- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] ac44db: Update tool_conf.xml.main to reflect main's curren...
by GitHub 07 Jul '17

07 Jul '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ac44dbb533284bb47e4190b16821311984129d8a https://github.com/galaxyproject/galaxy/commit/ac44dbb533284bb47e4190b16821… Author: Dave B <dave(a)bx.psu.edu> Date: 2017-07-07 (Fri, 07 Jul 2017) Changed paths: M config/tool_conf.xml.main Log Message: ----------- Update tool_conf.xml.main to reflect main's current state. Commit: c169c3a0908addeff88bae6a86f2e5ef199aeb3c https://github.com/galaxyproject/galaxy/commit/c169c3a0908addeff88bae6a86f2… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-07-07 (Fri, 07 Jul 2017) Changed paths: M config/tool_conf.xml.main Log Message: ----------- Merge pull request #4295 from davebx/update_main_tool_conf Update tool_conf.xml.main to reflect main's current state. Compare: https://github.com/galaxyproject/galaxy/compare/ba5549b47193...c169c3a0908a

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[galaxyproject/galaxy] 26d48c: Fix empty tabular output error when using discover...
by GitHub 06 Jul '17

06 Jul '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 26d48c876cd2bd39bd8c0e404d54e6de520ce1df https://github.com/galaxyproject/galaxy/commit/26d48c876cd2bd39bd8c0e404d54… Author: Pierrick Roger Mele <pierrick.rogermele(a)icloud.com> Date: 2017-06-26 (Mon, 26 Jun 2017) Changed paths: M lib/galaxy/datatypes/tabular.py A tools/mtbls-dwnld Log Message: ----------- Fix empty tabular output error when using discover_datasets. Commit: 4b9b3724e87e7ea0c6b81da36df5f6b00124c6c6 https://github.com/galaxyproject/galaxy/commit/4b9b3724e87e7ea0c6b81da36df5… Author: Pierrick Roger Mele <pierrick.rogermele(a)icloud.com> Date: 2017-06-28 (Wed, 28 Jun 2017) Changed paths: R tools/mtbls-dwnld Log Message: ----------- Remove tool symbolic link added by accident. Commit: edbe273a95d727278b37c4457912e27355ec2cf3 https://github.com/galaxyproject/galaxy/commit/edbe273a95d727278b37c4457912… Author: Pierrick Roger Mele <pierrick.rogermele(a)icloud.com> Date: 2017-06-28 (Wed, 28 Jun 2017) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M .gitignore M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/panels/tool-panel.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/layout/panel.js M client/galaxy/scripts/mvc/grid/grid-view.js A client/galaxy/scripts/mvc/history/history-list.js M client/galaxy/scripts/mvc/history/history-view-edit-current.js M client/galaxy/scripts/mvc/history/options-menu.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/user/user-preferences.js M client/galaxy/scripts/mvc/webhooks.js M client/galaxy/scripts/mvc/workflow/workflow-configure-menu.js M client/galaxy/scripts/mvc/workflow/workflow.js M client/galaxy/scripts/onload.js M client/galaxy/scripts/utils/utils.js M client/galaxy/style/less/base.less M config/plugins/interactive_environments/neo/config/allowed_images.yml.sample M config/plugins/interactive_environments/neo/config/neo.ini.sample M config/plugins/interactive_environments/neo/config/neo.xml M config/plugins/webhooks/demo/search/config/searchover.yaml M config/plugins/webhooks/demo/search/static/script.js M config/plugins/webhooks/demo/tool_list/helper/__init__.py A config/plugins/webhooks/demo/tour_generator/config/tour_generator.yml A config/plugins/webhooks/demo/tour_generator/helper/__init__.py A config/plugins/webhooks/demo/tour_generator/static/script.js A config/plugins/webhooks/demo/tour_generator/static/styles.css M cron/updateucsc.sh.sample M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/registry.