- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 02f3a2: Bug fix for masthead webhook if Galaxy.page is und...
by GitHub 09 Mar '17

09 Mar '17

Branch: refs/heads/release_16.10 Home: https://github.com/galaxyproject/galaxy Commit: 02f3a2737dd1c48574df9bf8e51ce43e6789bf1e https://github.com/galaxyproject/galaxy/commit/02f3a2737dd1c48574df9bf8e51c… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-03-08 (Wed, 08 Mar 2017) Changed paths: M client/galaxy/scripts/layout/menu.js M static/maps/layout/menu.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/menu.js Log Message: ----------- Bug fix for masthead webhook if Galaxy.page is undefined for workflow, data libraries etc pages Commit: 1b9a2868a17899787bf65181f96892596b16b51b https://github.com/galaxyproject/galaxy/commit/1b9a2868a17899787bf65181f968… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-03-09 (Thu, 09 Mar 2017) Changed paths: M client/galaxy/scripts/layout/menu.js M static/maps/layout/menu.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/menu.js Log Message: ----------- Merge pull request #3728 from martenson/backport-masthead-fix [16.10] backport of webhook masthead fix for datalibs and workflows Compare: https://github.com/galaxyproject/galaxy/compare/b41b8e305bac...1b9a2868a178

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[galaxyproject/galaxy] 9928a7: Merge ConfiguresGalaxyMixin.reload_toolbox() in _c...
by GitHub 09 Mar '17

09 Mar '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 9928a74c6c1cb57edbfba4068616bd5b15f51093 https://github.com/galaxyproject/galaxy/commit/9928a74c6c1cb57edbfba4068616… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-03-09 (Thu, 09 Mar 2017) Changed paths: M lib/galaxy/config.py Log Message: ----------- Merge ConfiguresGalaxyMixin.reload_toolbox() in _configure_toolbox() It's called only once from there when app is initialised, real toolbox reloads are performed by executing reload_toolbox() from lib/galaxy/queue_worker.py . Commit: a89954c8928f0997aa9a5781a39d18339914b387 https://github.com/galaxyproject/galaxy/commit/a89954c8928f0997aa9a5781a39d… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-03-09 (Thu, 09 Mar 2017) Changed paths: M lib/galaxy/queue_worker.py Log Message: ----------- Fix 2 typos Commit: bcc4e025c36c3ee394c73cee06a8031cec6e9354 https://github.com/galaxyproject/galaxy/commit/bcc4e025c36c3ee394c73cee06a8… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-03-09 (Thu, 09 Mar 2017) Changed paths: M lib/galaxy/config.py M lib/galaxy/queue_worker.py Log Message: ----------- Merge pull request #3732 from nsoranzo/reload_toolbox_merge Merge ConfiguresGalaxyMixin.reload_toolbox() in _configure_toolbox() Compare: https://github.com/galaxyproject/galaxy/compare/704e6a6676c2...bcc4e025c36c

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[galaxyproject/galaxy] 845e43: Avoid autoconversion of boolean values when callin...
by GitHub 08 Mar '17

08 Mar '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 845e43c1e537f66c8208165a82583b4ca814b1f0 https://github.com/galaxyproject/galaxy/commit/845e43c1e537f66c8208165a8258… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-03-03 (Fri, 03 Mar 2017) Changed paths: M lib/galaxy/tools/parameters/basic.py M lib/galaxy/util/json.py Log Message: ----------- Avoid autoconversion of boolean values when calling json loads Remove unused import Fix Commit: cb27f921c7e82f09c675e1e472417ad47d65bfab https://github.com/galaxyproject/galaxy/commit/cb27f921c7e82f09c675e1e47241… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-03-03 (Fri, 03 Mar 2017) Changed paths: M lib/galaxy/util/json.py Log Message: ----------- Fix comment Commit: 704e6a6676c2aa6aafe4a283f50dcfd8a646682e https://github.com/galaxyproject/galaxy/commit/704e6a6676c2aa6aafe4a283f50d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-08 (Wed, 08 Mar 2017) Changed paths: M lib/galaxy/tools/parameters/basic.py M lib/galaxy/util/json.py Log Message: ----------- Merge pull request #3702 from guerler/fix_boolean_handling Properly handle boolean values when parsed to a string-based/default tool parameter Compare: https://github.com/galaxyproject/galaxy/compare/0118c57af3ea...704e6a6676c2

