galaxy-commits December 2018

galaxy-commits@lists.galaxyproject.org

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76 discussions

[galaxyproject/galaxy] 3d3738: Fix dataset discovery for YAML/dictified tools.
by GitHub 29 Dec '18

29 Dec '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 3d373827b3b1d59dd166ad6db1b95dedcb256004 https://github.com/galaxyproject/galaxy/commit/3d373827b3b1d59dd166ad6db1b9… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-12-26 (Wed, 26 Dec 2018) Changed paths: M lib/galaxy/tools/parser/output_collection_def.py M lib/galaxy/tools/parser/util.py M lib/galaxy/tools/parser/yaml.py M test/unit/tools/test_collect_primary_datasets.py Log Message: ----------- Fix dataset discovery for YAML/dictified tools. Commit: 4c741ef00ef0fcde5af1b2e270acc0f0f2f407ec https://github.com/galaxyproject/galaxy/commit/4c741ef00ef0fcde5af1b2e270ac… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2018-12-29 (Sat, 29 Dec 2018) Changed paths: M lib/galaxy/tools/parser/output_collection_def.py M lib/galaxy/tools/parser/util.py M lib/galaxy/tools/parser/yaml.py M test/unit/tools/test_collect_primary_datasets.py Log Message: ----------- Merge pull request #7152 from jmchilton/fix_yaml_discovery Fix dataset discovery for YAML/dictified tools. Compare: https://github.com/galaxyproject/galaxy/compare/7b911c6fcd4b...4c741ef00ef0 **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] 647479: Fix for parsing collection outputs for YAML/dictif...
by GitHub 29 Dec '18

29 Dec '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 647479f40ae1c5e4c1569b173c7cc0ae8c029c93 https://github.com/galaxyproject/galaxy/commit/647479f40ae1c5e4c1569b173c7c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-12-26 (Wed, 26 Dec 2018) Changed paths: M lib/galaxy/tools/parser/yaml.py A test/functional/tools/collection_creates_pair_y.yml M test/unit/tools/test_parsing.py Log Message: ----------- Fix for parsing collection outputs for YAML/dictified tools. Commit: 7b911c6fcd4b6fca661275afee13c247b766c169 https://github.com/galaxyproject/galaxy/commit/7b911c6fcd4b6fca661275afee13… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2018-12-29 (Sat, 29 Dec 2018) Changed paths: M lib/galaxy/tools/parser/yaml.py A test/functional/tools/collection_creates_pair_y.yml M test/unit/tools/test_parsing.py Log Message: ----------- Merge pull request #7153 from jmchilton/fix_output_collection_yaml Fix for parsing collection outputs for YAML/dictified tools. Compare: https://github.com/galaxyproject/galaxy/compare/471d54c27af2...7b911c6fcd4b **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] 234d3e: Remove redundant Task code.
by GitHub 27 Dec '18

27 Dec '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 234d3ee8a6c4979aeeea4bbd9a07d875c379f0be https://github.com/galaxyproject/galaxy/commit/234d3ee8a6c4979aeeea4bbd9a07… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-12-26 (Wed, 26 Dec 2018) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Remove redundant Task code. get_job is overridden in Task, that should be sufficient I suspect. Commit: 47d8fedfa4d4b84ef47fcebd2b0f5536b919c353 https://github.com/galaxyproject/galaxy/commit/47d8fedfa4d4b84ef47fcebd2b0f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-12-26 (Wed, 26 Dec 2018) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Reuse get_param_dict in job wrapper. There is a comment to this, listen to the smart comment and then delete. Commit: 471d54c27af26699be234155585bc488b5d16f65 https://github.com/galaxyproject/galaxy/commit/471d54c27af26699be234155585b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-12-27 (Thu, 27 Dec 2018) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Merge pull request #7155 from jmchilton/reuse_get_params Small de-duplication cleanups to galaxy.jobs Compare: https://github.com/galaxyproject/galaxy/compare/26c950f56911...471d54c27af2 **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] 356d94: Allow pulsar jobs to be resubmitted on connection ...
by GitHub 21 Dec '18

21 Dec '18

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.

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[galaxyproject/galaxy] 1c82d0: adds Aequatus visualisation plugin
by GitHub 21 Dec '18

21 Dec '18

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.

