Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 356d949199359a974a96d531db0dc39d97007df6
https://github.com/galaxyproject/galaxy/commit/356d949199359a974a96d531db0d…
Author: Nuwan Goonasekera <2070605+nuwang(a)users.noreply.github.com>
Date: 2018-11-28 (Wed, 28 Nov 2018)
Changed paths:
M lib/galaxy/jobs/runners/pulsar.py
Log Message:
-----------
Allow pulsar jobs to be resubmitted on connection failures
Commit: 263d10ca1c7577f3138df83f19468c1c20b85ea0
https://github.com/galaxyproject/galaxy/commit/263d10ca1c7577f3138df83f1946…
Author: Nuwan Goonasekera <2070605+nuwang(a)users.noreply.github.com>
Date: 2018-11-28 (Wed, 28 Nov 2018)
Changed paths:
A test/integration/resubmission_pulsar_job_conf.xml
M test/integration/test_job_resubmission.py
Log Message:
-----------
Added test for pulsar resubmission
Commit: 2632c071cdf1f6f49c30d243eea4931ee6fcaab2
https://github.com/galaxyproject/galaxy/commit/2632c071cdf1f6f49c30d243eea4…
Author: Nuwan Goonasekera <2070605+nuwang(a)users.noreply.github.com>
Date: 2018-11-28 (Wed, 28 Nov 2018)
Changed paths:
M lib/galaxy/jobs/mapper.py
M test/unit/jobs/test_mapper.py
M test/unit/jobs/test_rules/10_site.py
Log Message:
-----------
Added referrer parameter for dynamic destinations + test
Commit: cd119d641ad59a9da008875b5c32f20127bcbd65
https://github.com/galaxyproject/galaxy/commit/cd119d641ad59a9da008875b5c32…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-12-21 (Fri, 21 Dec 2018)
Changed paths:
M client/README.md
M client/galaxy/scripts/app/singleton.js
M client/galaxy/scripts/apps/analysis.js
A client/galaxy/scripts/components/GalaxyLoader.vue
M client/galaxy/scripts/layout/menu.js
M client/galaxy/scripts/layout/panel.js
M client/galaxy/scripts/mvc/collection/collection-li.js
M client/galaxy/scripts/mvc/collection/collection-view.js
M client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js
M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js
M client/galaxy/scripts/mvc/dataset/dataset-li.js
M client/galaxy/scripts/mvc/history/hdca-li.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/list/list-item.js
M client/galaxy/scripts/mvc/list/list-view.js
M client/galaxy/scripts/mvc/tool/tool-form.js
M client/galaxy/scripts/mvc/ui/ui-frames.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/package.json
M config/datatypes_conf.xml.sample
M config/galaxy.yml.sample
M config/job_conf.xml.sample_advanced
M config/job_resource_params_conf.xml.sample
M config/plugins/interactive_environments/neo/config/allowed_images.yml.sample
M config/plugins/interactive_environments/neo/config/neo.ini.sample
M config/tool_conf.xml.sample
M config/workflow_resource_params_conf.xml.sample
M config/workflow_schedulers_conf.xml.sample
M doc/source/admin/framework_dependencies.rst
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/datatypes/binary.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/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/jobs/runners/__init__.py
M lib/galaxy/jobs/runners/drmaa.py
M lib/galaxy/jobs/runners/pulsar.py
M lib/galaxy/managers/configuration.py
M lib/galaxy/managers/datasets.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/0145_add_workflow_step_input.py
A lib/galaxy/model/migrate/versions/0146_workflow_paths.py
M lib/galaxy/objectstore/__init__.py
M lib/galaxy/objectstore/azure_blob.py
M lib/galaxy/objectstore/cloud.py
M lib/galaxy/objectstore/pithos.py
M lib/galaxy/objectstore/s3.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/tools/deps/singularity_util.py
M lib/galaxy/tools/filter_from_file.xml
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/verify/__init__.py
M lib/galaxy/tools/xsd/galaxy.xsd
M lib/galaxy/util/__init__.py
M lib/galaxy/util/facts.py
M lib/galaxy/util/handlers.py
M lib/galaxy/visualization/plugins/interactive_environments.py
M lib/galaxy/web/base/controller.py
M lib/galaxy/web/stack/__init__.py
M lib/galaxy/web/stack/transport.py
M lib/galaxy/webapps/galaxy/api/cloud.py
M lib/galaxy/webapps/galaxy/api/jobs.py
M lib/galaxy/webapps/galaxy/api/workflows.py
