Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 60d0d9d5ec36fb1e6a79a4f51ab919325687b10d
https://github.com/galaxyproject/galaxy/commit/60d0d9d5ec36fb1e6a79a4f51ab9…
Author: Pierrick Roger <pk.roger(a)icloud.com>
Date: 2018-06-07 (Thu, 07 Jun 2018)
Changed paths:
M tools/data_source/upload.py
Log Message:
-----------
Add grooming for composite files.
Add call to groom_dataset_content() for composite files.
Commit: 665e11facbf0b9b86fbcde04593fcd49ebe96777
https://github.com/galaxyproject/galaxy/commit/665e11facbf0b9b86fbcde04593f…
Author: Pierrick Roger <pk.roger(a)icloud.com>
Date: 2018-06-07 (Thu, 07 Jun 2018)
Changed paths:
M config/datatypes_conf.xml.sample
A lib/galaxy/datatypes/isa.py
M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt
Log Message:
-----------
Add ISA composite data type.
Add new data types isa-tab and isa-json.
Add isa-rwval library (isatools Python 2 version) in requirements.
Commit: 1fb63a1369e8fa75b1f7825693ef286682659a64
https://github.com/galaxyproject/galaxy/commit/1fb63a1369e8fa75b1f7825693ef…
Author: Pablo Moreno <pcm32(a)users.noreply.github.com>
Date: 2018-06-07 (Thu, 07 Jun 2018)
Changed paths:
M lib/galaxy/datatypes/isa.py
Log Message:
-----------
[ISA datatype] adds logger setting for isatools.isatab to avoid failing uploads when no pandas (#31)
* [ISA datatype] adds logger setting for isatools.isatab to avoid failing uploads when no pandas.
* Update isa.py
Commit: fe139ad8dfe6c83188c33498d8d2854b33670c04
https://github.com/galaxyproject/galaxy/commit/fe139ad8dfe6c83188c33498d8d2…
Author: Pablo Moreno <pcm32(a)users.noreply.github.com>
Date: 2018-06-07 (Thu, 07 Jun 2018)
Changed paths:
A lib/galaxy/dependencies/pinned-requirements.txt
R lib/galaxy/dependencies/pinned-requirements.txt
Log Message:
-----------
Installs isa-rwval from develop
Otherwise failing currently when building in the container.
Commit: 06c57810d9050ffd4c81ce8e189741f255d6eafc
https://github.com/galaxyproject/galaxy/commit/06c57810d9050ffd4c81ce8e1897…
Author: Pierrick Roger <pk.roger(a)icloud.com>
Date: 2018-06-07 (Thu, 07 Jun 2018)
Changed paths:
M lib/galaxy/datatypes/isa.py
Log Message:
-----------
Correct linting issues detected by Travis-CI run.
Commit: 5babb80fc24febbbbed1af5b0bf56c84f16ab8a4
https://github.com/galaxyproject/galaxy/commit/5babb80fc24febbbbed1af5b0bf5…
Author: Pierrick Roger <pk.roger(a)icloud.com>
Date: 2018-06-07 (Thu, 07 Jun 2018)
Changed paths:
M lib/galaxy/datatypes/isa.py
Log Message:
-----------
Correct again lint errors for Travis-CI.
Commit: 84c002283209a5717682c31d1013034e9cfc828b
https://github.com/galaxyproject/galaxy/commit/84c002283209a5717682c31d1013…
Author: Pierrick Roger <pk.roger(a)icloud.com>
Date: 2018-06-07 (Thu, 07 Jun 2018)
Changed paths:
M lib/galaxy/datatypes/isa.py
Log Message:
-----------
Correct some more lint errors for Travis-CI.
Commit: b9c63df60e12b6220f088645c17bf6d8bd68ab1b
https://github.com/galaxyproject/galaxy/commit/b9c63df60e12b6220f088645c17b…
Author: Pierrick Roger <pk.roger(a)icloud.com>
Date: 2018-06-07 (Thu, 07 Jun 2018)
Changed paths:
M lib/galaxy/datatypes/isa.py
Log Message:
-----------
Change ISA Tools web site link.
Replace ISA Tools .org web site that has just been hacked, by the GitHub
page of the organization.
Commit: cf7034399083c77d38e29c2832339776df103983
https://github.com/galaxyproject/galaxy/commit/cf7034399083c77d38e29c283233…
Author: Pierrick Roger <pk.roger(a)icloud.com>
Date: 2018-06-07 (Thu, 07 Jun 2018)
Changed paths:
M lib/galaxy/datatypes/isa.py
Log Message:
-----------
Escape filename in primary file.
Commit: a50537cd5a2cb1039bcc7b0fa215d523c6e97499
https://github.com/galaxyproject/galaxy/commit/a50537cd5a2cb1039bcc7b0fa215…
Author: Pierrick Roger <pk.roger(a)icloud.com>
Date: 2018-06-07 (Thu, 07 Jun 2018)
Changed paths:
M lib/galaxy/datatypes/isa.py
Log Message:
-----------
Escape assay information in ISA display_data().
Commit: 86de0d3bc431404d6fca26e7506ec11415411788
https://github.com/galaxyproject/galaxy/commit/86de0d3bc431404d6fca26e7506e…
Author: Pierrick Roger <pk.roger(a)icloud.com>
Date: 2018-06-07 (Thu, 07 Jun 2018)
Changed paths:
M lib/galaxy/datatypes/isa.py
Log Message:
-----------
Remove unused method _list_archive_files().
Commit: 62ff476a7c3eeaca51147b5ae0cac753b71ba9ee
https://github.com/galaxyproject/galaxy/commit/62ff476a7c3eeaca51147b5ae0ca…
Author: Pierrick Roger <pk.roger(a)icloud.com>
Date: 2018-06-07 (Thu, 07 Jun 2018)
Changed paths:
M lib/galaxy/datatypes/isa.py
Log Message:
-----------
Use CompressedFile class.
Replace unzip custom code by Galaxy call to CompressedFile class.
Commit: abd22c12f22b15c010bcfe6b7dca63d1c2135d18
https://github.com/galaxyproject/galaxy/commit/abd22c12f22b15c010bcfe6b7dca…
Author: Pierrick Roger <pk.roger(a)icloud.com>
Date: 2018-06-07 (Thu, 07 Jun 2018)
Changed paths:
M lib/galaxy/datatypes/isa.py
Log Message:
-----------
Remove logger configuration.
Commit: 55bae21f77c03ebb1d114e9dbe593490b3e07993
https://github.com/galaxyproject/galaxy/commit/55bae21f77c03ebb1d114e9dbe59…
Author: Pierrick Roger <pk.roger(a)icloud.com>
Date: 2018-06-07 (Thu, 07 Jun 2018)
Changed paths:
M lib/galaxy/datatypes/isa.py
Log Message:
-----------
Comment out raw files listing in ISA type.