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[galaxyproject/galaxy] aa0af3: Add a simple UI to manage tool dependencies
by GitHub 08 Mar '17

08 Mar '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: aa0af352cdd034872d24b3a5f497a04204c9c017 https://github.com/galaxyproject/galaxy/commit/aa0af352cdd034872d24b3a5f497… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-03-08 (Wed, 08 Mar 2017) Changed paths: M lib/galaxy/web/base/controllers/admin.py M templates/webapps/galaxy/admin/index.mako A templates/webapps/galaxy/admin/manage_dependencies.mako M templates/webapps/tool_shed/repository/common.mako Log Message: ----------- Add a simple UI to manage tool dependencies This page simply lists all loaded tools and their dependency status. On the left are checkboxes to select multiple tools, and at the bottom is a button to install the selected tool dependencies. Commit: 818c10832a1429b79e65906d106b6fda0ed28a35 https://github.com/galaxyproject/galaxy/commit/818c10832a1429b79e65906d106b… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-03-08 (Wed, 08 Mar 2017) Changed paths: M lib/galaxy/web/base/controllers/admin.py M templates/webapps/galaxy/admin/manage_dependencies.mako Log Message: ----------- Build the dependency status more efficiently: Pass a dictionary with ToolRequirements object as key and requirements status as value Commit: f882a14886de65b0079d5eea72a7bea044ab4a02 https://github.com/galaxyproject/galaxy/commit/f882a14886de65b0079d5eea72a7… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-03-08 (Wed, 08 Mar 2017) Changed paths: M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/web/base/controllers/admin.py M templates/webapps/galaxy/admin/manage_dependencies.mako Log Message: ----------- Add new view that primarily manages dependencies Commit: f1bb5a6a7114f1aa4dc331622183432604e9dbc7 https://github.com/galaxyproject/galaxy/commit/f1bb5a6a7114f1aa4dc331622183… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-03-08 (Wed, 08 Mar 2017) Changed paths: M templates/webapps/galaxy/admin/manage_dependencies.mako Log Message: ----------- close opened div Commit: 96ae2893b3610e28101445f58966cffd61f873eb https://github.com/galaxyproject/galaxy/commit/96ae2893b3610e28101445f58966… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-03-08 (Wed, 08 Mar 2017) Changed paths: M templates/webapps/galaxy/admin/manage_dependencies.mako Log Message: ----------- improve the markup and UX a bit Commit: 5dc73b7966d3c9e90e0a58823e34bc26663d5d71 https://github.com/galaxyproject/galaxy/commit/5dc73b7966d3c9e90e0a58823e34… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-03-08 (Wed, 08 Mar 2017) Changed paths: M templates/webapps/galaxy/admin/manage_dependencies.mako Log Message: ----------- Add title and explanation for Manage Tool Dependencies page. Commit: 0118c57af3ea2bae8b5c8c72fa45f431afb4aa8f https://github.com/galaxyproject/galaxy/commit/0118c57af3ea2bae8b5c8c72fa45… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-03-08 (Wed, 08 Mar 2017) Changed paths: M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/web/base/controllers/admin.py M templates/webapps/galaxy/admin/index.mako A templates/webapps/galaxy/admin/manage_dependencies.mako M templates/webapps/tool_shed/repository/common.mako Log Message: ----------- Merge pull request #3479 from mvdbeek/manage_tool_dependencies Add a simple UI to manage tool dependencies Compare: https://github.com/galaxyproject/galaxy/compare/07490e428dc0...0118c57af3ea

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[galaxyproject/galaxy] ba8d03: Adding overlay search feature to webhooks
by GitHub 08 Mar '17