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[galaxyproject/galaxy] fbf671: added store library to exported libs in bundleEntr...
by GitHub 21 Dec '18

21 Dec '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: fbf67196fff08a8c7a04d23703082cd77893e815 https://github.com/galaxyproject/galaxy/commit/fbf67196fff08a8c7a04d2370308… Author: Mason <nerdinacan(a)gmail.com> Date: 2018-12-21 (Fri, 21 Dec 2018) Changed paths: M client/galaxy/scripts/apps/extended.js Log Message: ----------- added store library to exported libs in bundleEntries Commit: e8d95fba71a44b128dd873c336d95b7e551607a7 https://github.com/galaxyproject/galaxy/commit/e8d95fba71a44b128dd873c336d9… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-12-21 (Fri, 21 Dec 2018) Changed paths: M client/galaxy/scripts/apps/extended.js Log Message: ----------- Merge pull request #7149 from Nerdinacan/include_store_in_bundleEntries added store library to exported libs in bundleEntries Compare: https://github.com/galaxyproject/galaxy/compare/9de86adc06dc...e8d95fba71a4 **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] 9bbdb3: Remove unneeded session flushes and adds when coll...
by GitHub 21 Dec '18

21 Dec '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 9bbdb34fb6f0676675851691280f261a3f37bb9e https://github.com/galaxyproject/galaxy/commit/9bbdb34fb6f0676675851691280f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-12-19 (Wed, 19 Dec 2018) Changed paths: M lib/galaxy/tools/parameters/output_collect.py Log Message: ----------- Remove unneeded session flushes and adds when collecting primary datasets. Commit: 9de86adc06dc3fa0d071d84252fd9c9b4befd2a0 https://github.com/galaxyproject/galaxy/commit/9de86adc06dc3fa0d071d84252fd… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-12-21 (Fri, 21 Dec 2018) Changed paths: M lib/galaxy/tools/parameters/output_collect.py Log Message: ----------- Merge pull request #7134 from jmchilton/remove_flushes Remove unneeded session flushes and adds when discovering outputs. Compare: https://github.com/galaxyproject/galaxy/compare/3af7a5c1a754...9de86adc06dc **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] 3af7a5: Client format I intended to lump into display appl...
by GitHub 21 Dec '18

21 Dec '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 3af7a5c1a754a72c3dab94fde0eb1cc3476405fe https://github.com/galaxyproject/galaxy/commit/3af7a5c1a754a72c3dab94fde0eb… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-12-21 (Fri, 21 Dec 2018) Changed paths: M client/galaxy/scripts/components/admin/AdminServices.js M client/galaxy/scripts/components/admin/DisplayApplications.vue Log Message: ----------- Client format I intended to lump into display applications merge. **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] de3b7b: Add display applications api endpoint
by GitHub 21 Dec '18

