Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 08547faddd42858c072c7eca6f45b7422cd4b710
https://github.com/galaxyproject/galaxy/commit/08547faddd42858c072c7eca6f45…
Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com>
Date: 2018-06-30 (Sat, 30 Jun 2018)
Changed paths:
M config/datatypes_conf.xml.sample
M config/tool_conf.xml.main
M config/tool_conf.xml.sample
M config/tool_data_table_conf.xml.sample
A display_applications/intermine/intermine_simple.xml
A tools/data_source/intermine.xml
Log Message:
-----------
Intermine from Hack
Commit: 433d4648706be8902f609a4cba1a0d941acb7a0d
https://github.com/galaxyproject/galaxy/commit/433d4648706be8902f609a4cba1a…
Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com>
Date: 2018-07-01 (Sun, 01 Jul 2018)
Changed paths:
M config/tool_conf.xml.sample
M tools/data_source/intermine.xml
Log Message:
-----------
Update InterMine
Commit: 5b0088ae43c748edaaccbaa363e0d0c86756a66a
https://github.com/galaxyproject/galaxy/commit/5b0088ae43c748edaaccbaa363e0…
Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com>
Date: 2018-07-01 (Sun, 01 Jul 2018)
Changed paths:
M config/tool_conf.xml.sample
Log Message:
-----------
Update InterMine
Commit: 58c68d408f2eec0c787ad176dabb3330a322d582
https://github.com/galaxyproject/galaxy/commit/58c68d408f2eec0c787ad176dabb…
Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com>
Date: 2018-07-06 (Fri, 06 Jul 2018)
Changed paths:
A tool-data/intermine_simple_display.loc.sample
Log Message:
-----------
add missing intermine_simple_display.loc.sample
Commit: 8df7cafe3ac6d700f2637f0c41d0dfba8a360076
https://github.com/galaxyproject/galaxy/commit/8df7cafe3ac6d700f2637f0c41d0…
Author: Dannon <dannon.baker(a)gmail.com>
Date: 2018-07-06 (Fri, 06 Jul 2018)
Changed paths:
M config/datatypes_conf.xml.sample
M config/tool_conf.xml.main
M config/tool_conf.xml.sample
M config/tool_data_table_conf.xml.sample
A display_applications/intermine/intermine_simple.xml
A tool-data/intermine_simple_display.loc.sample
A tools/data_source/intermine.xml
Log Message:
-----------
Merge pull request #6444 from blankenberg/intermine
Intermine Enhancements
Compare: https://github.com/galaxyproject/galaxy/compare/0b98e3ed13fe...8df7cafe3ac6
**NOTE:** This service 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: 1a2cd725bb303e8db6fa07118f4714b7c0516e60
https://github.com/galaxyproject/galaxy/commit/1a2cd725bb303e8db6fa07118f47…
Author: M Bernt <m.bernt(a)ufz.de>
Date: 2018-06-20 (Wed, 20 Jun 2018)
Changed paths:
M config/datatypes_conf.xml.sample
M lib/galaxy/datatypes/binary.py
Log Message:
-----------
added daa (diamond alignment) datatype
Commit: 68dc4c26508087829150b8e5c6d3530a47202304
https://github.com/galaxyproject/galaxy/commit/68dc4c26508087829150b8e5c6d3…
Author: M Bernt <m.bernt(a)ufz.de>
Date: 2018-06-20 (Wed, 20 Jun 2018)
Changed paths:
M lib/galaxy/datatypes/binary.py
Log Message:
-----------
removed try-except and used with
Commit: 3b6ab3ecd087786113daa81e8cb0beda9a8eff82
https://github.com/galaxyproject/galaxy/commit/3b6ab3ecd087786113daa81e8cb0…
Author: M Bernt <m.bernt(a)ufz.de>
Date: 2018-06-20 (Wed, 20 Jun 2018)
Changed paths:
M lib/galaxy/datatypes/binary.py
Log Message:
-----------
shortened code
Commit: e636bf00c64354bea8236cbfec81074f19b6a295
https://github.com/galaxyproject/galaxy/commit/e636bf00c64354bea8236cbfec81…
Author: M Bernt <m.bernt(a)ufz.de>
Date: 2018-06-20 (Wed, 20 Jun 2018)
Changed paths:
A lib/galaxy/datatypes/test/diamond.daa
Log Message:
-----------
added missing test file
Commit: a651b6af1ea04041aa4fa4230786e255b5fb954a
https://github.com/galaxyproject/galaxy/commit/a651b6af1ea04041aa4fa4230786…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-06-20 (Wed, 20 Jun 2018)
Changed paths:
M lib/galaxy/datatypes/binary.py
Log Message:
-----------
Minor cosmetics on diamond datatypes
Commit: 46788b99b2386c165a9edc899d9a0a7fdafaba05