Commit: e9f00065ee190ebdeca5c02d21c068d815674999
https://github.com/galaxyproject/galaxy/commit/e9f00065ee190ebdeca5c02d21c0…
Author: Pierrick Roger <pk.roger(a)icloud.com>
Date: 2018-06-07 (Thu, 07 Jun 2018)
Changed paths:
M lib/galaxy/datatypes/isa.py
Log Message:
-----------
Remove dynamical setting of study name for ISA.
Commit: 2be9e1f637180d04d4e085b1c91292df3e09c72e
https://github.com/galaxyproject/galaxy/commit/2be9e1f637180d04d4e085b1c912…
Author: djcomlab <djcomlab(a)gmail.com>
Date: 2018-06-07 (Thu, 07 Jun 2018)
Changed paths:
M lib/galaxy/datatypes/isa.py
Log Message:
-----------
Add new lazy table parsing for isa-tab datatype and reintroduce data files
Commit: 87cdd2156d46036807134f8d91fde4fcc2ac10de
https://github.com/galaxyproject/galaxy/commit/87cdd2156d46036807134f8d91fd…
Author: Pierrick Roger <pk.roger(a)icloud.com>
Date: 2018-06-07 (Thu, 07 Jun 2018)
Changed paths:
A test-data/MTBLS6.zip
M test/api/test_tools_upload.py
Log Message:
-----------
Start writing upload test for isa-tab.
Do not know how to read zip file content and submit it to uploader for a
composite type.
Commit: 08ce54fe6e0f3cc178ad41a6fa3c00177cfbfef1
https://github.com/galaxyproject/galaxy/commit/08ce54fe6e0f3cc178ad41a6fa3c…
Author: djcomlab <djcomlab(a)gmail.com>
Date: 2018-06-07 (Thu, 07 Jun 2018)
Changed paths:
M lib/galaxy/datatypes/isa.py
M lib/galaxy/dependencies/pinned-requirements.txt
Log Message:
-----------
Introduce new table parsers to get data files back; temporarily puts dependency back to Git repo to test against (updated PyPI package for isa-rwval will be pushed soon).
Commit: eac29d55f9567b68ca94b3c2e468c380a64261ba
https://github.com/galaxyproject/galaxy/commit/eac29d55f9567b68ca94b3c2e468…
Author: djcomlab <djcomlab(a)gmail.com>
Date: 2018-06-07 (Thu, 07 Jun 2018)
Changed paths:
M lib/galaxy/dependencies/pinned-requirements.txt
Log Message:
-----------
Fix requirements again for isa-rwval==0.10.1
Commit: b4fa3d28064e1c527a3b1a3232d10873490b6825
https://github.com/galaxyproject/galaxy/commit/b4fa3d28064e1c527a3b1a3232d1…
Author: djcomlab <djcomlab(a)gmail.com>
Date: 2018-06-07 (Thu, 07 Jun 2018)
Changed paths:
M lib/galaxy/datatypes/isa.py
Log Message:
-----------
Cleanup presentation of data files (unused rendering using datafile id)
Commit: 832f51b5168cc9751eecb77a62ff7a06807f92ed
https://github.com/galaxyproject/galaxy/commit/832f51b5168cc9751eecb77a62ff…
Author: Pierrick Roger <pk.roger(a)icloud.com>
Date: 2018-06-07 (Thu, 07 Jun 2018)
Changed paths:
A lib/galaxy/dependencies/pinned-requirements.txt
R lib/galaxy/dependencies/pinned-requirements.txt
Log Message:
-----------
Pinned requirements as a symbolic link as done in dev branch.
Commit: 39d4447a97ab8fe8359d3fd2a1df2815014570ea
https://github.com/galaxyproject/galaxy/commit/39d4447a97ab8fe8359d3fd2a1df…
Author: djcomlab <djcomlab(a)gmail.com>
Date: 2018-06-07 (Thu, 07 Jun 2018)
Changed paths:
M lib/galaxy/datatypes/isa.py
Log Message:
-----------
Add check so that empty filenames not added to file list.
Commit: a98cc55db25492217ff5cb6d91716122e39347fb
https://github.com/galaxyproject/galaxy/commit/a98cc55db25492217ff5cb6d9171…
Author: djcomlab <djcomlab(a)gmail.com>
Date: 2018-06-29 (Fri, 29 Jun 2018)
Changed paths:
M test/api/test_tools_upload.py
Log Message:
-----------
Fix upload test for isa-tab datatype
Commit: f2176d395478fe4c4ad41ae3f03747b3967abc6d
https://github.com/galaxyproject/galaxy/commit/f2176d395478fe4c4ad41ae3f037…
Author: djcomlab <djcomlab(a)gmail.com>
Date: 2018-06-29 (Fri, 29 Jun 2018)
Changed paths:
M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt
Log Message:
-----------
Update isa-rwval version as new update fixes a bug
Commit: efc7864cabb0f7adc65929f3bff2f56c3ef14041
https://github.com/galaxyproject/galaxy/commit/efc7864cabb0f7adc65929f3bff2…
Author: Pierrick ROGER <pk.roger(a)icloud.com>
Date: 2018-10-18 (Thu, 18 Oct 2018)
Changed paths:
M .ci/flake8_blacklist.txt
A .ci/jenkins/api-py3/run_tests.sh
M .ci/jenkins/api/run_tests.sh
A .ci/jenkins/framework-py3/run_tests.sh
M .ci/jenkins/framework/run_tests.sh
A .ci/jenkins/integration-py3/run_tests.sh
A .ci/jenkins/main-tools-py3/run_tests.sh
A .ci/jenkins/main-tools/run_tests.sh
A .ci/jenkins/selenium-py3/run_tests.sh
M .ci/jenkins/selenium/run_tests.sh
M .ci/jenkins/toolshed/run_tests.sh
M .coveragerc
M .gitignore
M .travis.yml
M client/README.md
A client/galaxy/docs/README.md
M client/galaxy/docs/bootstrap.md
A client/galaxy/docs/galaxy-buttons.md
A client/galaxy/docs/galaxy-forms.md
A client/galaxy/docs/galaxy-masthead.md
A client/galaxy/docs/galaxy-menus.md
A client/galaxy/docs/galaxy-messages.md
A client/galaxy/docs/galaxy-panels.md
R client/galaxy/docs/galaxy-styles.md
A client/galaxy/docs/galaxy-tables.md
A client/galaxy/docs/galaxy-tabs.md
M client/galaxy/scripts/admin.toolshed.js
M client/galaxy/scripts/apps/admin.js
M client/galaxy/scripts/apps/analysis.js
M client/galaxy/scripts/apps/panels/admin-panel.js
M client/galaxy/scripts/apps/panels/tool-panel.js
M client/galaxy/scripts/components/Citations.vue
A client/galaxy/scripts/components/DataDialog.vue
M client/galaxy/scripts/components/DisplayStructured.vue
M client/galaxy/scripts/components/HistoryImport.vue
M client/galaxy/scripts/components/HistoryView.vue
M client/galaxy/scripts/components/PluginList.vue
M client/galaxy/scripts/components/RuleCollectionBuilder.vue
M client/galaxy/scripts/components/Sharing.vue
M client/galaxy/scripts/components/WorkflowImport.vue
M client/galaxy/scripts/components/admin/BaseGrid.vue
A client/galaxy/scripts/components/admin/DataTypes.vue
R client/galaxy/scripts/components/admin/UserAPIKeys.vue
M client/galaxy/scripts/galaxy.pages.js
A client/galaxy/scripts/layout/data.js
