April 2017 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] c85738: Merge ToolConfWatchers and separate from Toolbox
by GitHub 07 Apr '17

07 Apr '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c8573888232f15ef3641bfeb2f0d92a7aa80387f https://github.com/galaxyproject/galaxy/commit/c8573888232f15ef3641bfeb2f0d… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-03-27 (Mon, 27 Mar 2017) Changed paths: M lib/galaxy/app.py M lib/galaxy/queue_worker.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/data_manager/manager.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/watcher.py Log Message: ----------- Merge ToolConfWatchers and separate from Toolbox This should avoid some complexities associated with managing threads. I would also like to eliminate the separate reload_tool_data_tables and reload_data_managers callbacks and do this when reloading the toolbox, but every tool data table reload triggers twice the download of http://igv.broadinstitute.org/genomes/genomes.txt, which each time takes 2 seconds. Commit: 1a5e337420e4832593b6e30089c0022291fd6078 https://github.com/galaxyproject/galaxy/commit/1a5e337420e4832593b6e30089c0… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-04-03 (Mon, 03 Apr 2017) Changed paths: M .ci/flake8_lint_include_list.txt M lib/galaxy/app.py M lib/galaxy/tools/toolbox/watcher.py A lib/galaxy/webapps/galaxy/config_watchers.py Log Message: ----------- Move ConfigWatchers into galaxy.webapps.galaxy.config_watchers Commit: f79fb9075a4f724d5bad95163a6450c9ffb89b84 https://github.com/galaxyproject/galaxy/commit/f79fb9075a4f724d5bad95163a64… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-04-03 (Mon, 03 Apr 2017) Changed paths: M lib/galaxy/app.py M lib/galaxy/config.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/webapps/galaxy/config_watchers.py M test/unit/tools/test_toolbox.py Log Message: ----------- Move ToolWatcher from Toolbox to ConfigWatchers class Commit: 63f1efd15a6903526406ff8d643fb3d6f4a5e678 https://github.com/galaxyproject/galaxy/commit/63f1efd15a6903526406ff8d643f… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-04-03 (Mon, 03 Apr 2017) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Fix toolshed startup Commit: c4e6671ce50a64ba561a3ef815816426183adf4d https://github.com/galaxyproject/galaxy/commit/c4e6671ce50a64ba561a3ef81581… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-04-03 (Mon, 03 Apr 2017) Changed paths: M lib/galaxy/webapps/galaxy/config_watchers.py Log Message: ----------- Fix import order in config_watchers.py Commit: b037332e943edbf9cf65f4799a1226bf53e8476a https://github.com/galaxyproject/galaxy/commit/b037332e943edbf9cf65f4799a12… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-04-03 (Mon, 03 Apr 2017) Changed paths: M lib/galaxy/webapps/galaxy/config_watchers.py Log Message: ----------- Avoid race-condition between multiple instances of ToolConfWatchers Commit: 2c7089df46fa0a5178a1e0f72cc87514e8a97142 https://github.com/galaxyproject/galaxy/commit/2c7089df46fa0a5178a1e0f72cc8… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-04-03 (Mon, 03 Apr 2017) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Fix TS tests Commit: e7a4ae5c154e5a9a9d2767c76ea043c5fd846fe8 https://github.com/galaxyproject/galaxy/commit/e7a4ae5c154e5a9a9d2767c76ea0… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-04-07 (Fri, 07 Apr 2017) Changed paths: M .ci/flake8_lint_include_list.txt M lib/galaxy/app.py M lib/galaxy/config.py M lib/galaxy/queue_worker.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/data_manager/manager.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/watcher.py A lib/galaxy/webapps/galaxy/config_watchers.py M test/unit/tools/test_toolbox.py Log Message: ----------- Merge pull request #3821 from mvdbeek/repository_updates Merge ToolConfWatchers and separate from Toolbox Compare: https://github.com/galaxyproject/galaxy/compare/b5323e714726...e7a4ae5c154e

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[galaxyproject/galaxy] 82fe42: Hardklor and kronik datatypes for proteomics
by GitHub 07 Apr '17