M lib/galaxy/webapps/galaxy/config_schema.yml
M lib/galaxy/webapps/galaxy/controllers/admin.py
M lib/galaxy/webapps/galaxy/controllers/dataset.py
M lib/galaxy/webapps/galaxy/controllers/history.py
M lib/galaxy/workflow/scheduling_manager.py
M lib/galaxy_ext/metadata/set_metadata.py
M scripts/common_startup.sh
M scripts/common_startup_functions.sh
M scripts/grt/export.py
M scripts/grt/grt.yml.sample
M templates/admin/tool_shed_repository/manage_repository.mako
M test/api/test_workflows.py
M test/base/populators.py
M test/base/workflow_fixtures.py
M test/functional/tools/for_workflows/head.xml
M test/functional/tools/samples_tool_conf.xml
A test/functional/tools/tool_provided_metadata_10.xml
A test/functional/tools/tool_provided_metadata_11.xml
A test/functional/tools/tool_provided_metadata_12.xml
M test/integration/test_dockerized_jobs.py
A test/integration/test_workflow_sync.py
A test/unit/jobs/handler_template_job_conf.xml
M test/unit/jobs/test_job_configuration.py
M test/unit/jobs/test_job_wrapper.py
M test/unit/jobs/test_runner_local.py
M test/unit/test_objectstore.py
M test/unit/tools/test_actions.py
M test/unit/tools/test_parameter_parsing.py
M test/unit/tools/test_toolbox.py
M test/unit/tools/test_wrappers.py
M test/unit/unittest_utils/galaxy_mock.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/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 pulsar_resubmit
Commit: 0727f17ade3bb964a260907860a7ab0aee39a4b3
https://github.com/galaxyproject/galaxy/commit/0727f17ade3bb964a260907860a7…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-12-21 (Fri, 21 Dec 2018)
Changed paths:
M lib/galaxy/jobs/runners/pulsar.py
M test/integration/resubmission_pulsar_job_conf.xml
Log Message:
-----------
Fixes for Pulsar error handling.
More uniform error hanlding to fix test. Simplify test case of resubmission to test just jobs resubmit properly (no need to test Pulsar-to-Pulsar resubmission in particular here I don't think, maybe as a second test - but not a first?).
Commit: abf98be7833f1df15ad292b453f5b79899e8412f
https://github.com/galaxyproject/galaxy/commit/abf98be7833f1df15ad292b453f5…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-12-21 (Fri, 21 Dec 2018)
Changed paths:
M lib/galaxy/jobs/runners/pulsar.py
Log Message:
-----------
lint fix
Commit: 26c950f569111ccd61621849c0fc7aecbf70e76b
https://github.com/galaxyproject/galaxy/commit/26c950f569111ccd61621849c0fc…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-12-21 (Fri, 21 Dec 2018)
Changed paths:
M lib/galaxy/jobs/mapper.py
M lib/galaxy/jobs/runners/pulsar.py
A test/integration/resubmission_pulsar_job_conf.xml
M test/integration/test_job_resubmission.py
M test/unit/jobs/test_mapper.py
M test/unit/jobs/test_rules/10_site.py
Log Message:
-----------
Merge pull request #7053 from nuwang/pulsar_resubmit
Added resubmit handlers on Pulsar connection failures
Compare: https://github.com/galaxyproject/galaxy/compare/e4e2d9c09a45...26c950f56911
**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/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 1c82d08ab5c216ad568ec1d51d3398ffb0214c18
https://github.com/galaxyproject/galaxy/commit/1c82d08ab5c216ad568ec1d51d33…
Author: anilthanki <thanki.anil(a)gmail.com>
Date: 2018-12-20 (Thu, 20 Dec 2018)
Changed paths:
A config/plugins/visualizations/aequatus/README.md
A config/plugins/visualizations/aequatus/config/aequatus.xml
A config/plugins/visualizations/aequatus/static/aequatus-vis/LICENSE
A config/plugins/visualizations/aequatus/static/aequatus-vis/README.md
A config/plugins/visualizations/aequatus/static/aequatus-vis/_config.yml
A config/plugins/visualizations/aequatus/static/aequatus-vis/scripts/cigarUtils.js
A config/plugins/visualizations/aequatus/static/aequatus-vis/scripts/d3_tree.js
A config/plugins/visualizations/aequatus/static/aequatus-vis/scripts/drawCIGARs.js
A config/plugins/visualizations/aequatus/static/aequatus-vis/scripts/drawGene.js
A config/plugins/visualizations/aequatus/static/aequatus-vis/scripts/drawGeneExonOnly.js