M client/galaxy/scripts/layout/masthead.js
M client/galaxy/scripts/layout/menu.js
M client/galaxy/scripts/layout/modal.js
M client/galaxy/scripts/layout/page.js
M client/galaxy/scripts/layout/panel.js
M client/galaxy/scripts/layout/scratchbook.js
M client/galaxy/scripts/mvc/collection/list-collection-creator.js
M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js
M client/galaxy/scripts/mvc/collection/pair-collection-creator.js
M client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js
M client/galaxy/scripts/mvc/dataset/dataset-error.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/form/form-input.js
M client/galaxy/scripts/mvc/form/form-repeat.js
M client/galaxy/scripts/mvc/form/form-section.js
M client/galaxy/scripts/mvc/form/form-view.js
M client/galaxy/scripts/mvc/form/form-wrapper.js
M client/galaxy/scripts/mvc/history/history-contents.js
M client/galaxy/scripts/mvc/history/history-view-edit-current.js
M client/galaxy/scripts/mvc/history/history-view-edit.js
M client/galaxy/scripts/mvc/history/history-view.js
M client/galaxy/scripts/mvc/history/job-dag.js
M client/galaxy/scripts/mvc/history/job-states-model.js
M client/galaxy/scripts/mvc/lazy/lazy-limited.js
M client/galaxy/scripts/mvc/library/library-folderlist-view.js
M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
M client/galaxy/scripts/mvc/rules/rule-definitions.js
M client/galaxy/scripts/mvc/tool/tool-form-base.js
M client/galaxy/scripts/mvc/tool/tool-form-composite.js
M client/galaxy/scripts/mvc/tool/tool-form.js
M client/galaxy/scripts/mvc/tool/tools.js
M client/galaxy/scripts/mvc/toolshed/categories-view.js
R client/galaxy/scripts/mvc/toolshed/repo-queue-view.js
M client/galaxy/scripts/mvc/toolshed/repo-status-view.js
M client/galaxy/scripts/mvc/toolshed/repositories-view.js
M client/galaxy/scripts/mvc/toolshed/repository-queue-view.js
M client/galaxy/scripts/mvc/toolshed/repository-view.js
M client/galaxy/scripts/mvc/toolshed/shed-list-view.js
M client/galaxy/scripts/mvc/toolshed/toolshed-model.js
M client/galaxy/scripts/mvc/toolshed/util.js
M client/galaxy/scripts/mvc/toolshed/workflows-view.js
M client/galaxy/scripts/mvc/tours.js
M client/galaxy/scripts/mvc/ui/ui-buttons.js
M client/galaxy/scripts/mvc/ui/ui-list.js
M client/galaxy/scripts/mvc/ui/ui-misc.js
M client/galaxy/scripts/mvc/ui/ui-options.js
M client/galaxy/scripts/mvc/ui/ui-popover.js
M client/galaxy/scripts/mvc/ui/ui-portlet.js
M client/galaxy/scripts/mvc/ui/ui-rules-edit.js
M client/galaxy/scripts/mvc/ui/ui-select-content.js
M client/galaxy/scripts/mvc/ui/ui-select-default.js
M client/galaxy/scripts/mvc/ui/ui-select-genomespace.js
M client/galaxy/scripts/mvc/ui/ui-select-library.js
M client/galaxy/scripts/mvc/ui/ui-slider.js
M client/galaxy/scripts/mvc/ui/ui-table.js
M client/galaxy/scripts/mvc/ui/ui-tabs.js
R client/galaxy/scripts/mvc/ui/ui-thumbnails.js
M client/galaxy/scripts/mvc/upload/collection/collection-row.js
M client/galaxy/scripts/mvc/upload/collection/collection-view.js
M client/galaxy/scripts/mvc/upload/composite/composite-row.js
M client/galaxy/scripts/mvc/upload/composite/composite-view.js
M client/galaxy/scripts/mvc/upload/default/default-row.js
M client/galaxy/scripts/mvc/upload/default/default-view.js
M client/galaxy/scripts/mvc/upload/upload-extension.js
M client/galaxy/scripts/mvc/upload/upload-ftp.js
M client/galaxy/scripts/mvc/upload/upload-settings.js
M client/galaxy/scripts/mvc/upload/upload-view.js
M client/galaxy/scripts/mvc/user/user-custom-builds.js
M client/galaxy/scripts/mvc/user/user-preferences.js
M client/galaxy/scripts/mvc/visualization/chart/components/model.js
M client/galaxy/scripts/mvc/visualization/chart/views/description.js
M client/galaxy/scripts/mvc/visualization/chart/views/editor.js
M client/galaxy/scripts/mvc/visualization/chart/views/groups.js
M client/galaxy/scripts/mvc/visualization/chart/views/menu.js
M client/galaxy/scripts/mvc/visualization/chart/views/settings.js
M client/galaxy/scripts/mvc/workflow/workflow-canvas.js
M client/galaxy/scripts/mvc/workflow/workflow-connector.js
M client/galaxy/scripts/mvc/workflow/workflow-forms.js
M client/galaxy/scripts/mvc/workflow/workflow-manager.js
M client/galaxy/scripts/mvc/workflow/workflow-node.js
M client/galaxy/scripts/mvc/workflow/workflow-terminals.js
M client/galaxy/scripts/mvc/workflow/workflow-view-data.js
M client/galaxy/scripts/mvc/workflow/workflow-view-terminals.js
M client/galaxy/scripts/mvc/workflow/workflow-view.js
M client/galaxy/scripts/qunit/test.js
M client/galaxy/scripts/qunit/tests/form_tests.js
M client/galaxy/scripts/qunit/tests/masthead_tests.js
R client/galaxy/scripts/qunit/tests/popover_tests.js
M client/galaxy/scripts/qunit/tests/ui_tests.js
M client/galaxy/scripts/qunit/tests/upload_dialog_tests.js
M client/galaxy/scripts/reports/run_stats.js
M client/galaxy/scripts/ui/editable-text.js
M client/galaxy/scripts/ui/fa-icon-button.js
M client/galaxy/scripts/utils/config.js
M client/galaxy/scripts/utils/uploadbox.js
M client/galaxy/scripts/viz/circster.js
M client/galaxy/scripts/viz/sweepster.js
M client/galaxy/scripts/viz/trackster/painters.js
M client/galaxy/scripts/viz/trackster/tracks.js
M client/galaxy/scripts/viz/visualization.js
M client/galaxy/style/scss/base.scss
M client/galaxy/style/scss/charts.scss
M client/galaxy/style/scss/frame.scss
R client/galaxy/style/scss/galaxy_bootstrap/overrides.scss
R client/galaxy/style/scss/galaxy_bootstrap/variables.scss
R client/galaxy/style/scss/galaxy_variables.scss
M client/galaxy/style/scss/history.scss
M client/galaxy/style/scss/jstree.scss
M client/galaxy/style/scss/library.scss
M client/galaxy/style/scss/list-item.scss
A client/galaxy/style/scss/overrides.scss
M client/galaxy/style/scss/theme/blue.scss
R client/galaxy/style/scss/theme/plain.scss