07 Apr '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 82fe4262148ae462eb4fe5012e4c7c03ec9be7b8 https://github.com/galaxyproject/galaxy/commit/82fe4262148ae462eb4fe5012e4c… Author: Jorrit Boekel <jorrit.boekel(a)scilifelab.se> Date: 2017-04-05 (Wed, 05 Apr 2017) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Hardklor and kronik datatypes for proteomics Commit: c10a23b924983f11565c6a8976b80f6c65b97955 https://github.com/galaxyproject/galaxy/commit/c10a23b924983f11565c6a8976b8… Author: Jorrit Boekel <jorrit.boekel(a)scilifelab.se> Date: 2017-04-05 (Wed, 05 Apr 2017) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- More recognizable naming for datatype extensions Commit: b5323e7147266ccd14728e5b4783350c7704be30 https://github.com/galaxyproject/galaxy/commit/b5323e7147266ccd14728e5b4783… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-04-07 (Fri, 07 Apr 2017) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Merge pull request #3884 from glormph/kronik_proteomics_datatype Hardklor and kronik datatypes for proteomics Compare: https://github.com/galaxyproject/galaxy/compare/f5ade2b5daab...b5323e714726

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[galaxyproject/galaxy] 2b4b43: Add missing trigger event to drop handler in conte...
by GitHub 07 Apr '17

07 Apr '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 2b4b431d0a4f300c1af3d9ac4a105e7887ec09c6 https://github.com/galaxyproject/galaxy/commit/2b4b431d0a4f300c1af3d9ac4a10… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-04-06 (Thu, 06 Apr 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-content.js M static/maps/mvc/ui/ui-select-content.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/ui/ui-select-content.js Log Message: ----------- Add missing trigger event to drop handler in content selector Commit: ea17f2dacf8b00e579741676deb33a98d0c234ef https://github.com/galaxyproject/galaxy/commit/ea17f2dacf8b00e579741676deb3… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-04-06 (Thu, 06 Apr 2017) Changed paths: M client/galaxy/scripts/mvc/collection/collection-view-edit.js M client/galaxy/scripts/mvc/collection/collection-view.js M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/history/hda-li.js M client/galaxy/scripts/mvc/history/hdca-li.js M client/galaxy/scripts/mvc/tag.js M client/package.json M client/webpack.config.js M lib/galaxy/managers/collections.py M lib/galaxy/managers/hdas.py M lib/galaxy/managers/hdcas.py M lib/galaxy/managers/tags.py M lib/galaxy/tools/actions/__init__.py M static/maps/mvc/collection/collection-view-edit.js.map M static/maps/mvc/collection/collection-view.js.map M static/maps/mvc/dataset/dataset-li.js.map M static/maps/mvc/history/hda-li.js.map M static/maps/mvc/history/hdca-li.js.map M static/maps/mvc/tag.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/collection/collection-view-edit.js M static/scripts/mvc/collection/collection-view.js M static/scripts/mvc/dataset/dataset-li.js M static/scripts/mvc/history/hda-li.js M static/scripts/mvc/history/hdca-li.js M static/scripts/mvc/tag.js Log Message: ----------- Merge branch 'dev' into fix_refresh_trigger Commit: f5ade2b5daab6fbf3fa924cbda89fbf21e7373a9 https://github.com/galaxyproject/galaxy/commit/f5ade2b5daab6fbf3fa924cbda89… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-04-07 (Fri, 07 Apr 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-content.js M static/maps/mvc/ui/ui-select-content.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/ui/ui-select-content.js Log Message: ----------- Merge pull request #3897 from guerler/fix_refresh_trigger Add missing trigger event to drop handler in content selector Compare: https://github.com/galaxyproject/galaxy/compare/408906efb118...f5ade2b5daab

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[galaxyproject/galaxy] e085f8: Routes cleanup -- this adjust_hidden route is unne...
by GitHub 07 Apr '17

07 Apr '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e085f8cb41a00668efa6108b3caf9e7dbbc712f2 https://github.com/galaxyproject/galaxy/commit/e085f8cb41a00668efa6108b3caf… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-04-06 (Thu, 06 Apr 2017) Changed paths: M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Routes cleanup -- this adjust_hidden route is unnecessary and is handled by the normal controller logic. Commit: a2a64821b4511db810865e75e991e19fc365f6f9 https://github.com/galaxyproject/galaxy/commit/a2a64821b4511db810865e75e991… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-04-06 (Thu, 06 Apr 2017) Changed paths: M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- This login route is also unnecessary Commit: 408906efb118dc4f36d134c632667101d34a666e https://github.com/galaxyproject/galaxy/commit/408906efb118dc4f36d134c63266… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-04-07 (Fri, 07 Apr 2017) Changed paths: M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Merge pull request #3895 from dannon/routes_cleanup Routes cleanup Compare: https://github.com/galaxyproject/galaxy/compare/5b880697c23e...408906efb118

