request #7082 from jmchilton/legacy_hacks Remove legacy job handling hacks. Compare: https://github.com/galaxyproject/galaxy/compare/11428a03b819...10aa953a40e1 **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.

1 0

[galaxyproject/usegalaxy-playbook] 3ae75e: Update MTS
by GitHub 11 Dec '18

11 Dec '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 3ae75e93d54584e6d250f745f6d1a176cf73ba22 https://github.com/galaxyproject/usegalaxy-playbook/commit/3ae75e93d54584e6… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-12-11 (Tue, 11 Dec 2018) Changed paths: M env/toolshed/group_vars/toolshedservers/vars.yml Log Message: ----------- Update MTS **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.

1 0

[galaxyproject/galaxy] 9bac3c: Path-aware workflows.
by GitHub 07 Dec '18

07 Dec '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 9bac3c44faf51e0e4c396d7f1d3470f7aa4a588e https://github.com/galaxyproject/galaxy/commit/9bac3c44faf51e0e4c396d7f1d34… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-11-20 (Tue, 20 Nov 2018) Changed paths: M lib/galaxy/managers/workflows.py M lib/galaxy/model/mapping.py A lib/galaxy/model/migrate/versions/0146_workflow_paths.py M lib/galaxy/web/base/controller.py M lib/galaxy/webapps/galaxy/api/workflows.py M test/api/test_workflows.py M test/base/populators.py M test/base/workflow_fixtures.py M test/integration/test_dockerized_jobs.py A test/integration/test_workflow_sync.py Log Message: ----------- Path-aware workflows. - Allow workflows to be uploaded via path using the GUI and and API for admins. - Track the path and resync workflows on save (both .ga and format 2 workflows) - this will allow Planemo to leverage the Galaxy workflow editor to interactively save workflows. Commit: 11428a03b8193ff50c35d9dd7069789ca2ba6cc7 https://github.com/galaxyproject/galaxy/commit/11428a03b8193ff50c35d9dd7069… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-12-07 (Fri, 07 Dec 2018) Changed paths: M lib/galaxy/managers/workflows.py M lib/galaxy/model/mapping.py A lib/galaxy/model/migrate/versions/0146_workflow_paths.py M lib/galaxy/web/base/controller.py M lib/galaxy/webapps/galaxy/api/workflows.py M test/api/test_workflows.py M test/base/populators.py M test/base/workflow_fixtures.py M test/integration/test_dockerized_jobs.py A test/integration/test_workflow_sync.py Log Message: ----------- Merge pull request #7019 from jmchilton/path-aware-workflows File-based Workflow Editor Compare: https://github.com/galaxyproject/galaxy/compare/ad42f9410204...11428a03b819 **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.

1 0

[galaxyproject/usegalaxy-playbook] 60fbfd: Remove older and insecure versions of SRA tools.
by GitHub 07 Dec '18

07 Dec '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 60fbfd0e4349e3b623d7dc963d03729843c415cd https://github.com/galaxyproject/usegalaxy-playbook/commit/60fbfd0e4349e3b6… Author: Dave B <dave(a)bx.psu.edu> Date: 2018-12-07 (Fri, 07 Dec 2018) Changed paths: M env/main/files/galaxy/var/integrated_tool_panel.xml M env/main/files/galaxy/var/shed_tool_conf.xml Log Message: ----------- Remove older and insecure versions of SRA tools. **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.

1 0

[galaxyproject/galaxy] 83417c: Add styled loader vue component
by GitHub 07 Dec '18

07 Dec '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 83417cab622309f9b53d8881c6946bc11e6cb3ba https://github.com/galaxyproject/galaxy/commit/83417cab622309f9b53d8881c694… Author: Ivan Kuzmin <inkuzm(a)gmail.com> Date: 2018-11-28 (Wed, 28 Nov 2018) Changed paths: A client/galaxy/scripts/components/GalaxyLoader.vue Log Message: ----------- Add styled loader vue component Commit: ad42f94102048a4c3a3695aaf88a333794aef0f7 https://github.com/galaxyproject/galaxy/commit/ad42f94102048a4c3a3695aaf88a… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-12-07 (Fri, 07 Dec 2018) Changed paths: A client/galaxy/scripts/components/GalaxyLoader.vue Log Message: ----------- Merge pull request #7052 from inkuzmin/dev Add styled loader vue component Compare: https://github.com/galaxyproject/galaxy/compare/1ca77d53ef2b...ad42f9410204 **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.

1 0

[galaxyproject/galaxy] c4c8af: doc: updated error parsing docs
by GitHub 07 Dec '18

07 Dec '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c4c8af036fda560d5340e77d9f38782754729eb1 https://github.com/galaxyproject/galaxy/commit/c4c8af036fda560d5340e77d9f38… Author: M Bernt <m.bernt(a)ufz.de> Date: 2018-11-27 (Tue, 27 Nov 2018) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- doc: updated error parsing docs see https://github.com/galaxyproject/galaxy/pull/697://github.com/galaxyproject… Commit: 1ca77d53ef2bc1067db5c3a3b5d1c36b28aeaa1b https://github.com/galaxyproject/galaxy/commit/1ca77d53ef2bc1067db5c3a3b5d1… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-12-07 (Fri, 07 Dec 2018) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Merge pull request #7049 from bernt-matthias/topic/doc-errors-detection doc: updated error parsing docs Compare: https://github.com/galaxyproject/galaxy/compare/f09d7b7d9346...1ca77d53ef2b **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.

1 0

[galaxyproject/galaxy] 5c384e: Fix via refactor set_metadata so more output metad...
by GitHub 07 Dec '18

07 Dec '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 5c384efb8d2ad42d6dfafa84fc09bc02d3f462e8 https://github.com/galaxyproject/galaxy/commit/5c384efb8d2ad42d6dfafa84fc09… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-12-07 (Fri, 07 Dec 2018) Changed paths: M lib/galaxy_ext/metadata/set_metadata.py Log Message: ----------- Fix via refactor set_metadata so more output metadata pruned properly. Commit: f09d7b7d93463590dc8434376260248d0f3d4171 https://github.com/galaxyproject/galaxy/commit/f09d7b7d93463590dc8434376260… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-12-07 (Fri, 07 Dec 2018) Changed paths: M lib/galaxy_ext/metadata/set_metadata.py Log Message: ----------- Merge pull request #7084 from jmchilton/fix_set_metadata Fix via refactor set_metadata so more output metadata pruned properly. Compare: https://github.com/galaxyproject/galaxy/compare/e8d2b334a03c...f09d7b7d9346 **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.

1 0