M client/galaxy/style/scss/ui.scss
M client/galaxy/style/scss/upload.scss
A client/galaxy/style/source_material/error_icon.svg
M client/galaxy/style/source_material/galaxy_icons.svg
A client/galaxy/style/source_material/info_icon.svg
A client/galaxy/style/source_material/ok_icon.svg
A client/galaxy/style/source_material/wait_icon.svg
A client/galaxy/style/source_material/warn_icon.svg
M client/gulpfile.js
M client/package.json
M client/styleguide.config.js
M client/webpack.config.js
M client/yarn.lock
A config/container_resolvers_conf.xml.sample
M config/containers_conf.yml.sample
M config/datatypes_conf.xml.sample
M config/error_report.yml.sample
M config/galaxy.yml.sample
M config/job_conf.xml.sample_advanced
M config/oidc_backends_config.xml.sample
M config/openid_conf.xml.sample
M config/plugins/interactive_environments/bam_iobio/templates/bam_iobio.mako
M config/plugins/interactive_environments/hicbrowser/templates/hicbrowser.mako
M config/plugins/interactive_environments/neo/templates/neo.mako
M config/plugins/tours/core.galaxy_ui.yaml
M config/plugins/visualizations/graphviz/config/graphviz.xml
M config/plugins/visualizations/msa/config/msa.xml
M config/plugins/webhooks/demo/tour_generator/__init__.py
M config/reports.yml.sample
M config/tool_conf.xml.main
M config/tool_conf.xml.sample
M config/tool_data_table_conf.xml.sample
M config/tool_shed.yml.sample
M contrib/nagios/check_galaxy.py
M cron/build_chrom_db.py
M cron/parse_builds_3_sites.py
A display_applications/intermine/intermine_simple.xml
M doc/parse_gx_xsd.py
M doc/schema_template.md
M doc/source/admin/cluster.md
M doc/source/admin/conda_faq.rst
M doc/source/admin/config.rst
M doc/source/admin/dependency_resolvers.rst
M doc/source/admin/framework_dependencies.rst
M doc/source/admin/galaxy_options.rst
M doc/source/admin/jobs.md
M doc/source/admin/production.md
M doc/source/admin/scaling.md
M doc/source/admin/special_topics/interactive_environments.rst
M doc/source/admin/special_topics/performance_tracking.rst
M doc/source/api_doc.rst
M doc/source/conf.py
M doc/source/dev/index.rst
M doc/source/dev/interactive_environments.rst
M doc/source/lib/galaxy.actions.rst
M doc/source/lib/galaxy.auth.rst
A doc/source/lib/galaxy.authnz.rst
M doc/source/lib/galaxy.containers.rst
M doc/source/lib/galaxy.datatypes.converters.rst
M doc/source/lib/galaxy.datatypes.rst
R doc/source/lib/galaxy.external_services.result_handlers.rst
R doc/source/lib/galaxy.external_services.rst
R doc/source/lib/galaxy.jobs.deferred.rst
M doc/source/lib/galaxy.jobs.metrics.instrumenters.rst
M doc/source/lib/galaxy.jobs.rst
R doc/source/lib/galaxy.jobs.runners.util.drmaa.rst
M doc/source/lib/galaxy.jobs.runners.util.rst
M doc/source/lib/galaxy.managers.rst
M doc/source/lib/galaxy.objectstore.rst
M doc/source/lib/galaxy.rst
R doc/source/lib/galaxy.sample_tracking.rst
M doc/source/lib/galaxy.tools.cwl.rst
M doc/source/lib/galaxy.tools.deps.resolvers.rst
M doc/source/lib/galaxy.tools.deps.rst
A doc/source/lib/galaxy.tools.error_reports.plugins.rst
A doc/source/lib/galaxy.tools.error_reports.rst
M doc/source/lib/galaxy.tools.parser.rst
M doc/source/lib/galaxy.tools.rst
M doc/source/lib/galaxy.tools.toolbox.lineages.rst
M doc/source/lib/galaxy.tools.toolbox.rst
M doc/source/lib/galaxy.tools.verify.rst
R doc/source/lib/galaxy.util.backports.rst
R doc/source/lib/galaxy.util.log.rst
A doc/source/lib/galaxy.util.logging.rst
A doc/source/lib/galaxy.util.path.rst
M doc/source/lib/galaxy.util.rst
M doc/source/lib/galaxy.visualization.plugins.rst
R doc/source/lib/galaxy.web.base.controllers.rst
M doc/source/lib/galaxy.web.base.rst
M doc/source/lib/galaxy.web.framework.helpers.rst
M doc/source/lib/galaxy.web.framework.middleware.rst
M doc/source/lib/galaxy.web.framework.rst
M doc/source/lib/galaxy.web.stack.rst
M doc/source/lib/galaxy.webapps.galaxy.api.rst
M doc/source/lib/galaxy.webapps.galaxy.controllers.rst
M doc/source/lib/galaxy.webapps.reports.controllers.rst
A doc/source/lib/galaxy.webapps.reports.framework.rst
M doc/source/lib/galaxy.webapps.reports.rst
M doc/source/lib/galaxy.webapps.rst
A doc/source/lib/galaxy.workflow.resources.rst
M doc/source/lib/galaxy.workflow.rst
M doc/source/lib/tool_shed.util.rst
M doc/source/releases/16.04_announce.rst
M doc/source/releases/16.10.rst
A doc/source/releases/18.09.rst
A doc/source/releases/18.09_announce.rst
A doc/source/releases/19.01_announce.rst
M lib/galaxy/actions/library.py
M lib/galaxy/app.py
M lib/galaxy/authnz/managers.py
M lib/galaxy/authnz/psa_authnz.py
M lib/galaxy/config.py
M lib/galaxy/containers/docker_swarm.py
M lib/galaxy/dataset_collections/matching.py
M lib/galaxy/dataset_collections/structure.py
M lib/galaxy/datatypes/binary.py
A lib/galaxy/datatypes/converters/bam_to_bai.xml
M lib/galaxy/datatypes/converters/bam_to_bigwig_converter.xml
M lib/galaxy/datatypes/converters/sam_to_bigwig_converter.xml
M lib/galaxy/datatypes/data.py
M lib/galaxy/datatypes/display_applications/util.py
M lib/galaxy/datatypes/molecules.py
M lib/galaxy/datatypes/neo4j.py
M lib/galaxy/datatypes/proteomics.py
M lib/galaxy/datatypes/sequence.py
M lib/galaxy/datatypes/sniff.py
M lib/galaxy/datatypes/tabular.py
A lib/galaxy/datatypes/test/diamond.daa
A lib/galaxy/datatypes/test/empty.txt
A lib/galaxy/datatypes/test/md.cpt
A lib/galaxy/datatypes/test/md.trr
A lib/galaxy/datatypes/test/md.xtc
A lib/galaxy/datatypes/test/test.loom
A lib/galaxy/datatypes/test/test_charmm.vel
A lib/galaxy/datatypes/test/test_glucose_vacuum.dcd
M lib/galaxy/datatypes/text.py
M lib/galaxy/datatypes/triples.py
M lib/galaxy/datatypes/upload_util.py
M lib/galaxy/datatypes/util/gff_util.py
M lib/galaxy/dependencies/conda-file.sh
M lib/galaxy/dependencies/conditional-requirements.txt