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[galaxyproject/galaxy] ab1f7e: synchronise against latest UCSC versions
by GitHub 07 Apr '17

07 Apr '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ab1f7eae4d0f1836dad4e52a75dbc18f9bd20336 https://github.com/galaxyproject/galaxy/commit/ab1f7eae4d0f1836dad4e52a75db… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2017-04-05 (Wed, 05 Apr 2017) Changed paths: M tool-data/shared/ucsc/builds.txt.sample M tool-data/shared/ucsc/ucsc_build_sites.txt.sample Log Message: ----------- synchronise against latest UCSC versions Commit: cac9c980dfce7e22d076cec4032facd1c011d33f https://github.com/galaxyproject/galaxy/commit/cac9c980dfce7e22d076cec4032f… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-04-07 (Fri, 07 Apr 2017) Changed paths: M tool-data/shared/ucsc/ucsc_build_sites.txt.sample Log Message: ----------- remove obsolete line Commit: 5b880697c23e2cdf1c4339976db2bf7d6a9a1c62 https://github.com/galaxyproject/galaxy/commit/5b880697c23e2cdf1c4339976db2… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-04-07 (Fri, 07 Apr 2017) Changed paths: M tool-data/shared/ucsc/builds.txt.sample M tool-data/shared/ucsc/ucsc_build_sites.txt.sample Log Message: ----------- Merge pull request #3874 from bgruening/new_ucsc synchronise against latest UCSC versions Compare: https://github.com/galaxyproject/galaxy/compare/8ea4cf29f812...5b880697c23e

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[galaxyproject/infrastructure-playbook] 3a24bb: Docker SSL fixes (distribute from playbook if nece...
by GitHub 07 Apr '17

07 Apr '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 3a24bb310885f6a529e28aa6c8424e991223a45d https://github.com/galaxyproject/infrastructure-playbook/commit/3a24bb31088… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-04-07 (Fri, 07 Apr 2017) Changed paths: A common_env/group_vars/dockersslclients.yml A common_env/secret_group_vars/dockersslclients.yml M roles/docker/defaults/main.yml M roles/docker/tasks/ssl-ca.yml M roles/docker/tasks/ssl-client.yml M roles/docker/tasks/ssl-server.yml A taccenv/group_vars/dockersslclients.yml M taccenv/host_vars/galaxy07.tacc.utexas.edu.yml M taccenv/inventory M taccenv/playbook.yml A taccenv/secret_group_vars/dockersslclients.yml Log Message: ----------- Docker SSL fixes (distribute from playbook if necessary, e.g. for cases where the docker ssl master cannot ssh directly to ansible_user@client).

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[galaxyproject/galaxy] f88d89: Add HistoryDatasetCollectionAssociation as a possi...
by GitHub 06 Apr '17