https://github.com/galaxyproject/galaxy/commit/46788b99b2386c165a9edc899d9a…
Author: M Bernt <m.bernt(a)ufz.de>
Date: 2018-06-20 (Wed, 20 Jun 2018)
Changed paths:
M config/datatypes_conf.xml.sample
Log Message:
-----------
added sniffer entry in data_types.conf.sample
Commit: 891b8923bfbdd9c51e41f334185589b4ca87280d
https://github.com/galaxyproject/galaxy/commit/891b8923bfbdd9c51e41f3341855…
Author: M Bernt <m.bernt(a)ufz.de>
Date: 2018-06-21 (Thu, 21 Jun 2018)
Changed paths:
M lib/galaxy/datatypes/binary.py
Log Message:
-----------
fixed typo in test
this commit introduces also debug output for DAA and DMND snifferes
which needs to be removed before merging
Commit: 116c7051c9f4cc8e4b36577a3477a1bfcdc4b7d9
https://github.com/galaxyproject/galaxy/commit/116c7051c9f4cc8e4b36577a3477…
Author: M Bernt <m.bernt(a)ufz.de>
Date: 2018-06-22 (Fri, 22 Jun 2018)
Changed paths:
M lib/galaxy/datatypes/binary.py
Log Message:
-----------
daa detection: fixed typo and removed debug output
Commit: 14ef3b8643eb96a98b1f39391c1f385596d1cb42
https://github.com/galaxyproject/galaxy/commit/14ef3b8643eb96a98b1f39391c1f…
Author: Björn Grüning <bjoern(a)gruenings.eu>
Date: 2018-07-05 (Thu, 05 Jul 2018)
Changed paths:
M .ci/flake8_blacklist.txt
M .travis.yml
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/apps/admin.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
A client/galaxy/scripts/components/admin/DataTypes.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/modal.js
M client/galaxy/scripts/layout/page.js
M client/galaxy/scripts/layout/panel.js
M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js
M client/galaxy/scripts/mvc/history/history-view-edit.js
M client/galaxy/scripts/mvc/history/job-dag.js
M client/galaxy/scripts/mvc/library/library-folderlist-view.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/ui/ui-misc.js
M client/galaxy/scripts/mvc/ui/ui-options.js
M client/galaxy/scripts/mvc/visualization/chart/components/model.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-manager.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/reports/run_stats.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/galaxy_bootstrap/variables.scss
M client/galaxy/style/scss/galaxy_variables.scss
M client/galaxy/style/scss/theme/blue.scss
M client/galaxy/style/scss/ui.scss
M client/galaxy/style/scss/upload.scss
M client/package.json
M client/styleguide.config.js
M client/webpack.config.js
M client/yarn.lock
M config/datatypes_conf.xml.sample
M config/plugins/visualizations/msa/config/msa.xml
M lib/galaxy/datatypes/binary.py
A lib/galaxy/datatypes/converters/bam_to_bai.xml
M lib/galaxy/datatypes/data.py
M lib/galaxy/datatypes/proteomics.py
M lib/galaxy/datatypes/sniff.py
A lib/galaxy/datatypes/test/empty.txt
M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt
M lib/galaxy/dependencies/pipfiles/develop/Pipfile.lock
M lib/galaxy/dependencies/pipfiles/develop/pinned-requirements.txt
M lib/galaxy/dependencies/pipfiles/flake8/Pipfile.lock
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/output_checker.py
M lib/galaxy/jobs/runners/chronos.py
M lib/galaxy/jobs/runners/pulsar.py
M lib/galaxy/managers/rbac_secured.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/metadata.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/actions/__init__.py
M lib/galaxy/tools/deps/__init__.py
M lib/galaxy/tools/parameters/__init__.py
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/tools/parameters/output_collect.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/util.py
M lib/galaxy/tools/parser/xml.py
M lib/galaxy/tools/relabel_from_file.xml
M lib/galaxy/tools/util/maf_utilities.py
M lib/galaxy/tools/xsd/galaxy.xsd
M lib/galaxy/util/__init__.py
M lib/galaxy/util/checkers.py
M lib/galaxy/util/json.py
M lib/galaxy/visualization/plugins/interactive_environments.py
M lib/galaxy/visualization/plugins/plugin.py
M lib/galaxy/web/framework/webapp.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/controllers/admin.py