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/deps/mulled/invfile.lua M lib/galaxy/tools/deps/mulled/mulled_build.py M lib/galaxy/tools/deps/mulled/mulled_build_files.py M lib/galaxy/tools/deps/mulled/mulled_build_tool.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/wrappers.py M lib/galaxy/webapps/galaxy/api/webhooks.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M scripts/api/library_upload_dir.py M static/maps/layout/menu.js.map M static/maps/layout/page.js.map M static/maps/layout/panel.js.map M static/maps/mvc/grid/grid-view.js.map A static/maps/mvc/history/history-list.js.map M static/maps/mvc/history/history-view-edit-current.js.map M static/maps/mvc/history/options-menu.js.map M static/maps/mvc/tool/tool-form-base.js.map M static/maps/mvc/tool/tool-form-composite.js.map M static/maps/mvc/tool/tool-form.js.map M static/maps/mvc/user/user-preferences.js.map M static/maps/mvc/webhooks.js.map M static/maps/mvc/workflow/workflow-configure-menu.js.map M static/maps/mvc/workflow/workflow.js.map M static/maps/onload.js.map M static/maps/utils/utils.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.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/layout/menu.js M static/scripts/layout/page.js M static/scripts/layout/panel.js M static/scripts/mvc/grid/grid-view.js A static/scripts/mvc/history/history-list.js M static/scripts/mvc/history/history-view-edit-current.js M static/scripts/mvc/history/options-menu.js M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/tool/tool-form-composite.js M static/scripts/mvc/tool/tool-form.js M static/scripts/mvc/user/user-preferences.js M static/scripts/mvc/webhooks.js M static/scripts/mvc/workflow/workflow-configure-menu.js M static/scripts/mvc/workflow/workflow.js M static/scripts/onload.js M static/scripts/utils/utils.js M static/style/blue/base.css M templates/js-app.mako R templates/webapps/galaxy/history/grid.mako R templates/webapps/galaxy/history/grid_js.mako R templates/webapps/galaxy/visualization/list_published.mako R templates/webapps/galaxy/workflow/import.mako R templates/webapps/galaxy/workflow/list_published.mako R templates/webapps/galaxy/workflow/run.mako M test/functional/tools/sample_datatypes_conf.xml M test/functional/webhooks/phdcomics/helper/__init__.py M test/functional/webhooks/trans_object/helper/__init__.py M tools/filters/wc_gnu.xml Log Message: ----------- Merge branch 'dev' into issue-4231-fix-empty-tabular-output Commit: 8b0187317564d70b3a5bc5f67ee78461879fd43e https://github.com/galaxyproject/galaxy/commit/8b0187317564d70b3a5bc5f67ee7… Author: Pierrick Roger Mele <pierrick.rogermele(a)icloud.com> Date: 2017-07-06 (Thu, 06 Jul 2017) Changed paths: M lib/galaxy/datatypes/tabular.py Log Message: ----------- Implement Nicola Sorenzo's proposal for set_meta() method. Commit: 2a737d0b794d03d16774bcd6250561eda92d9abc https://github.com/galaxyproject/galaxy/commit/2a737d0b794d03d16774bcd62505… Author: Pierrick Roger Mele <pierrick.rogermele(a)icloud.com> Date: 2017-07-06 (Thu, 06 Jul 2017) Changed paths: M lib/galaxy/datatypes/tabular.py Log Message: ----------- Set two blank lines before class definition, in order for travis linting to pass. Commit: ba5549b47193f1ac87a2fa8d145e3d4d1541c554 https://github.com/galaxyproject/galaxy/commit/ba5549b47193f1ac87a2fa8d145e… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-07-06 (Thu, 06 Jul 2017) Changed paths: M lib/galaxy/datatypes/tabular.py Log Message: ----------- Merge pull request #4240 from pierrickrogermele/issue-4231-fix-empty-tabular-output Fix empty tabular output error when using discover_datasets. Compare: https://github.com/galaxyproject/galaxy/compare/e7731684518e...ba5549b47193

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[galaxyproject/galaxy] 3c488b: Return empty tool_version when tool is not loaded ...
by GitHub 06 Jul '17