06 Apr '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f88d893562112223553ba069eff2a1f42fe7d69b https://github.com/galaxyproject/galaxy/commit/f88d893562112223553ba069eff2… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-28 (Tue, 28 Mar 2017) Changed paths: M lib/galaxy/managers/tags.py Log Message: ----------- Add HistoryDatasetCollectionAssociation as a possible tagged item in the galaxy tag manager. Should refactor this down the road, feels weird to register everything here in the manager. Commit: 73bfb57abf5ba728e4145731f91d0b222d74f5df https://github.com/galaxyproject/galaxy/commit/73bfb57abf5ba728e4145731f91d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-28 (Tue, 28 Mar 2017) Changed paths: M lib/galaxy/managers/collections.py Log Message: ----------- Use the correct tag manager instance from the Collections manager. Commit: 5ceca34344b92d6bfa63ad1eb433a1cdea893f4f https://github.com/galaxyproject/galaxy/commit/5ceca34344b92d6bfa63ad1eb433… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-28 (Tue, 28 Mar 2017) Changed paths: M client/galaxy/scripts/mvc/collection/collection-view-edit.js M client/galaxy/scripts/mvc/collection/collection-view.js M lib/galaxy/managers/collections.py M static/maps/mvc/collection/collection-view-edit.js.map M static/maps/mvc/collection/collection-view.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/collection/collection-view-edit.js M static/scripts/mvc/collection/collection-view.js Log Message: ----------- Add basic tag rendering to expanded collection Commit: 821ee5bbcbfdd9a79c52ac60a20a51e20898b573 https://github.com/galaxyproject/galaxy/commit/821ee5bbcbfdd9a79c52ac60a20a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-28 (Tue, 28 Mar 2017) Changed paths: M client/galaxy/scripts/mvc/collection/collection-view-edit.js M static/maps/mvc/collection/collection-view-edit.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/collection/collection-view-edit.js Log Message: ----------- Simplify tags usage, since this editor's display is static. Commit: 4a45c9097e5c7d19977196d3ade1cd949af5af03 https://github.com/galaxyproject/galaxy/commit/4a45c9097e5c7d19977196d3ade1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-28 (Tue, 28 Mar 2017) Changed paths: M client/package.json M client/webpack.config.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map Log Message: ----------- Add babel loader. Commit: 2a86f8e54c95da45b59fe166d515fc40b06f3c26 https://github.com/galaxyproject/galaxy/commit/2a86f8e54c95da45b59fe166d515… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-28 (Tue, 28 Mar 2017) Changed paths: M lib/galaxy/managers/hdcas.py Log Message: ----------- Add tags to hdca serializer. TODO: Details only. Commit: 225393a30006ca0313585de1a4bd93b3f0d88566 https://github.com/galaxyproject/galaxy/commit/225393a30006ca0313585de1a4bd… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-28 (Tue, 28 Mar 2017) Changed paths: M lib/galaxy/managers/hdcas.py Log Message: ----------- Add nametags to dataset collection serializer Commit: c4fd96092bcabd869f8c4a4427489d0b2c6209a3 https://github.com/galaxyproject/galaxy/commit/c4fd96092bcabd869f8c4a442748… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-30 (Thu, 30 Mar 2017) Changed paths: M client/galaxy/scripts/mvc/tag.js M static/maps/mvc/tag.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tag.js Log Message: ----------- Make TagEditor label optional. Commit: c452af01bd16cf85e7459f767ee77c381e527a9a https://github.com/galaxyproject/galaxy/commit/c452af01bd16cf85e7459f767ee7… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-31 (Fri, 31 Mar 2017) Changed paths: M client/galaxy/scripts/mvc/history/hdca-li.js M static/maps/mvc/history/hdca-li.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/history/hdca-li.js Log Message: ----------- Render 'nametags' for hdcas Commit: 2f4aa1a763146e980f9c1c929f07ffd4b7bf7ff3 https://github.com/galaxyproject/galaxy/commit/2f4aa1a763146e980f9c1c929f07… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-31 (Fri, 31 Mar 2017) Changed paths: M client/galaxy/scripts/mvc/collection/collection-view-edit.js M static/maps/mvc/collection/collection-view-edit.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/collection/collection-view-edit.js Log Message: ----------- Toggle tags prompt on collection view Commit: 01655895174eb14530d27452789682335b2f7197 https://github.com/galaxyproject/galaxy/commit/01655895174eb14530d274527896… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-31 (Fri, 31 Mar 2017) Changed paths: M client/galaxy/scripts/mvc/collection/collection-view.js M static/maps/mvc/collection/collection-view.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/collection/collection-view.js Log Message: ----------- Tags editor location/styling fix for collection view. Commit: c9bbaa30f7400f547e8549ae8d0d3bed5ccbf0c5 https://github.com/galaxyproject/galaxy/commit/c9bbaa30f7400f547e8549ae8d0d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-04-04 (Tue, 04 Apr 2017) Changed paths: M .ci/flake8_lint_include_list.txt M CONTRIBUTING.md M client/galaxy/scripts/mvc/collection/base-creator.