M lib/galaxy/dependencies/dev-requirements.txt
M lib/galaxy/dependencies/pipfiles/default/Pipfile
A lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt
M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt
R lib/galaxy/dependencies/pipfiles/develop/Pipfile
R lib/galaxy/dependencies/pipfiles/develop/Pipfile.lock
R lib/galaxy/dependencies/pipfiles/develop/pinned-requirements.txt
R lib/galaxy/dependencies/pipfiles/flake8/Pipfile.lock
M lib/galaxy/dependencies/pipfiles/flake8/pinned-requirements.txt
M lib/galaxy/dependencies/pipfiles/update.sh
R lib/galaxy/dependencies/requirements.txt
M lib/galaxy/exceptions/__init__.py
M lib/galaxy/exceptions/error_codes.json
M lib/galaxy/exceptions/error_codes.py
M lib/galaxy/jobs/__init__.py
M lib/galaxy/jobs/dynamic_tool_destination.py
R lib/galaxy/jobs/error_level.py
M lib/galaxy/jobs/handler.py
M lib/galaxy/jobs/output_checker.py
M lib/galaxy/jobs/rule_helper.py
M lib/galaxy/jobs/runners/__init__.py
M lib/galaxy/jobs/runners/chronos.py
M lib/galaxy/jobs/runners/condor.py
M lib/galaxy/jobs/runners/local.py
M lib/galaxy/jobs/runners/pulsar.py
M lib/galaxy/jobs/runners/slurm.py
M lib/galaxy/jobs/runners/state_handlers/_safe_eval.py
A lib/galaxy/jobs/runners/util/cli/job/lsf.py
M lib/galaxy/jobs/runners/util/cli/shell/local.py
M lib/galaxy/jobs/runners/util/cli/shell/rsh.py
M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh
M lib/galaxy/jobs/runners/util/job_script/__init__.py
M lib/galaxy/jobs/runners/util/kill.py
M lib/galaxy/jobs/splitters/multi.py
M lib/galaxy/managers/base.py
A lib/galaxy/managers/cloud.py
A lib/galaxy/managers/cloudauthzs.py
M lib/galaxy/managers/collections.py
M lib/galaxy/managers/collections_util.py
M lib/galaxy/managers/context.py
M lib/galaxy/managers/datasets.py
M lib/galaxy/managers/folders.py
M lib/galaxy/managers/hdas.py
M lib/galaxy/managers/hdcas.py
M lib/galaxy/managers/jobs.py
M lib/galaxy/managers/lddas.py
M lib/galaxy/managers/libraries.py
M lib/galaxy/managers/library_datasets.py
M lib/galaxy/managers/rbac_secured.py
M lib/galaxy/managers/sharable.py
M lib/galaxy/managers/tags.py
M lib/galaxy/managers/users.py
M lib/galaxy/managers/workflows.py
M lib/galaxy/model/__init__.py
M lib/galaxy/model/custom_types.py
M lib/galaxy/model/item_attrs.py
M lib/galaxy/model/mapping.py
M lib/galaxy/model/metadata.py
M lib/galaxy/model/migrate/versions/0136_collection_and_workflow_state.py
A lib/galaxy/model/migrate/versions/0143_add_cloudauthz_tables.py
M lib/galaxy/model/orm/scripts.py
M lib/galaxy/model/search.py
M lib/galaxy/objectstore/__init__.py
M lib/galaxy/objectstore/cloud.py
M lib/galaxy/security/__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/model_operations.py
M lib/galaxy/tools/actions/upload.py
M lib/galaxy/tools/actions/upload_common.py
M lib/galaxy/tools/apply_rules.xml
A lib/galaxy/tools/build_list.xml
M lib/galaxy/tools/cache.py
M lib/galaxy/tools/cwl/cwltool_deps.py
M lib/galaxy/tools/cwl/parser.py
M lib/galaxy/tools/cwl/schema.py
M lib/galaxy/tools/cwl/util.py
M lib/galaxy/tools/data/__init__.py
M lib/galaxy/tools/data_fetch.py
M lib/galaxy/tools/data_fetch.xml
M lib/galaxy/tools/data_manager/manager.py
M lib/galaxy/tools/deps/__init__.py
M lib/galaxy/tools/deps/conda_util.py
M lib/galaxy/tools/deps/container_resolvers/mulled.py
M lib/galaxy/tools/deps/containers.py
M lib/galaxy/tools/deps/docker_util.py
M lib/galaxy/tools/deps/mulled/mulled_build.py
M lib/galaxy/tools/deps/mulled/mulled_build_channel.py
M lib/galaxy/tools/deps/resolvers/conda.py
M lib/galaxy/tools/error_reports/plugins/sentry.py
M lib/galaxy/tools/evaluation.py
M lib/galaxy/tools/execute.py
A lib/galaxy/tools/extract_dataset.xml
A lib/galaxy/tools/filter_empty_collection.xml
M lib/galaxy/tools/filter_failed_collection.xml
M lib/galaxy/tools/imp_exp/export_history.py
M lib/galaxy/tools/imp_exp/imp_history_from_archive.xml
M lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py
M lib/galaxy/tools/lint.py
M lib/galaxy/tools/linters/stdio.py
M lib/galaxy/tools/linters/tests.py
M lib/galaxy/tools/parameters/__init__.py
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/tools/parameters/dataset_matcher.py
M lib/galaxy/tools/parameters/dynamic_options.py
M lib/galaxy/tools/parameters/grouping.py
M lib/galaxy/tools/parameters/history_query.py
M lib/galaxy/tools/parameters/meta.py
M lib/galaxy/tools/parameters/output_collect.py
M lib/galaxy/tools/parameters/wrapped.py
M lib/galaxy/tools/parameters/wrapped_json.py
M lib/galaxy/tools/parser/cwl.py
A lib/galaxy/tools/parser/error_level.py
M lib/galaxy/tools/parser/interface.py
M lib/galaxy/tools/parser/output_actions.py
M lib/galaxy/tools/parser/output_collection_def.py
M lib/galaxy/tools/parser/output_objects.py
M lib/galaxy/tools/parser/util.py
M lib/galaxy/tools/parser/xml.py
M lib/galaxy/tools/relabel_from_file.xml
M lib/galaxy/tools/search/__init__.py
M lib/galaxy/tools/tag_collection_from_file.xml
M lib/galaxy/tools/test.py
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/tools/toolbox/filters/examples.py.sample
M lib/galaxy/tools/util/maf_utilities.py
M lib/galaxy/tools/verify/__init__.py
M lib/galaxy/tools/verify/interactor.py
M lib/galaxy/tools/verify/test_data.py
M lib/galaxy/tools/wrappers.py
M lib/galaxy/tools/xsd/galaxy.xsd
M lib/galaxy/util/__init__.py
M lib/galaxy/util/bunch.py
M lib/galaxy/util/checkers.py
M lib/galaxy/util/compression_utils.py
M lib/galaxy/util/create_history_template.py
M lib/galaxy/util/expressions.py
M lib/galaxy/util/hash_util.py
M lib/galaxy/util/json.py
M lib/galaxy/util/monitors.py
M lib/galaxy/util/none_like.py
M lib/galaxy/util/object_wrapper.py
M lib/galaxy/util/permutations.py
M lib/galaxy/util/renamed_temporary_file.py
M lib/galaxy/util/rules_dsl.py
M lib/galaxy/util/streamball.py