06 Jul '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 3c488b24d0c5dd2460a7f82346c5dde5bb8bae78 https://github.com/galaxyproject/galaxy/commit/3c488b24d0c5dd2460a7f82346c5… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-07-06 (Thu, 06 Jul 2017) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Return empty tool_version when tool is not loaded into tool panel Commit: e7731684518eec8336234994f32dda7246a5f5e0 https://github.com/galaxyproject/galaxy/commit/e7731684518eec8336234994f32d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-07-06 (Thu, 06 Jul 2017) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge pull request #4285 from mvdbeek/fix_wf_editor_crash_uninstalled_tool Return empty tool_version when tool is not loaded into tool panel Compare: https://github.com/galaxyproject/galaxy/compare/8b3c10553b26...e7731684518e

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[galaxyproject/galaxy] eb5843: Remove p style under blockquote
by GitHub 06 Jul '17

06 Jul '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: eb5843643298e0c8ac5f2a568ffed1cba47adb21 https://github.com/galaxyproject/galaxy/commit/eb5843643298e0c8ac5f2a568ffe… Author: E Rasche <hxr(a)hx42.org> Date: 2017-07-04 (Tue, 04 Jul 2017) Changed paths: M client/galaxy/style/less/galaxy_bootstrap/overrides.less M static/scripts/bundled/admin.bundled.js.map 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 M static/style/blue/base.css Log Message: ----------- Remove p style under blockquote Commit: 8b3c10553b26fed01c6825c47df397bacdf5d5a2 https://github.com/galaxyproject/galaxy/commit/8b3c10553b26fed01c6825c47df3… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-07-06 (Thu, 06 Jul 2017) Changed paths: M client/galaxy/style/less/galaxy_bootstrap/overrides.less M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/style/blue/base.css Log Message: ----------- Merge remote-tracking branch 'erasche/blockquotep' into dev (rebuilt client as well) Compare: https://github.com/galaxyproject/galaxy/compare/1ecaa0698732...8b3c10553b26

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[galaxyproject/galaxy] efc877: Adding showBootstrap feature for Phylocanvas viz
by GitHub 06 Jul '17