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/history/history-contents.js M client/galaxy/scripts/mvc/history/history-view-edit.js M client/galaxy/scripts/mvc/tool/tools.js M client/galaxy/scripts/mvc/ui/ui-options.js A client/galaxy/scripts/mvc/upload/collection/collection-row.js A client/galaxy/scripts/mvc/upload/collection/collection-view.js M client/galaxy/scripts/mvc/upload/upload-view.js M client/galaxy/style/less/ui/paired-collection-creator.less M client/galaxy/style/less/upload.less M config/datatypes_conf.xml.sample M config/galaxy.ini.sample A config/plugins/interactive_environments/ethercalc/config/allowed_images.yml.sample M config/plugins/interactive_environments/ethercalc/config/ethercalc.ini.sample A config/plugins/visualizations/charts/static/repository/build/biojs_phylocanvas.js A config/plugins/visualizations/charts/static/repository/build/biojs_phylocanvas.js.map R config/plugins/visualizations/charts/static/repository/build/cytoscape_basic.js R config/plugins/visualizations/charts/static/repository/build/cytoscape_basic.js.map A config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js A config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js.map M config/plugins/visualizations/charts/static/repository/build/registry.js M config/plugins/visualizations/charts/static/repository/build/registry.js.map M config/plugins/visualizations/charts/static/repository/build/registry.tmp.js A config/plugins/visualizations/charts/static/repository/plugins/biojs/phylocanvas/phylocanvas.js M config/plugins/visualizations/charts/static/repository/registry.json A config/plugins/visualizations/charts/static/repository/utilities/sifjson.js M config/plugins/visualizations/charts/static/repository/utilities/utils.js A config/plugins/visualizations/charts/static/repository/visualizations/biojs/phylocanvas/config.js A config/plugins/visualizations/charts/static/repository/visualizations/biojs/phylocanvas/logo.png A config/plugins/visualizations/charts/static/repository/visualizations/biojs/phylocanvas/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/basic/config.js R config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/basic/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/basic/wrapper.js A config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/config.js A config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/logo.png A config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/wrapper.js M display_applications/igv/bigwig.xml M doc/source/admin/framework_dependencies.rst M doc/source/admin/index.rst A doc/source/admin/reports.md M doc/source/admin/useful_scripts.rst A doc/source/api/api.rst A doc/source/api/ts_api.rst M doc/source/api_doc.rst M doc/source/conf.py M doc/source/index.rst R doc/source/lib/galaxy.webapps.galaxy.api.rst R doc/source/lib/galaxy.webapps.tool_shed.api.rst M doc/source/releases/_header.rst M doc/source/ts_api_doc.rst M lib/galaxy/config.py M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/util/gff_util.py M lib/galaxy/jobs/__init__.py M lib/galaxy/managers/collections.py M lib/galaxy/managers/collections_util.py M lib/galaxy/managers/datasets.py M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/deps/views.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/web/base/controllers/admin.py M lib/galaxy/webapps/galaxy/api/folder_contents.py M lib/galaxy/webapps/galaxy/api/library_contents.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run.py M lib/galaxy/workflow/scheduling_manager.py M static/maps/mvc/collection/base-creator.js.map M static/maps/mvc/collection/list-collection-creator.js.map M static/maps/mvc/collection/list-of-pairs-collection-creator.js.map M static/maps/mvc/collection/pair-collection-creator.js.map M static/maps/mvc/history/history-contents.js.map M static/maps/mvc/history/history-view-edit.js.map M static/maps/mvc/tool/tools.js.map M static/maps/mvc/ui/ui-options.js.map A static/maps/mvc/upload/collection/collection-row.js.map A static/maps/mvc/upload/collection/collection-view.js.map M static/maps/mvc/upload/upload-view.