08 Mar '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ba8d03624cad0b0d78d11f07ee9b05446977e6a0 https://github.com/galaxyproject/galaxy/commit/ba8d03624cad0b0d78d11f07ee9b… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-01-08 (Sun, 08 Jan 2017) Changed paths: M client/galaxy/scripts/onload.js A config/plugins/webhooks/demo/search/config/searchover.yaml A config/plugins/webhooks/demo/search/static/script.js A config/plugins/webhooks/demo/search/static/styles.css M static/maps/onload.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/onload.js Log Message: ----------- Adding overlay search feature to webhooks Commit: d66e2f912964fdc05c239b52f2dab440313513b5 https://github.com/galaxyproject/galaxy/commit/d66e2f912964fdc05c239b52f2da… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-01-09 (Mon, 09 Jan 2017) Changed paths: M config/plugins/webhooks/demo/search/config/searchover.yaml Log Message: ----------- Updating the logic to pull search plugin static code Commit: f6e0d65efcb517634540d5392d7d0c44e4f25bc2 https://github.com/galaxyproject/galaxy/commit/f6e0d65efcb517634540d5392d7d… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-01-10 (Tue, 10 Jan 2017) Changed paths: M config/plugins/webhooks/demo/search/static/script.js M config/plugins/webhooks/demo/search/static/styles.css Log Message: ----------- Adding items to the favorites when pinned and filter is home Commit: 07d9b63d09f2e3918a96b6be6f4778ac97a747d2 https://github.com/galaxyproject/galaxy/commit/07d9b63d09f2e3918a96b6be6f47… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-01-10 (Tue, 10 Jan 2017) Changed paths: M config/plugins/webhooks/demo/search/config/searchover.yaml M config/plugins/webhooks/demo/search/static/script.js Log Message: ----------- Synchronising pin/ unpin actions in the favorites section Commit: 839c9091dd39056243f6d75ea4a0797749882ee3 https://github.com/galaxyproject/galaxy/commit/839c9091dd39056243f6d75ea4a0… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-01-10 (Tue, 10 Jan 2017) Changed paths: M config/plugins/webhooks/demo/search/static/styles.css Log Message: ----------- Updating styles for tiles Commit: 5ad2e5ce66a36644eead2c50f51f971363b210e1 https://github.com/galaxyproject/galaxy/commit/5ad2e5ce66a36644eead2c50f51f… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-01-11 (Wed, 11 Jan 2017) Changed paths: M config/plugins/webhooks/demo/search/static/script.js M config/plugins/webhooks/demo/search/static/styles.css Log Message: ----------- Synchronising the deletion of item in favourites with pinned item in search results if any Commit: 3b6ddb992f1c0824e688ed7c9ab913d68826eda3 https://github.com/galaxyproject/galaxy/commit/3b6ddb992f1c0824e688ed7c9ab9… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-01-13 (Fri, 13 Jan 2017) Changed paths: M config/plugins/webhooks/demo/search/static/script.js Log Message: ----------- Fixing bug with aligning items in tools section Commit: 9dc814e81171f873fce15a63210138bc239f8063 https://github.com/galaxyproject/galaxy/commit/9dc814e81171f873fce15a632101… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-01-13 (Fri, 13 Jan 2017) Changed paths: M config/plugins/webhooks/demo/search/static/styles.css Log Message: ----------- Adding hover styles for tiles Commit: 78f29eab856220bd0fe44566cba7f850a91f6e41 https://github.com/galaxyproject/galaxy/commit/78f29eab856220bd0fe44566cba7… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-01-14 (Sat, 14 Jan 2017) Changed paths: M config/plugins/webhooks/demo/search/static/styles.css Log Message: ----------- Moving the pin icon to the left of tiles Commit: 34be05339915df8554a619a086214974f98e5bcb https://github.com/galaxyproject/galaxy/commit/34be05339915df8554a619a08621… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-01-21 (Sat, 21 Jan 2017) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/jenkins/selenium/run_galaxy.bash M .ci/py3_sources.txt M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/ui/ui-misc.js M config/datatypes_conf.xml.sample M config/plugins/interactive_environments/rstudio/templates/rstudio.mako M config/plugins/visualizations/charts/templates/charts.mako M config/plugins/visualizations/csg/templates/csg.mako M config/plugins/visualizations/graphviz/templates/graphviz.mako M config/plugins/visualizations/scatterplot/templates/scatterplot.mako M config/plugins/webhooks/demo/phdcomics/helper/__init__.py M config/plugins/webhooks/demo/phdcomics/static/script.js M doc/schema_template.md M doc/source/admin/webhooks.rst M doc/source/api/guidelines.rst M lib/galaxy/datatypes/binary.py A lib/galaxy/datatypes/converters/fastqbz2_to_fastq.xml A lib/galaxy/datatypes/converters/fastqcssangerbz2_to_fastqcssanger.xml A lib/galaxy/datatypes/converters/fastqcssangergz_to_fastqcssanger.xml A lib/galaxy/datatypes/converters/fastqgz_to_fastq.xml A lib/galaxy/datatypes/converters/fastqilluminabz2_to_fastqillumina.xml A lib/galaxy/datatypes/converters/fastqilluminagz_to_fastqillumina.xml A lib/galaxy/datatypes/converters/fastqsangerbz2_to_fastqsanger.xml A lib/galaxy/datatypes/converters/fastqsangergz_to_fastqsanger.xml A lib/galaxy/datatypes/converters/fastqsolexabz2_to_fastqsolexa.xml A lib/galaxy/datatypes/converters/fastqsolexagz_to_fastqsolexa.xml M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py A lib/galaxy/datatypes/test/diamond_db.dmnd M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/actions/post.