06 Jul '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: efc877ab29b86e897552e4822d0a05c6fa796902 https://github.com/galaxyproject/galaxy/commit/efc877ab29b86e897552e4822d0a… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-07-05 (Wed, 05 Jul 2017) Changed paths: M config/plugins/visualizations/charts/static/repository/build/biojs_phylocanvas.js M config/plugins/visualizations/charts/static/repository/build/biojs_phylocanvas.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/visualizations/biojs/phylocanvas/config.js M config/plugins/visualizations/charts/static/repository/visualizations/biojs/phylocanvas/wrapper.js M static/scripts/bundled/admin.bundled.js.map 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: ----------- Adding showBootstrap feature for Phylocanvas viz Commit: 065ab584c7bd6fa15c3cadc2cc9ef2ef57921f3b https://github.com/galaxyproject/galaxy/commit/065ab584c7bd6fa15c3cadc2cc9e… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-07-05 (Wed, 05 Jul 2017) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M .gitignore M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/history/history-list.js M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/style/less/ui.less M config/datatypes_conf.xml.sample M lib/galaxy/config.py M lib/galaxy/dataset_collections/matching.py M lib/galaxy/dataset_collections/registry.py M lib/galaxy/dataset_collections/structure.py M lib/galaxy/dataset_collections/types/list.py M lib/galaxy/dataset_collections/types/paired.py M lib/galaxy/datatypes/blast.py M lib/galaxy/datatypes/chrominfo.py M lib/galaxy/datatypes/converters/bedgraph_to_array_tree_converter.py M lib/galaxy/datatypes/converters/fasta_to_tabular_converter.py M lib/galaxy/datatypes/converters/interval_to_fli.py M lib/galaxy/datatypes/converters/pbed_ldreduced_converter.py M lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.py M lib/galaxy/datatypes/converters/sam_to_bam.py M lib/galaxy/datatypes/converters/vcf_to_interval_index_converter.py M lib/galaxy/datatypes/converters/wiggle_to_array_tree_converter.py M lib/galaxy/datatypes/converters/wiggle_to_simple_converter.py M lib/galaxy/datatypes/coverage.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/dataproviders/chunk.py M lib/galaxy/datatypes/dataproviders/column.py M lib/galaxy/datatypes/dataproviders/dataset.py M lib/galaxy/datatypes/dataproviders/decorators.py M lib/galaxy/datatypes/dataproviders/external.py M lib/galaxy/datatypes/dataproviders/hierarchy.py M lib/galaxy/datatypes/dataproviders/line.py M lib/galaxy/datatypes/display_applications/application.py M lib/galaxy/datatypes/display_applications/parameters.py M lib/galaxy/datatypes/graph.py M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/molecules.py M lib/galaxy/datatypes/mothur.py M lib/galaxy/datatypes/neo4j.py M lib/galaxy/datatypes/plant_tribes.py M lib/galaxy/datatypes/qualityscore.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/tabular.py A lib/galaxy/datatypes/test/1.ptkscmp M lib/galaxy/datatypes/triples.py M lib/galaxy/datatypes/util/gff_util.py M lib/galaxy/datatypes/xml.py M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conda-environment.txt M lib/galaxy/jobs/__init__.py M lib/galaxy/model/__init__.py M lib/galaxy/model/base.py M lib/galaxy/model/custom_types.py M lib/galaxy/model/search.py M lib/galaxy/model/tool_shed_install/__init__.py M lib/galaxy/model/tool_shed_install/mapping.py M lib/galaxy/model/tool_shed_install/migrate/check.py M lib/galaxy/queue_worker.py M lib/galaxy/security/__init__.py M lib/galaxy/security/passwords.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/lineages/__init__.py M lib/galaxy/tools/toolbox/lineages/factory.py M lib/galaxy/tools/toolbox/lineages/interface.py R lib/galaxy/tools/toolbox/lineages/stock.py R lib/galaxy/tools/toolbox/lineages/tool_shed.py A lib/galaxy/util/tool_version.py M lib/galaxy/webapps/galaxy/api/jobs.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/api/users.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/library.py M lib/galaxy/webhooks/__init__.py M lib/galaxy/work/context.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/render.py M lib/galaxy/workflow/run_request.py M lib/galaxy/workflow/scheduling_manager.py M lib/log_tempfile.py M lib/tool_shed/galaxy_install/installed_repository_manager.py M lib/tool_shed/tools/tool_version_manager.py M static/maps/layout/menu.js.map M static/maps/mvc/collection/collection-model.js.map M static/maps/mvc/history/history-list.js.map M static/maps/mvc/history/options-menu.js.map M static/maps/mvc/tool/tool-form-base.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/collection/collection-model.js M static/scripts/mvc/history/history-list.js M static/scripts/mvc/history/options-menu.js M static/scripts/mvc/tool/tool-form-base.js M static/style/blue/base.css M templates/base.mako M templates/base/base_panels.mako M templates/display_base.mako M templates/js-app.mako M templates/user/logout.mako M templates/webapps/galaxy/admin/center.mako M templates/webapps/galaxy/base_panels.mako M templates/webapps/galaxy/dataset/display.mako M templates/webapps/galaxy/dataset/errors.mako M templates/webapps/galaxy/galaxy.panels.mako M templates/webapps/galaxy/history/list_published.mako R templates/webapps/galaxy/history/shared_grid.mako M templates/webapps/galaxy/mobile/form.mako M templates/webapps/galaxy/mobile/index.mako M templates/webapps/galaxy/root/tool_runner.mako M templates/webapps/reports/base_panels.mako M templates/webapps/tool_shed/admin/center.mako M templates/webapps/tool_shed/base_panels.mako M templates/webapps/tool_shed/repository/tool_form.mako M test/api/test_dataset_collections.py M test/functional/tools/sample_datatypes_conf.xml A test/integration/test_config_options_users.py A test/unit/shed_unit/test_installed_repository_manager.py M test/unit/shed_unit/test_tool_panel_manager.py M test/unit/tools/test_toolbox.py M test/unit/tools_support.py Log Message: ----------- Merging with dev Commit: 1ecaa06987325100fa9bb0334a9be2d212ee0d9e https://github.com/galaxyproject/galaxy/commit/1ecaa06987325100fa9bb0334a9b… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2017-07-06 (Thu, 06 Jul 2017) Changed paths: M config/plugins/visualizations/charts/static/repository/build/biojs_phylocanvas.js M config/plugins/visualizations/charts/static/repository/build/biojs_phylocanvas.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/visualizations/biojs/phylocanvas/config.js M config/plugins/visualizations/charts/static/repository/visualizations/biojs/phylocanvas/wrapper.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Merge pull request #4284 from bgruening/enhancement_phylocanvas Enhancement for Phylocanvas plugin Compare: https://github.com/galaxyproject/galaxy/compare/9a65d9b2ab3f...1ecaa0698732