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/collection/base-creator.js M static/scripts/mvc/collection/list-collection-creator.js M static/scripts/mvc/collection/list-of-pairs-collection-creator.js M static/scripts/mvc/collection/pair-collection-creator.js M static/scripts/mvc/history/history-contents.js M static/scripts/mvc/history/history-view-edit.js M static/scripts/mvc/tool/tools.js M static/scripts/mvc/ui/ui-options.js A static/scripts/mvc/upload/collection/collection-row.js A static/scripts/mvc/upload/collection/collection-view.js M static/scripts/mvc/upload/upload-view.js M static/style/blue/base.css M templates/webapps/galaxy/admin/manage_dependencies.mako M test/api/test_history_contents.py M test/api/test_jobs.py M test/api/test_libraries.py M test/api/test_tools.py M test/api/test_users.py M test/api/test_workflows.py M test/api/test_workflows_from_yaml.py M test/base/api_asserts.py M test/base/data/test_workflow_pause.ga M test/base/driver_util.py M test/base/populators.py M test/functional/tools/create_10.xml A test/functional/tools/create_2.xml A test/functional/tools/identifier_multiple_in_conditional.xml A test/functional/tools/identifier_multiple_in_repeat.xml M test/functional/tools/samples_tool_conf.xml M test/galaxy_selenium/has_driver.py M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/sizzle.py A test/integration/test_maximum_worklfow_invocation_duration.py A test/integration/test_workflow_handler_configuration.py A test/integration/workflow_handler_configuration_job_conf.xml M test/qunit/test-data/paired-collection-creator.data.js M test/selenium_tests/test_collection_builders.py M test/selenium_tests/test_tool_form.py M test/selenium_tests/test_uploads.py M test/shed_functional/functional/test_1090_repository_dependency_handling.py Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into tags_improvements Commit: 439444e65ad9c79a0a2553a5eb916405b1910e93 https://github.com/galaxyproject/galaxy/commit/439444e65ad9c79a0a2553a5eb91… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-04-04 (Tue, 04 Apr 2017) Changed paths: M lib/galaxy/managers/collections.py M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Preserve tags for collection outputs. This is one step forward, also need to address non-output handled collectinos, like those automatically created in workflow execution with collection inputs. Commit: bfbca68b4e70cc380398e364dd8abdd5ac1a360e https://github.com/galaxyproject/galaxy/commit/bfbca68b4e70cc380398e364dd8a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-04-04 (Tue, 04 Apr 2017) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Don't wrap tags up in element_kwds -- this prevents them being sent to non-hda collections. Commit: 6ce47ddbf4ed0046f52cd6c7d4f140c893d9b1e3 https://github.com/galaxyproject/galaxy/commit/6ce47ddbf4ed0046f52cd6c7d4f1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-04-04 (Tue, 04 Apr 2017) Changed paths: M lib/galaxy/managers/collections.py Log Message: ----------- Also include implicit_collection_info in collection tag creation logic. Commit: bdcc474d3666fd08f0032629e1882a4441b35244 https://github.com/galaxyproject/galaxy/commit/bdcc474d3666fd08f0032629e188… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-04-05 (Wed, 05 Apr 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/mvc/ui/ui-table.js A client/galaxy/scripts/mvc/user/user-custom-builds.js M client/galaxy/scripts/mvc/user/user-preferences.js M client/galaxy/style/less/ui.less M lib/galaxy/web/framework/base.py M lib/galaxy/webapps/galaxy/api/histories.py M lib/galaxy/webapps/galaxy/api/users.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/user.py A static/GruntFile.js A static/GruntFile.js.map M static/maps/layout/menu.js.map M static/maps/mvc/form/form-parameters.js.map M static/maps/mvc/ui/ui-misc.js.map M static/maps/mvc/ui/ui-table.js.map A static/maps/mvc/user/user-custom-builds.js.map M static/maps/mvc/user/user-preferences.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/menu.js M static/scripts/mvc/form/form-parameters.js M static/scripts/mvc/ui/ui-misc.js M static/scripts/mvc/ui/ui-table.js A static/scripts/mvc/user/user-custom-builds.js M static/scripts/mvc/user/user-preferences.js M static/style/blue/base.css R templates/user/dbkeys.mako M tools/filters/trimmer.py M tools/filters/trimmer.xml Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into tags_improvements Commit: 54b7c32bd2913c236c4eacfaf45bdef3ba4c2e7d https://github.com/galaxyproject/galaxy/commit/54b7c32bd2913c236c4eacfaf45b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-04-05 (Wed, 05 Apr 2017) Changed paths: M client/galaxy/scripts/mvc/history/hda-li.js M client/galaxy/scripts/mvc/history/hdca-li.js M lib/galaxy/managers/hdas.py M lib/galaxy/managers/hdcas.py M static/maps/mvc/history/hda-li.js.map M static/maps/mvc/history/hdca-li.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/history/hda-li.js M static/scripts/mvc/history/hdca-li.js Log Message: ----------- Render nametags from core tag data instead of a different field. This actually should be somewhat faster, along with being easier to track/update. Commit: 2215869f2d68c1839091dc23cf303bf43fa29078 https://github.com/galaxyproject/galaxy/commit/2215869f2d68c1839091dc23cf30… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-04-05 (Wed, 05 Apr 2017) Changed paths: M client/galaxy/scripts/mvc/history/hda-li.js M client/galaxy/scripts/mvc/history/hdca-li.js M client/galaxy/scripts/mvc/tag.js M static/maps/mvc/history/hda-li.js.map M static/maps/mvc/history/hdca-li.js.map M static/maps/mvc/tag.