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/data/__init__.py 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/requirements.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/deps/resolvers/resolver_mixins.py M lib/galaxy/tools/deps/views.py M lib/galaxy/tools/errors.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/imp_exp/export_history.py M lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/dynamic_options.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/tools/parameters/meta.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/search/__init__.py M lib/galaxy/tools/util/galaxyops/__init__.py M lib/galaxy/tools/util/maf_utilities.py M lib/galaxy/tools/verify/asserts/__init__.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/object_wrapper.py M lib/galaxy/web/framework/middleware/remoteuser.py M lib/galaxy/webapps/galaxy/api/configuration.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/util/shed_util_common.py M run_tests.sh A static/maps/libs/showdown.js.map M static/maps/mvc/form/form-view.js.map M static/maps/mvc/ui/ui-misc.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map A static/scripts/libs/showdown.js M static/scripts/mvc/form/form-view.js M static/scripts/mvc/ui/ui-misc.js M templates/ind_share_base.mako M templates/webapps/galaxy/history/share.mako A test-data/1.fastqsanger.bz2 A test-data/1.fastqsanger.gz M test/api/test_workflows.py M test/docker/README.md M test/functional/tools/column_param.xml A test/functional/tools/compressed_bz2_fastq_conversion.xml A test/functional/tools/compressed_bz2_fastq_no_conversion.xml A test/functional/tools/compressed_gz_fastq_conversion.xml A test/functional/tools/compressed_gz_fastq_no_conversion.xml A test/functional/tools/explicit_conversion.xml A test/functional/tools/implicit_conversion.xml A test/functional/tools/mulled_example_conflict.xml M test/functional/tools/sample_datatypes_conf.xml M test/functional/tools/samples_tool_conf.xml M test/galaxy_selenium/navigates_galaxy.py M test/selenium_tests/test_history_dataset_state.py M test/selenium_tests/test_history_sharing.py M test/selenium_tests/test_tool_form.py M test/selenium_tests/test_workflow_editor.py M test/selenium_tests/test_workflow_management.py Log Message: ----------- Merging with dev Commit: 823ac3cc6172db54c35fdae43553af304a6a162b https://github.com/galaxyproject/galaxy/commit/823ac3cc6172db54c35fdae43553… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2017-02-11 (Sat, 11 Feb 2017) Changed paths: M config/plugins/webhooks/demo/search/static/script.js M config/plugins/webhooks/demo/search/static/styles.css Log Message: ----------- add new Search plugin styles Commit: 4120781713cc65d3c05064bee981cf826d5c4be8 https://github.com/galaxyproject/galaxy/commit/4120781713cc65d3c05064bee981… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2017-03-05 (Sun, 05 Mar 2017) Changed paths: M config/galaxy.ini.sample M config/plugins/webhooks/demo/search/static/styles.css Log Message: ----------- increase contrast and improve readability Commit: 0bfe9fa7ca1489d744351eecc4312838a20008eb https://github.com/galaxyproject/galaxy/commit/0bfe9fa7ca1489d744351eecc431… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-03-07 (Tue, 07 Mar 2017) Changed paths: M .ci/flake8_blacklist.txt M .ci/flake8_lint_include_list.txt M .ci/jenkins/selenium/run_tests.sh M .ci/py3_sources.txt M CONTRIBUTING.md M README.rst M client/galaxy/scripts/libs/jquery/jquery.autocomplete.js M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/grid/grid-view.js M client/galaxy/scripts/mvc/history/hda-li.js M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/history-view.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 R client/galaxy/scripts/mvc/tool/tool-form-workflow.js M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/mvc/ui/ui-portlet.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/upload/upload-ftp.js M client/galaxy/scripts/mvc/user/user-quotameter.js M client/galaxy/scripts/mvc/workflow/workflow-canvas.js A 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-view-node.