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[galaxyproject/galaxy] 0bc2d9: Uniform html titles
by GitHub 05 Jul '17

05 Jul '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 0bc2d9c96abf0f0a85f6e804ff9c892649b28cb9 https://github.com/galaxyproject/galaxy/commit/0bc2d9c96abf0f0a85f6e804ff9c… Author: E Rasche <hxr(a)hx42.org> Date: 2017-07-02 (Sun, 02 Jul 2017) Changed paths: M templates/base.mako M templates/base/base_panels.mako M templates/display_base.mako M templates/js-app.mako M templates/user/logout.mako M templates/webapps/galaxy/admin/center.mako M templates/webapps/galaxy/base_panels.mako M templates/webapps/galaxy/dataset/display.mako M templates/webapps/galaxy/dataset/errors.mako M templates/webapps/galaxy/galaxy.panels.mako M templates/webapps/galaxy/history/list_published.mako M templates/webapps/galaxy/mobile/form.mako M templates/webapps/galaxy/mobile/index.mako M templates/webapps/galaxy/root/tool_runner.mako M templates/webapps/reports/base_panels.mako M templates/webapps/tool_shed/admin/center.mako M templates/webapps/tool_shed/base_panels.mako M templates/webapps/tool_shed/repository/tool_form.mako Log Message: ----------- Uniform html titles Commit: 3f03774616634a6126405c1ff934f0f338197c8b https://github.com/galaxyproject/galaxy/commit/3f03774616634a6126405c1ff934… Author: E Rasche <hxr(a)hx42.org> Date: 2017-07-02 (Sun, 02 Jul 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/library.py Log Message: ----------- Redundant Commit: e88986f3897aa661197bcaf22077e5f3cc515cef https://github.com/galaxyproject/galaxy/commit/e88986f3897aa661197bcaf22077… Author: E Rasche <hxr(a)hx42.org> Date: 2017-07-02 (Sun, 02 Jul 2017) Changed paths: M templates/js-app.mako Log Message: ----------- Accidental inclusion Commit: 9a65d9b2ab3fd8169ee196c068af2bf3ba3a66eb https://github.com/galaxyproject/galaxy/commit/9a65d9b2ab3fd8169ee196c068af… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-07-05 (Wed, 05 Jul 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/library.py M templates/base.mako M templates/base/base_panels.mako M templates/display_base.mako M templates/js-app.mako M templates/user/logout.mako M templates/webapps/galaxy/admin/center.mako M templates/webapps/galaxy/base_panels.mako M templates/webapps/galaxy/dataset/display.mako M templates/webapps/galaxy/dataset/errors.mako M templates/webapps/galaxy/galaxy.panels.mako M templates/webapps/galaxy/history/list_published.mako M templates/webapps/galaxy/mobile/form.mako M templates/webapps/galaxy/mobile/index.mako M templates/webapps/galaxy/root/tool_runner.mako M templates/webapps/reports/base_panels.mako M templates/webapps/tool_shed/admin/center.mako M templates/webapps/tool_shed/base_panels.mako M templates/webapps/tool_shed/repository/tool_form.mako Log Message: ----------- Merge pull request #4272 from erasche/uniform-titles Uniform titles Compare: https://github.com/galaxyproject/galaxy/compare/bec227436c00...9a65d9b2ab3f