21 Dec '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: de3b7bb55fd4949456bfb61637cb67b1fd367d6e https://github.com/galaxyproject/galaxy/commit/de3b7bb55fd4949456bfb61637cb… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-12-11 (Tue, 11 Dec 2018) Changed paths: A lib/galaxy/webapps/galaxy/api/display_applications.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Add display applications api endpoint Commit: 6546e35bff27a60b09bf30ca68c2beb62a61acd4 https://github.com/galaxyproject/galaxy/commit/6546e35bff27a60b09bf30ca68c2… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-12-11 (Tue, 11 Dec 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/display_applications.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Add reload feature to display applications api endpoint Commit: eb0c0ad9ab204cee83233523c01b11aa040a6388 https://github.com/galaxyproject/galaxy/commit/eb0c0ad9ab204cee83233523c01b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-12-11 (Tue, 11 Dec 2018) Changed paths: M client/galaxy/scripts/apps/admin.js A client/galaxy/scripts/components/admin/DisplayApplications.vue M lib/galaxy/webapps/galaxy/api/display_applications.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Add display application vue component Commit: 727ab11480962ec31387cc6934c0fcec14a4ead0 https://github.com/galaxyproject/galaxy/commit/727ab11480962ec31387cc6934c0… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-12-11 (Tue, 11 Dec 2018) Changed paths: M client/galaxy/scripts/apps/panels/admin-panel.js Log Message: ----------- Fix spacing in admin app router Commit: 35d2cd9bf62a748bc3dd5963a3246b5a5a7e2a18 https://github.com/galaxyproject/galaxy/commit/35d2cd9bf62a748bc3dd5963a324… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-12-11 (Tue, 11 Dec 2018) Changed paths: M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/components/admin/DisplayApplications.vue Log Message: ----------- Load display application data and display number of available applications Commit: 505e4288eebabf4ff3a317a90785cc6906941e53 https://github.com/galaxyproject/galaxy/commit/505e4288eebabf4ff3a317a90785… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-12-11 (Tue, 11 Dec 2018) Changed paths: M client/galaxy/scripts/components/admin/DisplayApplications.vue Log Message: ----------- Add display application vue component Commit: 218a02f3dccd8ccb5c6aa3df6c81764cb5e7a793 https://github.com/galaxyproject/galaxy/commit/218a02f3dccd8ccb5c6aa3df6c81… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-12-11 (Tue, 11 Dec 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py R templates/webapps/galaxy/admin/view_display_applications.mako Log Message: ----------- Remove legacy display applications mako and controller endpoints Commit: 4b097acffe77ab8348b4497cc9032011e2469825 https://github.com/galaxyproject/galaxy/commit/4b097acffe77ab8348b4497cc903… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-12-11 (Tue, 11 Dec 2018) Changed paths: M client/galaxy/scripts/components/admin/DisplayApplications.vue M lib/galaxy/webapps/galaxy/api/display_applications.py Log Message: ----------- Submit reload requests to new display application api endpoint Commit: b3f4d9b699e7a137dce7d130fe629aa01fc81292 https://github.com/galaxyproject/galaxy/commit/b3f4d9b699e7a137dce7d130fe62… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-12-11 (Tue, 11 Dec 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/display_applications.py Log Message: ----------- Remove debug outputs Commit: e8739a6cf530426bcd6f8c1c3964d7c31fb2a487 https://github.com/galaxyproject/galaxy/commit/e8739a6cf530426bcd6f8c1c3964… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-12-11 (Tue, 11 Dec 2018) Changed paths: M client/galaxy/scripts/components/admin/DisplayApplications.vue Log Message: ----------- Use bootstrap vues table component to render display applications table Commit: 39870a0d06647cf378ceae8b99065fbb09a8eefb https://github.com/galaxyproject/galaxy/commit/39870a0d06647cf378ceae8b9906… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-12-11 (Tue, 11 Dec 2018) Changed paths: M client/galaxy/scripts/components/admin/DisplayApplications.vue M lib/galaxy/webapps/galaxy/api/display_applications.py Log Message: ----------- Highlight reloaded/failed display application rows individually Commit: f68fa47f295f3d743d7de97521fcf97f78cf0248 https://github.com/galaxyproject/galaxy/commit/f68fa47f295f3d743d7de97521fc… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-12-11 (Tue, 11 Dec 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/display_applications.py Log Message: ----------- Fix linting Commit: 06deee06a48ae263a8ad396aac210ff9093ad6c6 https://github.com/galaxyproject/galaxy/commit/06deee06a48ae263a8ad396aac21… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-12-12 (Wed, 12 Dec 2018) Changed paths: M client/galaxy/scripts/components/admin/DisplayApplications.vue M test/selenium_tests/test_admin_app.py Log Message: ----------- Fix selenium test case for display application visibility Commit: 5b677cfd52e35e4b325dcd7fe426446c9c695262 https://github.com/galaxyproject/galaxy/commit/5b677cfd52e35e4b325dcd7fe426… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-12-13 (Thu, 13 Dec 2018) Changed paths: M client/galaxy/scripts/components/admin/DisplayApplications.vue M test/selenium_tests/test_admin_app.py Log Message: ----------- Fix selenium test, add missing applications message Commit: e3ef379674784f766d94c8e126f3744af4f5c9a7 https://github.com/galaxyproject/galaxy/commit/e3ef379674784f766d94c8e126f3… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-12-13 (Thu, 13 Dec 2018) Changed paths: M client/galaxy/scripts/components/admin/DisplayApplications.vue Log Message: ----------- Show warning message after requesting display applications Commit: f5a3ab464743a0d47672c00ce611520d846d6241 https://github.com/galaxyproject/galaxy/commit/f5a3ab464743a0d47672c00ce611… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-12-13 (Thu, 13 Dec 2018) Changed paths: A client/galaxy/scripts/components/admin/AdminServices.js M client/galaxy/scripts/components/admin/DisplayApplications.vue Log Message: ----------- Separate api requests from vue component for admin services Commit: 255418d158fd0d4a77bd9e56f18c15ec56bac02d https://github.com/galaxyproject/galaxy/commit/255418d158fd0d4a77bd9e56f18c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-12-13 (Thu, 13 Dec 2018) Changed paths: M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Fix comment header for display applications api Commit: f5b7553fea0f08c1bb37ce43172b91feed15bb44 https://github.com/galaxyproject/galaxy/commit/f5b7553fea0f08c1bb37ce43172b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-12-17 (Mon, 17 Dec 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/display_applications.py Log Message: ----------- Add require admin to display applications api Commit: a00d013fd14ecc1eca59b8d572c1ec5a673bce74 https://github.com/galaxyproject/galaxy/commit/a00d013fd14ecc1eca59b8d572c1… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-12-18 (Tue, 18 Dec 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/display_applications.py Log Message: ----------- Remove admin requirment from index endpoint of display applications Commit: e237bcfd16d6a72e78afe1405e4eaeb05a91af20 https://github.com/galaxyproject/galaxy/commit/e237bcfd16d6a72e78afe1405e4e… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-12-19 (Wed, 19 Dec 2018) Changed paths: M client/galaxy/scripts/components/admin/DisplayApplications.vue Log Message: ----------- Use b-alert instead of basic bootstrap alert messages Commit: 558aca71d69ea81746013489be52ee5813ecc43c https://github.com/galaxyproject/galaxy/commit/558aca71d69ea81746013489be52… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-12-19 (Wed, 19 Dec 2018) Changed paths: M client/galaxy/scripts/components/admin/DisplayApplications.vue Log Message: ----------- Replace default links with bootstrap vue buttons Commit: 3c2858ab0c9d79de18e28abfcef89de789e2c70c https://github.com/galaxyproject/galaxy/commit/3c2858ab0c9d79de18e28abfcef8… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-12-21 (Fri, 21 Dec 2018) Changed paths: M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/panels/admin-panel.js A client/galaxy/scripts/components/admin/AdminServices.js A client/galaxy/scripts/components/admin/DisplayApplications.vue A lib/galaxy/webapps/galaxy/api/display_applications.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin.py R templates/webapps/galaxy/admin/view_display_applications.mako M test/selenium_tests/test_admin_app.py Log Message: ----------- Merge pull request #7097 from guerler/display_applications Replace display applications mako with vue component Compare: https://github.com/galaxyproject/galaxy/compare/38687ff15a09...3c2858ab0c9d **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] 5d8e0b: Correct code error in 'build job runner' tutorial
by GitHub 21 Dec '18