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/scripts/ui/autocom_tagging.js M client/galaxy/scripts/viz/trackster/tracks.js M client/galaxy/style/less/base.less M client/galaxy/style/less/history.less M client/galaxy/style/less/ui.less A config/build_sites.yml.sample M config/datatypes_conf.xml.sample M config/galaxy.ini.sample A config/local_conda_mapping.yml.sample M config/plugins/interactive_environments/bam_iobio/config/bam_iobio.ini.sample M config/plugins/interactive_environments/jupyter/config/allowed_images.yml.sample M config/plugins/interactive_environments/jupyter/config/jupyter.ini.sample M config/plugins/interactive_environments/jupyter/config/jupyter.xml M config/plugins/interactive_environments/neo/config/neo.ini.sample M config/plugins/interactive_environments/phinch/config/phinch.ini.sample M config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample M config/plugins/tours/core.galaxy_ui.yaml M config/plugins/tours/core.history.yaml A config/plugins/visualizations/charts/static/repository/build/ngl_viewer.js A config/plugins/visualizations/charts/static/repository/build/ngl_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/ngl/viewer.js M config/plugins/visualizations/charts/static/repository/registry.json A 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templates/webapps/galaxy/workflow/editor_generic_form.mako R templates/webapps/galaxy/workflow/editor_tool_form.mako M templates/webapps/tool_shed/repository/tool_form.mako A test-data/simple.xml M test/TESTING.md M test/api/test_datatypes.py M test/api/test_histories.py M test/api/test_history_contents.py M test/api/test_tools.py A test/api/test_webhooks.py M test/api/test_workflow_extraction.py M test/api/test_workflows.py M test/base/driver_util.py M test/base/populators.py M test/docker/base/run_test_wrapper.sh M test/functional/tools/checksum.xml A test/functional/tools/is_valid_xml.xml A test/functional/tools/legacy_r.xml M test/functional/tools/md5sum.xml A test/functional/tools/mulled_example_multi_incomplete.xml A test/functional/tools/output_format_deprecated_when.xml A test/functional/tools/param_text_option.xml M test/functional/tools/samples_tool_conf.xml A test/functional/webhooks/history_test1/config/history_test1.yml A test/functional/webhooks/history_test2/config/history_test2.yml A test/functional/webhooks/masthead_test/config/masthead_test.yml A test/functional/webhooks/phdcomics/config/phdcomics.yaml A test/functional/webhooks/phdcomics/helper/__init__.py A test/functional/webhooks/phdcomics/static/script.js A test/functional/webhooks/phdcomics/static/styles.css A test/functional/webhooks/trans_object/config/trans_object.yaml A test/functional/webhooks/trans_object/helper/__init__.py A test/functional/webhooks/xkcd/config/xkcd.yml A test/functional/webhooks/xkcd/static/script.js A test/functional/webhooks/xkcd/static/styles.css M test/galaxy_selenium/has_driver.py M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation-data.yml M test/galaxy_selenium/sizzle.py M test/integration/test_resolvers.py M test/qunit/tests/form_tests.js M test/qunit/tests/workflow_editor_tests.js M test/selenium_tests/framework.py A test/selenium_tests/test_collection_builders.py M test/selenium_tests/test_stock_tours.py M test/selenium_tests/test_uploads.py M test/selenium_tests/test_workflow_editor.py M test/unit/managers/test_HDAManager.py M test/unit/managers/test_HistoryManager.py M test/unit/tools/test_conda_resolution.py M test/unit/tools/test_data_parameters.py M test/unit/tools/test_execution.py M test/unit/tools/test_tool_deps.py M test/unit/workflows/test_modules.py M test/unit/workflows/test_workflow_progress.py M tools/data_source/upload.py M tools/evolution/add_scores.xml M tools/extract/extract_genomic_dna.xml M tools/filters/pasteWrapper.xml M tools/maf/genebed_maf_to_fasta.xml M tools/maf/interval2maf.xml M tools/maf/interval2maf_pairwise.xml M tools/maf/interval_maf_to_merged_fasta.xml M tools/maf/macros.xml M tools/maf/maf_by_block_number.xml M tools/maf/maf_filter.xml M tools/maf/maf_limit_size.xml M tools/maf/maf_limit_to_species.xml M tools/maf/maf_reverse_complement.xml M tools/maf/maf_split_by_species.xml M tools/maf/maf_stats.xml M tools/maf/maf_thread_for_species.xml M tools/maf/maf_to_bed.xml M tools/maf/maf_to_fasta.xml M tools/maf/maf_to_interval.xml M tools/maf/vcf_to_maf_customtrack.xml M tools/metag_tools/shrimp_color_wrapper.xml M tools/metag_tools/shrimp_wrapper.xml M tools/next_gen_conversion/fastq_gen_conv.xml M tools/plotting/bar_chart.xml M tools/stats/aggregate_binned_scores_in_intervals.xml M tox.ini Log Message: ----------- Merging with dev Commit: 07490e428dc0a3596d7623a7a787443494626c63 https://github.com/galaxyproject/galaxy/commit/07490e428dc0a3596d7623a7a787… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-08 (Wed, 08 Mar 2017) Changed paths: M client/galaxy/scripts/onload.js M config/galaxy.ini.sample A config/plugins/webhooks/demo/search/config/searchover.yaml A config/plugins/webhooks/demo/search/static/script.js A config/plugins/webhooks/demo/search/static/styles.css M static/maps/onload.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/onload.js Log Message: ----------- Merge pull request #3460 from bgruening/search_overlay Overlay search for tools, wf, libraries and histories Compare: https://github.com/galaxyproject/galaxy/compare/b9c1abd43a69...07490e428dc0