M lib/galaxy/util/template.py
M lib/galaxy/util/ucsc.py
M lib/galaxy/util/xml_macros.py
M lib/galaxy/version.py
M lib/galaxy/visualization/plugins/interactive_environments.py
M lib/galaxy/visualization/plugins/plugin.py
M lib/galaxy/web/base/controller.py
M lib/galaxy/web/form_builder.py
M lib/galaxy/web/framework/base.py
M lib/galaxy/web/framework/decorators.py
M lib/galaxy/web/framework/helpers/__init__.py
M lib/galaxy/web/framework/helpers/grids.py
M lib/galaxy/web/framework/middleware/batch.py
M lib/galaxy/web/framework/middleware/static.py
M lib/galaxy/web/framework/webapp.py
M lib/galaxy/web/security/__init__.py
M lib/galaxy/web/stack/__init__.py
M lib/galaxy/web/stack/transport.py
M lib/galaxy/webapps/config_manage.py
M lib/galaxy/webapps/galaxy/api/authenticate.py
A lib/galaxy/webapps/galaxy/api/cloud.py
A lib/galaxy/webapps/galaxy/api/cloudauthz.py
M lib/galaxy/webapps/galaxy/api/configuration.py
M lib/galaxy/webapps/galaxy/api/datasets.py
M lib/galaxy/webapps/galaxy/api/folder_contents.py
M lib/galaxy/webapps/galaxy/api/folders.py
M lib/galaxy/webapps/galaxy/api/forms.py
M lib/galaxy/webapps/galaxy/api/groups.py
M lib/galaxy/webapps/galaxy/api/histories.py
M lib/galaxy/webapps/galaxy/api/history_contents.py
M lib/galaxy/webapps/galaxy/api/jobs.py
M lib/galaxy/webapps/galaxy/api/libraries.py
M lib/galaxy/webapps/galaxy/api/library_contents.py
M lib/galaxy/webapps/galaxy/api/library_datasets.py
M lib/galaxy/webapps/galaxy/api/pages.py
M lib/galaxy/webapps/galaxy/api/roles.py
M lib/galaxy/webapps/galaxy/api/search.py
M lib/galaxy/webapps/galaxy/api/tool_data.py
M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py
M lib/galaxy/webapps/galaxy/api/tools.py
M lib/galaxy/webapps/galaxy/api/toolshed.py
M lib/galaxy/webapps/galaxy/api/uploads.py
M lib/galaxy/webapps/galaxy/api/users.py
M lib/galaxy/webapps/galaxy/api/webhooks.py
M lib/galaxy/webapps/galaxy/api/workflows.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/config_schema.yml
M lib/galaxy/webapps/galaxy/controllers/admin.py
M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
M lib/galaxy/webapps/galaxy/controllers/authnz.py
M lib/galaxy/webapps/galaxy/controllers/data_manager.py
M lib/galaxy/webapps/galaxy/controllers/dataset.py
M lib/galaxy/webapps/galaxy/controllers/history.py
M lib/galaxy/webapps/galaxy/controllers/page.py
M lib/galaxy/webapps/galaxy/controllers/root.py
M lib/galaxy/webapps/galaxy/controllers/tag.py
M lib/galaxy/webapps/galaxy/controllers/tool_runner.py
M lib/galaxy/webapps/galaxy/controllers/user.py
M lib/galaxy/webapps/galaxy/controllers/workflow.py
M lib/galaxy/webapps/tool_shed/api/categories.py
M lib/galaxy/webapps/tool_shed/api/groups.py
M lib/galaxy/webapps/tool_shed/api/repositories.py
M lib/galaxy/webapps/tool_shed/api/repository_revisions.py
M lib/galaxy/webapps/tool_shed/buildapp.py
M lib/galaxy/webapps/tool_shed/config_schema.yml
M lib/galaxy/webapps/tool_shed/controllers/repository.py
M lib/galaxy/webapps/tool_shed/controllers/repository_review.py
M lib/galaxy/webapps/tool_shed/controllers/upload.py
M lib/galaxy/webapps/tool_shed/controllers/user.py
M lib/galaxy/webapps/tool_shed/model/__init__.py
M lib/galaxy/webapps/uwsgi_schema.yml
M lib/galaxy/workflow/extract.py
M lib/galaxy/workflow/modules.py
M lib/galaxy/workflow/resources/example.py.sample
M lib/galaxy/workflow/run.py
M lib/galaxy/workflow/run_request.py
M lib/galaxy/workflow/steps.py
M lib/galaxy_ext/metadata/set_metadata.py
M lib/tool_shed/capsule/capsule_manager.py
M lib/tool_shed/dependencies/attribute_handlers.py
M lib/tool_shed/dependencies/repository/relation_builder.py
M lib/tool_shed/galaxy_install/install_manager.py
M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py
M lib/tool_shed/galaxy_install/tools/data_manager.py
M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py
M lib/tool_shed/grids/repository_grids.py
M lib/tool_shed/grids/repository_review_grids.py
M lib/tool_shed/grids/util.py
M lib/tool_shed/managers/groups.py
M lib/tool_shed/metadata/metadata_generator.py
M lib/tool_shed/metadata/repository_metadata_manager.py
M lib/tool_shed/repository_registry.py
M lib/tool_shed/repository_types/metadata.py
M lib/tool_shed/repository_types/repository_suite_definition.py
M lib/tool_shed/repository_types/tool_dependency_definition.py
M lib/tool_shed/tools/tool_validator.py
M lib/tool_shed/tools/tool_version_manager.py
M lib/tool_shed/util/commit_util.py
M lib/tool_shed/util/common_util.py
M lib/tool_shed/util/encoding_util.py
M lib/tool_shed/util/hg_util.py
M lib/tool_shed/util/metadata_util.py
M lib/tool_shed/util/readme_util.py
M lib/tool_shed/util/repository_content_util.py
M lib/tool_shed/util/repository_util.py
M lib/tool_shed/util/review_util.py
M lib/tool_shed/util/shed_util_common.py
M lib/tool_shed/util/web_util.py
R openid/aol.xml
A pytest.ini
M run_tests.sh
M scripts/api/README
M scripts/api/common.py
M scripts/api/library_upload_dir.py
M scripts/apply_tags.py
M scripts/bootstrap_history.py
M scripts/check_galaxy.py
M scripts/check_python.py
M scripts/cleanup_datasets/pgcleanup.py
M scripts/common_startup.sh
M scripts/common_startup_functions.sh
M scripts/functional_tests.py
M scripts/galaxy-main
M scripts/get_uwsgi_args.py
M scripts/grt/export.py
M scripts/grt/grt.yml.sample
M scripts/grt/upload.py
M scripts/loc_files/create_all_fasta_loc.py
M scripts/microbes/util.py
A scripts/pages_identifier_conversion.py
A scripts/plugin_staging.py
M scripts/secret_decoder_ring.py
M scripts/slideshow/example.md
M static/style/blue/base.css
A static/style/blue/info_icon.svg
M static/style/blue/library.css
R templates/admin/impersonate.mako
M templates/admin/jobs.mako
M templates/admin/review_tool_migration_stages.mako