A config/plugins/visualizations/aequatus/static/aequatus-vis/scripts/geneView.js
A config/plugins/visualizations/aequatus/static/aequatus-vis/scripts/init.js
A config/plugins/visualizations/aequatus/static/aequatus-vis/scripts/jquery/jquery-ui-1.12.1.min.css
A config/plugins/visualizations/aequatus/static/aequatus-vis/scripts/jquery/jquery.svg.css
A config/plugins/visualizations/aequatus/static/aequatus-vis/scripts/jquery/js/jquery-3.3.1.min.js
A config/plugins/visualizations/aequatus/static/aequatus-vis/scripts/jquery/js/jquery-migrate-1.4.1.min.js
A config/plugins/visualizations/aequatus/static/aequatus-vis/scripts/jquery/js/jquery-ui-1.12.1.min.js
A config/plugins/visualizations/aequatus/static/aequatus-vis/scripts/jquery/js/jquery.cookie.js
A config/plugins/visualizations/aequatus/static/aequatus-vis/scripts/jquery/js/jquery.svg.js
A config/plugins/visualizations/aequatus/static/aequatus-vis/scripts/newick.js
A config/plugins/visualizations/aequatus/static/aequatus-vis/scripts/scriptaculous/prototype.js
A config/plugins/visualizations/aequatus/static/aequatus-vis/scripts/util.js
A config/plugins/visualizations/aequatus/static/aequatus-vis/styles/font-awesome-5.6.1/css/fontawesome.min.css
A config/plugins/visualizations/aequatus/static/aequatus-vis/styles/font-awesome-5.6.1/css/solid.min.css
A config/plugins/visualizations/aequatus/static/aequatus-vis/styles/font-awesome-5.6.1/webfonts/FontAwesome.otf
A config/plugins/visualizations/aequatus/static/aequatus-vis/styles/font-awesome-5.6.1/webfonts/fa-solid-900.eot
A config/plugins/visualizations/aequatus/static/aequatus-vis/styles/font-awesome-5.6.1/webfonts/fa-solid-900.svg
A config/plugins/visualizations/aequatus/static/aequatus-vis/styles/font-awesome-5.6.1/webfonts/fa-solid-900.ttf
A config/plugins/visualizations/aequatus/static/aequatus-vis/styles/font-awesome-5.6.1/webfonts/fa-solid-900.woff
A config/plugins/visualizations/aequatus/static/aequatus-vis/styles/font-awesome-5.6.1/webfonts/fa-solid-900.woff2
A config/plugins/visualizations/aequatus/static/aequatus-vis/styles/font-awesome-5.6.1/webfonts/fontawesome-webfont.eot
A config/plugins/visualizations/aequatus/static/aequatus-vis/styles/font-awesome-5.6.1/webfonts/fontawesome-webfont.svg
A config/plugins/visualizations/aequatus/static/aequatus-vis/styles/font-awesome-5.6.1/webfonts/fontawesome-webfont.ttf
A config/plugins/visualizations/aequatus/static/aequatus-vis/styles/font-awesome-5.6.1/webfonts/fontawesome-webfont.woff
A config/plugins/visualizations/aequatus/static/aequatus-vis/styles/style.css
A config/plugins/visualizations/aequatus/static/scripts/controls.js
A config/plugins/visualizations/aequatus/static/scripts/popup.js
A config/plugins/visualizations/aequatus/static/scripts/readSQLite.js
A config/plugins/visualizations/aequatus/static/scripts/sql.js
A config/plugins/visualizations/aequatus/static/scripts/worker.js
A config/plugins/visualizations/aequatus/static/scripts/worker.sql.js
A config/plugins/visualizations/aequatus/static/styles/aequatus.css
A config/plugins/visualizations/aequatus/templates/aequatus.mako
M lib/galaxy/datatypes/binary.py
Log Message:
-----------
adds Aequatus visualisation plugin
updates Aequatus control panel-settings font size
Update README.md
fix path to aequatus static scripts
updates with upstream
removes console
removes installation guide
removes demo
removes duplicates
removes d3.js
removes bootstrap
prunes font-awesome
removes less of font-awesome
removes scss of font-awesome
uses font-swesome min
removes bootstrap
removes leftandright css class
updates jQuery and changes css class for popup
updates jQuery
updates fontawesome to 5.6.1
restore galaxy.yml.sample
add missing resource
update paths after updating font
remove console log
switch to minified jquery ui
Commit: e4e2d9c09a45375faeb3e52d16beac87d4df1f99
https://github.com/galaxyproject/galaxy/commit/e4e2d9c09a45375faeb3e52d16be…
Author: Dannon <dannon.baker(a)gmail.com>
Date: 2018-12-21 (Fri, 21 Dec 2018)
Changed paths:
A config/plugins/visualizations/aequatus/README.md