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[galaxyproject/galaxy] caffea: Search collections by tags
by GitHub 05 Jul '17

05 Jul '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: caffea12536e085e6bfa094615066f76fdd87aff https://github.com/galaxyproject/galaxy/commit/caffea12536e085e6bfa09461506… Author: Peter van Heusden <pvh(a)sanbi.ac.za> Date: 2017-07-05 (Wed, 05 Jul 2017) Changed paths: M client/galaxy/scripts/mvc/collection/collection-model.js Log Message: ----------- Search collections by tags Commit: 601c136247fedadb6bf889187346481fb533882d https://github.com/galaxyproject/galaxy/commit/601c136247fedadb6bf889187346… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-07-05 (Wed, 05 Jul 2017) Changed paths: M client/galaxy/scripts/mvc/collection/collection-model.js Log Message: ----------- Merge remote-tracking branch 'pvanheus/collection_tag_searchable' into dev Commit: bec227436c00f74e2999f766db34ea8019092a5e https://github.com/galaxyproject/galaxy/commit/bec227436c00f74e2999f766db34… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-07-05 (Wed, 05 Jul 2017) Changed paths: M static/maps/mvc/collection/collection-model.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-model.js Log Message: ----------- Client build as part of merge. Compare: https://github.com/galaxyproject/galaxy/compare/a42abc03e0b0...bec227436c00

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[galaxyproject/galaxy] c2897c: Replace ShedToolLineage with enhanced StockLineage
by GitHub 05 Jul '17