M templates/admin/tool_shed_repository/browse_repository.mako
M templates/admin/tool_shed_repository/browse_tool_dependency.mako
M templates/admin/tool_shed_repository/deactivate_or_uninstall_repository.mako
M templates/admin/tool_shed_repository/install_tool_dependencies_with_update.mako
M templates/admin/tool_shed_repository/manage_repository.mako
M templates/admin/tool_shed_repository/manage_repository_tool_dependencies.mako
M templates/admin/tool_shed_repository/monitor_repository_installation.mako
M templates/admin/tool_shed_repository/purge_repository_confirmation.mako
M templates/admin/tool_shed_repository/reselect_tool_panel_section.mako
M templates/admin/tool_shed_repository/reset_metadata_on_selected_repositories.mako
M templates/admin/tool_shed_repository/select_tool_panel_section.mako
M templates/admin/tool_shed_repository/uninstall_tool_dependencies.mako
M templates/admin/tool_shed_repository/view_tool_metadata.mako
M templates/admin/tool_shed_repository/view_workflow.mako
R templates/admin/view_datatypes_registry.mako
M templates/base/base_panels.mako
M templates/display_base.mako
M templates/display_common.mako
M templates/galaxy_client_app.mako
M templates/ind_share_base.mako
M templates/legacy/grid_base.mako
M templates/message.mako
M templates/show_params.mako
M templates/tagging_common.mako
M templates/user/info.mako
M templates/user/register.mako
M templates/webapps/galaxy/admin/center.mako
M templates/webapps/galaxy/admin/manage_dependencies.mako
M templates/webapps/galaxy/admin/sanitize_whitelist.mako
M templates/webapps/galaxy/admin/view_display_applications.mako
M templates/webapps/galaxy/galaxy.masthead.mako
M templates/webapps/galaxy/galaxy.panels.mako
M templates/webapps/galaxy/history/display.mako
M templates/webapps/galaxy/history/share.mako
M templates/webapps/galaxy/page/editor.mako
M templates/webapps/galaxy/visualization/display.mako
M templates/webapps/galaxy/visualization/display_in_frame.mako
M templates/webapps/galaxy/workflow/display.mako
M templates/webapps/galaxy/workflow/editor.mako
M templates/webapps/tool_shed/base_panels.mako
M templates/webapps/tool_shed/common/repository_actions_menu.mako
M templates/webapps/tool_shed/common/reset_metadata_on_selected_repositories.mako
M templates/webapps/tool_shed/repository/manage_repository.mako
M templates/webapps/tool_shed/repository/tool_form.mako
M templates/webapps/tool_shed/repository/view_repository.mako
M templates/webapps/tool_shed/role/role.mako
M templates/webapps/tool_shed/user/username.mako
A test-data/11.tabular
A test-data/configfile.json
A test-data/rules/treated1fb.txt
A test-data/rules/treated2fb.txt
A test-data/rules/treated3fb.txt
A test-data/rules/untreated1fb.txt
A test-data/rules/untreated2fb.txt
A test-data/rules/untreated3fb.txt
A test-data/rules/untreated4fb.txt
A test-data/safetar_with_symlink.tar
A test-data/testdir.tar
A test-data/unsafe.tar
A test-data/unsafe.zip
A test-data/unsafe_relative_symlink.tar
M test/api/test_api_batch.py
M test/api/test_authenticate.py
M test/api/test_dataset_collections.py
M test/api/test_histories.py
M test/api/test_history_contents.py
M test/api/test_jobs.py
M test/api/test_libraries.py
M test/api/test_pages.py
A test/api/test_roles.py
M test/api/test_tool_data.py
M test/api/test_tools.py
M test/api/test_tools_upload.py
M test/api/test_workflow_extraction.py
M test/api/test_workflows.py
M test/api/test_workflows_from_yaml.py
M test/base/api.py
M test/base/data/rules_dsl_spec.yml
M test/base/data/test_workflow_topoambigouity.ga
M test/base/data/test_workflow_topoambigouity_auto_laidout.ga
M test/base/data/test_workflow_with_runtime_input.ga
M test/base/driver_util.py
M test/base/integration_util.py
M test/base/populators.py
M test/base/rules_test_data.py
A test/base/ssh_util.py
M test/base/workflow_fixtures.py
R test/base/workflows_format_2/README.txt
R test/base/workflows_format_2/__init__.py
R test/base/workflows_format_2/converter.py
R test/base/workflows_format_2/interface.py
R test/base/workflows_format_2/main.py
M test/docker/base/Dockerfile
M test/docker/base/run_test_wrapper.sh
A test/functional/conftest.py
A test/functional/known_broken_tools.txt
M test/functional/test_data_managers.py
M test/functional/test_toolbox.py
A test/functional/test_toolbox_pytest.py
A test/functional/tools/collection_cat_group_tag.xml
A test/functional/tools/collection_cat_group_tag_multiple.xml
A test/functional/tools/collection_type_source_map_over.xml
A test/functional/tools/column_param_configfile.xml
M test/functional/tools/disambiguate_cond.xml
M test/functional/tools/for_workflows/cat_collection.xml
A test/functional/tools/for_workflows/mapper_two.xml
A test/functional/tools/identifier_in_conditional.xml
A test/functional/tools/inputs_as_json_with_paths.xml
M test/functional/tools/job_environment_default.xml
M test/functional/tools/job_environment_default_legacy.xml
M test/functional/tools/job_environment_explicit_shared_home.xml
M test/functional/tools/metadata_biom1.xml
M test/functional/tools/multi_data_optional.xml
M test/functional/tools/parallelism.xml
M test/functional/tools/parallelism_optional.xml
M test/functional/tools/samples_tool_conf.xml
M test/functional/tools/unicode_stream.xml
R test/functional/twilltestcase.py
M test/galaxy_selenium/has_driver.py
M test/galaxy_selenium/navigates_galaxy.py
M test/galaxy_selenium/navigation.yml
M test/galaxy_selenium/smart_components.py
A test/integration/delay_job_conf.xml
A test/integration/delay_rules/__init__.py
A test/integration/delay_rules/rules.py
A test/integration/objectstore_selection_job_conf.xml
A test/integration/objectstore_selection_job_resource_parameters_conf.xml
A test/integration/objectstore_selection_rules/__init__.py