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[galaxyproject/galaxy]
by GitHub 08 Mar '17

08 Mar '17

Branch: refs/heads/datamanager_conda_install Home: https://github.com/galaxyproject/galaxy

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[galaxyproject/galaxy] b7820d: Allow display of install_resolver_checkbox when in...
by GitHub 08 Mar '17

08 Mar '17

Branch: refs/heads/datamanager_conda_install Home: https://github.com/galaxyproject/galaxy Commit: b7820d1269ca6bf7571ab6d0305504e9826a5872 https://github.com/galaxyproject/galaxy/commit/b7820d1269ca6bf7571ab6d03055… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-03-01 (Wed, 01 Mar 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M templates/admin/tool_shed_repository/select_shed_tool_panel_config.mako Log Message: ----------- Allow display of install_resolver_checkbox when installing data manager tools Commit: 2abc7b0d2b0c422a4f7c89ae7bdf767088323be2 https://github.com/galaxyproject/galaxy/commit/2abc7b0d2b0c422a4f7c89ae7bdf… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-03-08 (Wed, 08 Mar 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py R templates/admin/tool_shed_repository/select_shed_tool_panel_config.mako M templates/admin/tool_shed_repository/select_tool_panel_section.mako Log Message: ----------- Merge select_shed_tool_panel_config.mako functionality into select_tool_panel_section.mako Commit: 7d7e36e5d40c3418f5712d9f9a9e8bd4140c5bc5 https://github.com/galaxyproject/galaxy/commit/7d7e36e5d40c3418f5712d9f9a9e… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-03-08 (Wed, 08 Mar 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py Log Message: ----------- Remove checks for `includes_tools_for_display_in_tool_panel` and `includes_tools_for_display_in_tool_panel` when determining if initiate_repository_installation.mako should be posted to. It is sufficient to check that select_tool_panel_section_button has been clicked. Commit: 7372d5a339794f8eecc31afbc7f21c983c50b7a6 https://github.com/galaxyproject/galaxy/commit/7372d5a339794f8eecc31afbc7f2… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-03-08 (Wed, 08 Mar 2017) Changed paths: M test/shed_functional/functional/test_1150_datatype_converters.py Log Message: ----------- Adjust wording of datatype converter install test. Compare: https://github.com/galaxyproject/galaxy/compare/b7820d1269ca^...7372d5a33979