A config/plugins/visualizations/aequatus/config/aequatus.xml
A config/plugins/visualizations/aequatus/static/aequatus-vis/LICENSE
A config/plugins/visualizations/aequatus/static/aequatus-vis/README.md
A config/plugins/visualizations/aequatus/static/aequatus-vis/_config.yml
A config/plugins/visualizations/aequatus/static/aequatus-vis/scripts/cigarUtils.js
A config/plugins/visualizations/aequatus/static/aequatus-vis/scripts/d3_tree.js
A config/plugins/visualizations/aequatus/static/aequatus-vis/scripts/drawCIGARs.js
A config/plugins/visualizations/aequatus/static/aequatus-vis/scripts/drawGene.js
A config/plugins/visualizations/aequatus/static/aequatus-vis/scripts/drawGeneExonOnly.js
A config/plugins/visualizations/aequatus/static/aequatus-vis/scripts/geneView.js
A config/plugins/visualizations/aequatus/static/aequatus-vis/scripts/init.js
A config/plugins/visualizations/aequatus/static/aequatus-vis/scripts/jquery/jquery-ui-1.12.1.min.css
A config/plugins/visualizations/aequatus/static/aequatus-vis/scripts/jquery/jquery.svg.css
A config/plugins/visualizations/aequatus/static/aequatus-vis/scripts/jquery/js/jquery-3.3.1.min.js
A config/plugins/visualizations/aequatus/static/aequatus-vis/scripts/jquery/js/jquery-migrate-1.4.1.min.js
A config/plugins/visualizations/aequatus/static/aequatus-vis/scripts/jquery/js/jquery-ui-1.12.1.min.js
A config/plugins/visualizations/aequatus/static/aequatus-vis/scripts/jquery/js/jquery.cookie.js
A config/plugins/visualizations/aequatus/static/aequatus-vis/scripts/jquery/js/jquery.svg.js
A config/plugins/visualizations/aequatus/static/aequatus-vis/scripts/newick.js
A config/plugins/visualizations/aequatus/static/aequatus-vis/scripts/scriptaculous/prototype.js
A config/plugins/visualizations/aequatus/static/aequatus-vis/scripts/util.js
A config/plugins/visualizations/aequatus/static/aequatus-vis/styles/font-awesome-5.6.1/css/fontawesome.min.css
A config/plugins/visualizations/aequatus/static/aequatus-vis/styles/font-awesome-5.6.1/css/solid.min.css
A config/plugins/visualizations/aequatus/static/aequatus-vis/styles/font-awesome-5.6.1/webfonts/FontAwesome.otf
A config/plugins/visualizations/aequatus/static/aequatus-vis/styles/font-awesome-5.6.1/webfonts/fa-solid-900.eot
A config/plugins/visualizations/aequatus/static/aequatus-vis/styles/font-awesome-5.6.1/webfonts/fa-solid-900.svg
A config/plugins/visualizations/aequatus/static/aequatus-vis/styles/font-awesome-5.6.1/webfonts/fa-solid-900.ttf
A config/plugins/visualizations/aequatus/static/aequatus-vis/styles/font-awesome-5.6.1/webfonts/fa-solid-900.woff
A config/plugins/visualizations/aequatus/static/aequatus-vis/styles/font-awesome-5.6.1/webfonts/fa-solid-900.woff2
A config/plugins/visualizations/aequatus/static/aequatus-vis/styles/font-awesome-5.6.1/webfonts/fontawesome-webfont.eot
A config/plugins/visualizations/aequatus/static/aequatus-vis/styles/font-awesome-5.6.1/webfonts/fontawesome-webfont.svg
A config/plugins/visualizations/aequatus/static/aequatus-vis/styles/font-awesome-5.6.1/webfonts/fontawesome-webfont.ttf
A config/plugins/visualizations/aequatus/static/aequatus-vis/styles/font-awesome-5.6.1/webfonts/fontawesome-webfont.woff
A config/plugins/visualizations/aequatus/static/aequatus-vis/styles/style.css
A config/plugins/visualizations/aequatus/static/scripts/controls.js
A config/plugins/visualizations/aequatus/static/scripts/popup.js
A config/plugins/visualizations/aequatus/static/scripts/readSQLite.js
A config/plugins/visualizations/aequatus/static/scripts/sql.js
A config/plugins/visualizations/aequatus/static/scripts/worker.js
A config/plugins/visualizations/aequatus/static/scripts/worker.sql.js
A config/plugins/visualizations/aequatus/static/styles/aequatus.css
A config/plugins/visualizations/aequatus/templates/aequatus.mako
M lib/galaxy/datatypes/binary.py
Log Message:
-----------
Merge pull request #6484 from anilthanki/aequatus-vis
Adds Aequatus visualisation plugin
Compare: https://github.com/galaxyproject/galaxy/compare/e8d95fba71a4...e4e2d9c09a45
**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.