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/history/hda-li.js M static/scripts/mvc/history/hdca-li.js M static/scripts/mvc/tag.js Log Message: ----------- Listen to tag change events, rerender list item for nametags. Commit: 5a513b20bbc371cf9a51483b1cf468d9126a45fe https://github.com/galaxyproject/galaxy/commit/5a513b20bbc371cf9a51483b1cf4… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-04-05 (Wed, 05 Apr 2017) Changed paths: M client/galaxy/scripts/mvc/tag.js M static/maps/mvc/tag.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tag.js Log Message: ----------- Remove (previously) never-invoked change code which now double-invokes. Parents will handle this. Commit: d41a4efd8822c46aa9f236937d4fc74678ba0dfd https://github.com/galaxyproject/galaxy/commit/d41a4efd8822c46aa9f236937d4f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-04-05 (Wed, 05 Apr 2017) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li.js M static/maps/mvc/dataset/dataset-li.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/dataset/dataset-li.js Log Message: ----------- For datasets, only rerender title bar if tags have changed (for nametags) Commit: 2ab68fea8b20c256c30afd7e18bcf2647c978396 https://github.com/galaxyproject/galaxy/commit/2ab68fea8b20c256c30afd7e18bc… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-04-05 (Wed, 05 Apr 2017) Changed paths: M client/galaxy/scripts/mvc/history/hda-li.js M static/maps/mvc/history/hda-li.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/history/hda-li.js Log Message: ----------- Remove redundant listener, handled in parent. Commit: 9e9a2d8312990c11ff7d9df6e71927bdc3210514 https://github.com/galaxyproject/galaxy/commit/9e9a2d8312990c11ff7d9df6e719… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-04-05 (Wed, 05 Apr 2017) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li.js M static/maps/mvc/dataset/dataset-li.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/dataset/dataset-li.js Log Message: ----------- Rerender specifically subtitle iff it's the only changed attribute. Commit: cad62b1f8b5d289dc27ec88303118dadddbbbc52 https://github.com/galaxyproject/galaxy/commit/cad62b1f8b5d289dc27ec8830311… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-04-06 (Thu, 06 Apr 2017) Changed paths: M client/galaxy/scripts/mvc/history/history-view-edit.js M client/galaxy/scripts/mvc/ui/ui-select-content.js M client/galaxy/style/less/ui.less M config/tool_destinations.yml.sample M lib/galaxy/jobs/dynamic_tool_destination.py M lib/galaxy/tools/wrappers.py M lib/galaxy/webapps/galaxy/api/histories.py M lib/galaxy/webapps/galaxy/api/users.py M lib/galaxy/webapps/galaxy/buildapp.py R lib/galaxy/webapps/galaxy/controllers/search.py M run_tests.sh M static/maps/mvc/history/history-view-edit.js.map M static/maps/mvc/ui/ui-select-content.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/history/history-view-edit.js M static/scripts/mvc/ui/ui-select-content.js M static/style/blue/base.css Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into tags_improvements Commit: 1a5d570704da50bdca0ca3194f5549f1338f2c6b https://github.com/galaxyproject/galaxy/commit/1a5d570704da50bdca0ca3194f55… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-04-06 (Thu, 06 Apr 2017) Changed paths: M client/galaxy/scripts/mvc/collection/collection-view-edit.js M static/maps/mvc/collection/collection-view-edit.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Remove comment, rebuild. Commit: 8ea4cf29f812d8ce29b31efa18495aad5d5fca44 https://github.com/galaxyproject/galaxy/commit/8ea4cf29f812d8ce29b31efa1849… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2017-04-06 (Thu, 06 Apr 2017) Changed paths: M client/galaxy/scripts/mvc/collection/collection-view-edit.js M client/galaxy/scripts/mvc/collection/collection-view.js M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/history/hda-li.js M client/galaxy/scripts/mvc/history/hdca-li.js M client/galaxy/scripts/mvc/tag.js M client/package.json M client/webpack.config.js M lib/galaxy/managers/collections.py M lib/galaxy/managers/hdas.py M lib/galaxy/managers/hdcas.py M lib/galaxy/managers/tags.py M lib/galaxy/tools/actions/__init__.py M static/maps/mvc/collection/collection-view-edit.js.map M static/maps/mvc/collection/collection-view.js.map M static/maps/mvc/dataset/dataset-li.js.map M static/maps/mvc/history/hda-li.js.map M static/maps/mvc/history/hdca-li.js.map M static/maps/mvc/tag.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/collection/collection-view-edit.js M static/scripts/mvc/collection/collection-view.js M static/scripts/mvc/dataset/dataset-li.js M static/scripts/mvc/history/hda-li.js M static/scripts/mvc/history/hdca-li.js M static/scripts/mvc/tag.js Log Message: ----------- Merge pull request #3868 from dannon/tags_improvements Adding tagging to collections. Compare: https://github.com/galaxyproject/galaxy/compare/483f25c5c2c8...8ea4cf29f812