05 Jul '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c2897c211b1d9a3743171e3e9b05c235b79c50f7 https://github.com/galaxyproject/galaxy/commit/c2897c211b1d9a3743171e3e9b05… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-06-20 (Tue, 20 Jun 2017) Changed paths: M lib/galaxy/config.py M lib/galaxy/model/tool_shed_install/__init__.py M lib/galaxy/queue_worker.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/lineages/__init__.py M lib/galaxy/tools/toolbox/lineages/factory.py M lib/galaxy/tools/toolbox/lineages/interface.py M lib/galaxy/tools/toolbox/lineages/stock.py R lib/galaxy/tools/toolbox/lineages/tool_shed.py A lib/galaxy/util/tool_version.py M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/tool_shed/tools/tool_version_manager.py M test/unit/tools/test_toolbox.py Log Message: ----------- Replace ShedToolLineage with enhanced StockLineage This means we don't rely on the Tool Shed metadata anymore and instead deduce the tool lineage via the tool_id, which contains the version. Version comparison then happens via LooseVersions. This works for toolshed and non-toolshed tools, restoring proper grouping in the tool panel and version switches, even for tool shed tools whose lineage is broken. Commit: 0017d167f100f84df95967a05b0551250828f7a4 https://github.com/galaxyproject/galaxy/commit/0017d167f100f84df95967a05b05… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-06-20 (Tue, 20 Jun 2017) Changed paths: M test/unit/shed_unit/test_tool_panel_manager.py Log Message: ----------- Use correct tool version for ToolPanelManager.test_add_twice test to pass Commit: db5d0095a6a426efcd587eca6808f350a6e126cf https://github.com/galaxyproject/galaxy/commit/db5d0095a6a426efcd587eca6808… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-06-20 (Tue, 20 Jun 2017) Changed paths: M test/unit/tools/test_toolbox.py Log Message: ----------- Fix grouping tests by setting up correct versions Commit: aabb933fdf69719adcb6fb9e9ba82d795a3b9b74 https://github.com/galaxyproject/galaxy/commit/aabb933fdf69719adcb6fb9e9ba8… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-06-20 (Tue, 20 Jun 2017) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/toolbox/lineages/stock.py M test/unit/tools/test_toolbox.py Log Message: ----------- Keep StockLineage versions sorted Commit: 77e016bbbd5de566484d1c74c4f5679354edf360 https://github.com/galaxyproject/galaxy/commit/77e016bbbd5de566484d1c74c4f5… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-06-20 (Tue, 20 Jun 2017) Changed paths: M lib/galaxy/model/tool_shed_install/__init__.py Log Message: ----------- Remove unused next/previous version methods Commit: 6864187725b0af03e2196d12722f78f71d84977e https://github.com/galaxyproject/galaxy/commit/6864187725b0af03e2196d12722f… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-06-20 (Tue, 20 Jun 2017) Changed paths: M lib/galaxy/tools/__init__.py M test/unit/tools_support.py Log Message: ----------- ToolVersion to StockLineage, drop ToolVersionCache remnant from unittests (thx @nsoranzo!). Commit: 81e73969dce5102dec799e3ca8b2a3056969f6a3 https://github.com/galaxyproject/galaxy/commit/81e73969dce5102dec799e3ca8b2… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-06-22 (Thu, 22 Jun 2017) Changed paths: M lib/galaxy/model/tool_shed_install/__init__.py M lib/galaxy/tools/toolbox/lineages/factory.py M lib/galaxy/tools/toolbox/lineages/stock.py M lib/galaxy/util/tool_version.py M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py Log Message: ----------- Remove duplication between ToolLineage and TVM Getting tool versions and tool ids is now done through the tool lineage. Also assume that the lineage can always be found for a given loaded tool in the ToolVersionListGrid class. Thanks @nsoranzo for these suggestions! Commit: 0830ea2e4172e3be51ae081f9578c2c582f12a7e https://github.com/galaxyproject/galaxy/commit/0830ea2e4172e3be51ae081f9578… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-06-22 (Thu, 22 Jun 2017) Changed paths: M lib/galaxy/util/tool_version.py Log Message: ----------- Remove unused `get_version_from_guid` function Commit: db5e41c186d4c4b452ee4b7e83a0b26474d72873 https://github.com/galaxyproject/galaxy/commit/db5e41c186d4c4b452ee4b7e83a0… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-06-22 (Thu, 22 Jun 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Remove unused tool_id variable Commit: 0257248152db3edb493bfd4420f105a19000ae89 https://github.com/galaxyproject/galaxy/commit/0257248152db3edb493bfd4420f1… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-06-22 (Thu, 22 Jun 2017) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/toolbox/lineages/factory.py M lib/galaxy/tools/toolbox/lineages/interface.py R lib/galaxy/tools/toolbox/lineages/stock.py Log Message: ----------- Rename StockLineage to ToolLineage and merge stock.py contents into interface.py Commit: 68981c16cc708514e879941f152be9a60f7ad290 https://github.com/galaxyproject/galaxy/commit/68981c16cc708514e879941f152b… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-06-22 (Thu, 22 Jun 2017) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Remove unused lineage_ids from Tool class Commit: e9658e8adb5d0bf0f8db42faa4d14cb50d4c90ce https://github.com/galaxyproject/galaxy/commit/e9658e8adb5d0bf0f8db42faa4d1… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-06-22 (Thu, 22 Jun 2017) Changed paths: M lib/galaxy/tools/toolbox/lineages/factory.py Log Message: ----------- Clarify when and why tool version is being registered Commit: 41d739bdb4d1ac622fb7fd78f8b3dbc9acd978ad https://github.com/galaxyproject/galaxy/commit/41d739bdb4d1ac622fb7fd78f8b3… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-06-23 (Fri, 23 Jun 2017) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/lineages/interface.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py Log Message: ----------- Move tool.tool_version to tool.lineage This change makes it obvious that a Lineage object will be returned. Also removes two unused methods from ToolLineageVersion. Commit: 84e0e7e01e732b28dedebdf8a3fbea8225fece9a https://github.com/galaxyproject/galaxy/commit/84e0e7e01e732b28dedebdf8a3fb… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-06-24 (Sat, 24 Jun 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py Log Message: ----------- Access tool.lineage only if tool was loaded Commit: a42abc03e0b018546137471f302e28a39f3f7b2b https://github.com/galaxyproject/galaxy/commit/a42abc03e0b018546137471f302e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-07-05 (Wed, 05 Jul 2017) Changed paths: M lib/galaxy/config.py M lib/galaxy/model/tool_shed_install/__init__.py M lib/galaxy/queue_worker.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/lineages/__init__.py M lib/galaxy/tools/toolbox/lineages/factory.py M lib/galaxy/tools/toolbox/lineages/interface.py R lib/galaxy/tools/toolbox/lineages/stock.py R lib/galaxy/tools/toolbox/lineages/tool_shed.py A lib/galaxy/util/tool_version.py M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/tool_shed/tools/tool_version_manager.py M test/unit/shed_unit/test_tool_panel_manager.py M test/unit/tools/test_toolbox.py M test/unit/tools_support.py Log Message: ----------- Merge pull request #4119 from mvdbeek/version_switch_fix Merge ShedToolLineage and StockLineage to ToolLineage Compare: https://github.com/galaxyproject/galaxy/compare/516f7bff63fe...a42abc03e0b0