A test/integration/objectstore_selection_rules/rules.py
A test/integration/test_cli_runners.py
M test/integration/test_data_manager_table_reload.py
M test/integration/test_job_environments.py
A test/integration/test_job_recovery.py
M test/integration/test_job_resubmission.py
M test/integration/test_mules_as_job_handlers.py
A test/integration/test_objectstore_jobs.py
A test/integration/test_objectstore_selection.py
M test/integration/test_scripts.py
M test/integration/test_upload_configuration_options.py
M test/integration/tool_sheds_conf.xml
M test/integration/uses_shed.py
M test/manual/workflows_scaling.py
M test/selenium_tests/framework.py
M test/selenium_tests/test_admin_app.py
M test/selenium_tests/test_collection_builders.py
M test/selenium_tests/test_history_panel_collections.py
M test/selenium_tests/test_history_sharing.py
M test/selenium_tests/test_published_histories_grid.py
M test/selenium_tests/test_saved_histories.py
M test/selenium_tests/test_stock_tours.py
M test/selenium_tests/test_tool_form.py
M test/selenium_tests/test_workflow_run.py
M test/shed_functional/base/twilltestcase.py
M test/unit/datatypes/dataproviders/test_base_dataproviders.py
M test/unit/datatypes/test_bam.py
M test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py
M test/unit/jobs/test_job_output_checker.py
M test/unit/jobs/test_job_wrapper.py
M test/unit/jobs/test_runner_params.py
M test/unit/managers/test_DatasetManager.py
M test/unit/managers/test_HistoryContentsManager.py
M test/unit/managers/test_HistoryManager.py
A test/unit/managers/test_TagManager.py
A test/unit/test_compression_util.py
M test/unit/test_galaxy_mapping.py
A test/unit/test_model_copy.py
M test/unit/test_objectstore.py
M test/unit/test_remote_shell.py
M test/unit/test_rule_utils.py
M test/unit/test_security_helper.py
A test/unit/test_utils.py
M test/unit/tools/test_actions.py
M test/unit/tools/test_collect_primary_datasets.py
M test/unit/tools/test_data_parameters.py
M test/unit/tools/test_dataset_matcher.py
M test/unit/tools/test_evaluation.py
M test/unit/tools/test_execution.py
M test/unit/tools/test_history_imp_exp.py
M test/unit/tools/test_parsing.py
M test/unit/tools/test_tool_dependency_description.py
M test/unit/tools/test_tool_deps.py
M test/unit/tools/test_toolbox.py
M test/unit/tools/test_toolbox_filters.py
M test/unit/tools/test_wrappers.py
M test/unit/unittest_utils/galaxy_mock.py
M test/unit/unittest_utils/tempfilecache.py
M test/unit/visualizations/plugins/test_VisualizationsRegistry.py
M test/unit/web/framework/test_webapp.py
M test/unit/workflows/test_extract_summary.py
M test/unit/workflows/test_modules.py
M test/unit/workflows/test_workflow_progress.py
A tool-data/intermine_simple_display.loc.sample
M tool-data/shared/ucsc/builds.txt.sample
M tool-data/shared/ucsc/ucsc_build_sites.txt.sample
A tools/data_source/intermine.xml
M tools/data_source/ucsc_tablebrowser_test.xml
M tools/data_source/upload.py
M tools/filters/bed_to_bigbed.xml
M tools/filters/join.py
M tools/filters/joinWrapper.py
M tools/filters/random_lines_two_pass.py
M tools/filters/randomlines.xml
M tools/filters/secure_hash_message_digest.py
M tools/filters/sff_extract.py
M tools/filters/sff_extractor.xml
M tools/filters/tailWrapper.xml
M tools/filters/uniq.xml
M tools/filters/wc_gnu.xml
M tools/filters/wig_to_bigwig.xml
M tools/genomespace/genomespace_importer.py
M tools/maf/maf_limit_to_species.py
M tools/maf/maf_split_by_species.xml
M tools/maf/maf_to_bed.py
M tools/maf/maf_to_bed.xml
M tools/maf/maf_to_fasta_multiple_sets.py
M tools/maf/maf_to_interval.py
M tools/maf/maf_to_interval.xml
M tools/next_gen_conversion/solid2fastq.xml
M tools/phenotype_association/gpass.xml
M tools/phenotype_association/ldtools.xml
M tools/phenotype_association/ldtools_wrapper.sh
M tools/phenotype_association/linkToGProfile.pl
M tools/phenotype_association/linkToGProfile.xml
M tools/phenotype_association/lps.xml
M tools/phenotype_association/master2gd_snp.xml
M tools/phenotype_association/master2pg.xml
M tools/phenotype_association/senatag.py
M tools/plotting/boxplot.xml
M tools/solid_tools/solid_qual_stats.py
M tools/solid_tools/solid_qual_stats.xml
M tools/stats/aggregate_binned_scores_in_intervals.xml
M tools/stats/aggregate_scores_in_intervals.py
M tools/stats/filtering.xml
M tools/stats/grouping.py
M tools/stats/gsummary.xml
M tox.ini
Log Message:
-----------
Merge branch 'dev' into feature/isa_data_type
Commit: 35093e38fcfe4f9efc3a2914d694cf4a11f24ace
https://github.com/galaxyproject/galaxy/commit/35093e38fcfe4f9efc3a2914d694…
Author: Pierrick ROGER <pk.roger(a)icloud.com>
Date: 2018-10-18 (Thu, 18 Oct 2018)
Changed paths:
M test/api/test_tools_upload.py
Log Message:
-----------
Remove spaces in blank line.
Commit: a9eb587a3e38849c5044700f9f01c47d53f55a87
https://github.com/galaxyproject/galaxy/commit/a9eb587a3e38849c5044700f9f01…
Author: Pierrick ROGER <pk.roger(a)icloud.com>
Date: 2018-10-18 (Thu, 18 Oct 2018)
Changed paths:
M lib/galaxy/datatypes/isa.py
Log Message:
-----------
Various corrections for py34-lint
Add second blank line.
Remove useless imports.
Commit: 99bc4b33d2fa14a42f9ee7f4a9afe4dcf867c851
https://github.com/galaxyproject/galaxy/commit/99bc4b33d2fa14a42f9ee7f4a9af…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2018-10-19 (Fri, 19 Oct 2018)
Changed paths:
M config/datatypes_conf.xml.sample
A lib/galaxy/datatypes/isa.py
M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt
A test-data/MTBLS6.zip
M test/api/test_tools_upload.py
M tools/data_source/upload.py
Log Message:
-----------
Merge pull request #5787 from phnmnl/feature/isa_data_type
Feature/isa data type
Compare: https://github.com/galaxyproject/galaxy/compare/81f31d1a29e1...99bc4b33d2fa
**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.