M lib/galaxy/webapps/galaxy/controllers/workflow.py
M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py
M scripts/grt/export.py
M static/style/blue/base.css
R templates/admin/view_datatypes_registry.mako
M templates/base/base_panels.mako
M templates/webapps/galaxy/galaxy.panels.mako
M templates/webapps/galaxy/workflow/editor.mako
M templates/webapps/tool_shed/base_panels.mako
M test/api/test_tools.py
M test/functional/test_data_managers.py
M test/functional/test_toolbox.py
M test/unit/datatypes/dataproviders/test_base_dataproviders.py
M test/unit/datatypes/test_bam.py
M test/unit/jobs/test_job_output_checker.py
M test/unit/jobs/test_runner_params.py
M test/unit/test_galaxy_mapping.py
M test/unit/test_security_helper.py
M test/unit/tools/test_evaluation.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/unittest_utils/galaxy_mock.py
M test/unit/unittest_utils/tempfilecache.py
M test/unit/visualizations/plugins/test_VisualizationsRegistry.py
M test/unit/workflows/test_extract_summary.py
M tools/data_source/upload.py
Log Message:
-----------
Merge branch 'dev' into topic/daa
Commit: 9a06474a30cb82122ee6a78c30eca601af9d6578
https://github.com/galaxyproject/galaxy/commit/9a06474a30cb82122ee6a78c30ec…
Author: Björn Grüning <bjoern(a)gruenings.eu>
Date: 2018-07-05 (Thu, 05 Jul 2018)
Changed paths:
M config/datatypes_conf.xml.sample
M lib/galaxy/datatypes/binary.py
A lib/galaxy/datatypes/test/diamond.daa
Log Message:
-----------
Merge pull request #6313 from bernt-matthias/topic/daa
added daa (diamond alignment) datatype
Compare: https://github.com/galaxyproject/galaxy/compare/1f57706abffb...9a06474a30cb
**NOTE:** This service 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: 21f42f5bb6f076b3b318f5f98657929d7f66102b
https://github.com/galaxyproject/galaxy/commit/21f42f5bb6f076b3b318f5f98657…
Author: caleb <caleb.easterly(a)gmail.com>
Date: 2018-07-04 (Wed, 04 Jul 2018)
Changed paths:
M lib/galaxy/tools/parser/interface.py
Log Message:
-----------
fixes test/unit/jobs/test_job_output_checker.py
Commit: fb0cc8bb1f8a786699f861256d5d25632b50af3f
https://github.com/galaxyproject/galaxy/commit/fb0cc8bb1f8a786699f861256d5d…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2018-07-04 (Wed, 04 Jul 2018)
Changed paths:
M lib/galaxy/tools/parser/interface.py
Log Message:
-----------
Use stdioerrorlevel constants to indicate FATAL
Commit: 0d59c9cd54d49fad31767f52c07c995ff963ce18
https://github.com/galaxyproject/galaxy/commit/0d59c9cd54d49fad31767f52c07c…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-07-04 (Wed, 04 Jul 2018)
Changed paths:
R lib/galaxy/jobs/error_level.py
M lib/galaxy/jobs/output_checker.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/util.py
M lib/galaxy/tools/parser/xml.py
M test/unit/jobs/test_job_output_checker.py
Log Message:
-----------
Refactor galaxy.jobs.error_level -> galaxy.tools.parser.error_level.
Needed after 46170e9bcdcc2eb104ebab72a7afc9b7238bc314 to keep galaxy-lib from importing things outside of galaxy-lib but clearly a good refactoring on its own since it eliminates mid-file imports that were there to prevent circular dependencies from loading Galaxy.
Commit: fb229c251f7487215a285967be8b7b331c1d21f2
https://github.com/galaxyproject/galaxy/commit/fb229c251f7487215a285967be8b…
Author: Nicola Soranzo <nicola.soranzo(a)gmail.com>
Date: 2018-07-04 (Wed, 04 Jul 2018)
Changed paths:
R lib/galaxy/jobs/error_level.py
M lib/galaxy/jobs/output_checker.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/util.py
M lib/galaxy/tools/parser/xml.py
M test/unit/jobs/test_job_output_checker.py
Log Message:
-----------
Merge pull request #6438 from caleb-easterly/test_job_output_checker_py3
fixes test/unit/jobs/test_job_output_checker.py; strange default?
Compare: https://github.com/galaxyproject/galaxy/compare/cc0022d5d1cc...fb229c251f74
**NOTE:** This service 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.