21 Dec '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 5d8e0bb049a5ffdc0197a1e8436f358d4352ce09 https://github.com/galaxyproject/galaxy/commit/5d8e0bb049a5ffdc0197a1e8436f… Author: Sergey Golitsynskiy <sgolitsynskiy(a)gmail.com> Date: 2018-12-21 (Fri, 21 Dec 2018) Changed paths: M doc/source/dev/build_a_job_runner.rst Log Message: ----------- Correct code error in 'build job runner' tutorial When __init__ is called, **kwargs (most likely) will not contain the 'runner_param_specs' key. And if so, calling update() on kwargs['runner_param_specs'] will cause an error. Check if key exists, then update or create. Commit: 0bd861aec759edb86a86e5e599e5b208dec48e43 https://github.com/galaxyproject/galaxy/commit/0bd861aec759edb86a86e5e599e5… Author: Sergey Golitsynskiy <sgolitsynskiy(a)gmail.com> Date: 2018-12-21 (Fri, 21 Dec 2018) Changed paths: M doc/source/dev/build_a_job_runner.rst Log Message: ----------- Code style improvement to previous commit Commit: 38687ff15a092477a798891eed572c7680e4d037 https://github.com/galaxyproject/galaxy/commit/38687ff15a092477a798891eed57… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-12-21 (Fri, 21 Dec 2018) Changed paths: M doc/source/dev/build_a_job_runner.rst Log Message: ----------- Merge pull request #7148 from ic4f/dev Correct code error in 'build job runner' tutorial Compare: https://github.com/galaxyproject/galaxy/compare/288453d4d017...38687ff15a09 **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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