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[galaxyproject/galaxy] 95fd21: Adding bug fix for SIF files
by GitHub 06 Apr '17

06 Apr '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 95fd21230b7f73434a4af60b6624b499efcaa1af https://github.com/galaxyproject/galaxy/commit/95fd21230b7f73434a4af60b6624… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-04-06 (Thu, 06 Apr 2017) Changed paths: M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js.map M config/plugins/visualizations/charts/static/repository/build/registry.js M config/plugins/visualizations/charts/static/repository/build/registry.js.map M config/plugins/visualizations/charts/static/repository/utilities/sifjson.js Log Message: ----------- Adding bug fix for SIF files Commit: ee66994c44cda791ab4c0d5c8fe72dff4edd2710 https://github.com/galaxyproject/galaxy/commit/ee66994c44cda791ab4c0d5c8fe7… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-04-06 (Thu, 06 Apr 2017) Changed paths: M lib/galaxy/tools/wrappers.py M lib/galaxy/webapps/galaxy/buildapp.py R lib/galaxy/webapps/galaxy/controllers/search.py M run_tests.sh Log Message: ----------- Merge branch 'dev' of https://github.com/bgruening/galaxy into bugfix_cytoscape Commit: 483f25c5c2c8d375d6096d9ca239618e413dde45 https://github.com/galaxyproject/galaxy/commit/483f25c5c2c8d375d6096d9ca239… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-04-06 (Thu, 06 Apr 2017) Changed paths: M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js.map M config/plugins/visualizations/charts/static/repository/build/registry.js M config/plugins/visualizations/charts/static/repository/build/registry.js.map M config/plugins/visualizations/charts/static/repository/utilities/sifjson.js Log Message: ----------- Merge pull request #3896 from bgruening/bugfix_cytoscape Cytoscape bugfix for SIF files Compare: https://github.com/galaxyproject/galaxy/compare/69ff6ab906d9...483f25c5c2c8

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[galaxyproject/ansible-galaxy]
by GitHub 06 Apr '17

06 Apr '17

Branch: refs/tags/0.7 Home: https://github.com/galaxyproject/ansible-galaxy

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[galaxyproject/ansible-galaxy] c9f923: Remove a lot of cruft, switch to yaml-style task p...
by GitHub 06 Apr '17

06 Apr '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/ansible-galaxy Commit: c9f923ad2691df71df75658cebd87f4249ab268c https://github.com/galaxyproject/ansible-galaxy/commit/c9f923ad2691df71df75… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-04-06 (Thu, 06 Apr 2017) Changed paths: M README.md M defaults/main.yml M files/makepyc.py M handlers/main.yml M tasks/clone.yml M tasks/database.yml M tasks/dependencies.yml M tasks/download.yml M tasks/main.yml M tasks/mutable_setup.yml M tasks/static_setup.yml M tasks/virtualenv.yml Log Message: ----------- Remove a lot of cruft, switch to yaml-style task params, and update for Ansible 2.2 compatibility

1 0