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[galaxyproject/galaxy] 422add: Fix problem in collection download tests related t...
by GitHub 05 Jul '17

05 Jul '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 422add1c480ff0726cd691bccb7a28ec479dcee0 https://github.com/galaxyproject/galaxy/commit/422add1c480ff0726cd691bccb7a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-07-05 (Wed, 05 Jul 2017) Changed paths: M test/api/test_dataset_collections.py Log Message: ----------- Fix problem in collection download tests related to ID references. DatasetsCollectionElement ids were being confused with HDA ids. Commit: 516f7bff63fe8339ec29ce544a509a228d903304 https://github.com/galaxyproject/galaxy/commit/516f7bff63fe8339ec29ce544a50… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2017-07-05 (Wed, 05 Jul 2017) Changed paths: M test/api/test_dataset_collections.py Log Message: ----------- Merge pull request #4281 from jmchilton/test_fixes Fix problem in collection download tests related to ID references. Compare: https://github.com/galaxyproject/galaxy/compare/3529897b8888...516f7bff63fe

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[galaxyproject/galaxy] c90b94: Instead of setting the tags from a list, workflow ...
by GitHub 05 Jul '17

05 Jul '17

Branch: refs/heads/release_17.05 Home: https://github.com/galaxyproject/galaxy Commit: c90b94311e5427da95a36a9661c1d0eb19e16fc2 https://github.com/galaxyproject/galaxy/commit/c90b94311e5427da95a36a9661c1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-06-13 (Tue, 13 Jun 2017) Changed paths: M lib/galaxy/jobs/actions/post.py M lib/galaxy/managers/tags.py Log Message: ----------- Instead of setting the tags from a list, workflow PJAs will now append tags, so propagating tags will work alongside this feature. Commit: 01510af8f57508877dda205cb0afdc144bfa73c2 https://github.com/galaxyproject/galaxy/commit/01510af8f57508877dda205cb0af… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-06-13 (Tue, 13 Jun 2017) Changed paths: M lib/galaxy/managers/tags.py Log Message: ----------- Consistent spacing (not a fan of the rule, but consistency is better) Commit: 472ff8ce520a6327179dd54c301db763ea7e979b https://github.com/galaxyproject/galaxy/commit/472ff8ce520a6327179dd54c301d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-06-13 (Tue, 13 Jun 2017) Changed paths: M lib/galaxy/managers/tags.py Log Message: ----------- Fix for when item.tags is undefined Commit: fc613d2d60c126b3b37c9ebe3ddbd9cc58803643 https://github.com/galaxyproject/galaxy/commit/fc613d2d60c126b3b37c9ebe3ddb… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-07-05 (Wed, 05 Jul 2017) Changed paths: M lib/galaxy/jobs/actions/post.py M lib/galaxy/managers/tags.py Log Message: ----------- Merge pull request #4188 from dannon/workflow_pja_add_not_set_tags [17.05] Hashtags w/ workflow-defined tags fix Compare: https://github.com/galaxyproject/galaxy/compare/d0893b91ae28...fc613d2d60c1

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