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[galaxyproject/galaxy] 072f99: Fix cycle detection for single node workflows.
by GitHub 08 Mar '17

08 Mar '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 072f998bbaaf74fbf4f6992d264af9a853f723ec https://github.com/galaxyproject/galaxy/commit/072f998bbaaf74fbf4f6992d264a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-27 (Tue, 27 Dec 2016) Changed paths: M lib/galaxy/workflow/steps.py Log Message: ----------- Fix cycle detection for single node workflows. Fixes #3236. Commit: b9c1abd43a69241accd54d3531442b56508efc0f https://github.com/galaxyproject/galaxy/commit/b9c1abd43a69241accd54d353144… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2017-03-07 (Tue, 07 Mar 2017) Changed paths: M lib/galaxy/workflow/steps.py Log Message: ----------- Merge pull request #3374 from jmchilton/singleton_workflow_cycles Fix cycle detection for single node workflows. Compare: https://github.com/galaxyproject/galaxy/compare/9aa911d509ac...b9c1abd43a69

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[galaxyproject/galaxy] 79945f: Do not require stored workflow id for subworkflows
by GitHub 07 Mar '17

07 Mar '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 79945f37c31d4d42be86bee352370af11b063271 https://github.com/galaxyproject/galaxy/commit/79945f37c31d4d42be86bee35237… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-03-07 (Tue, 07 Mar 2017) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Do not require stored workflow id for subworkflows Commit: 9aa911d509ac50f44ba4e6c5dca2cb9dba61ebbb https://github.com/galaxyproject/galaxy/commit/9aa911d509ac50f44ba4e6c5dca2… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-03-07 (Tue, 07 Mar 2017) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Merge pull request #3723 from guerler/fix_subworkflow_id Do not require stored workflow id for subworkflows Compare: https://github.com/galaxyproject/galaxy/compare/1b12259739e2...9aa911d509ac

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[galaxyproject/galaxy] a7ec0c: Add datatypes for soon coming PlantTribes Galaxy t...
by GitHub 07 Mar '17

07 Mar '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a7ec0c8579267adf6355e6f678b734e3f1b63cc9 https://github.com/galaxyproject/galaxy/commit/a7ec0c8579267adf6355e6f678b7… Author: Greg Von Kuster <ghv2(a)psu.edu> Date: 2017-03-02 (Thu, 02 Mar 2017) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/text.py Log Message: ----------- Add datatypes for soon coming PlantTribes Galaxy tools. Commit: 1b12259739e28bc69e68576a76aefcd61ee99358 https://github.com/galaxyproject/galaxy/commit/1b12259739e28bc69e68576a76ae… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-07 (Tue, 07 Mar 2017) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/text.py Log Message: ----------- Merge pull request #3698 from gregvonkuster/ptformats Add datatypes for soon coming PlantTribes Galaxy tools. Compare: https://github.com/galaxyproject/galaxy/compare/9ccb0953ad63...1b12259739e2

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[galaxyproject/galaxy] 570401: Implement initial collection builder UX test cases...
by GitHub 07 Mar '17

07 Mar '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 5704013301f8b185fbc55324a79ab58937a48230 https://github.com/galaxyproject/galaxy/commit/5704013301f8b185fbc55324a79a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-03-06 (Mon, 06 Mar 2017) Changed paths: M test/galaxy_selenium/has_driver.py M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation-data.yml A test/selenium_tests/test_collection_builders.py Log Message: ----------- Implement initial collection builder UX test cases. Exercise list and paired builder's most basic functionality. Commit: 8800376eb41d262b41862b3a1ad160218b47d45d https://github.com/galaxyproject/galaxy/commit/8800376eb41d262b41862b3a1ad1… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-03-06 (Mon, 06 Mar 2017) Changed paths: M test/galaxy_selenium/has_driver.py M test/galaxy_selenium/navigates_galaxy.py Log Message: ----------- Improved Selenium exception messages. For many common waiting operations used throughout many tests: ``` TimeoutException: Message: ``` Will become something like ``` TimeoutException: Message: Timeout waiting on CSS selector [#dataset-adb5f5c93f827949.state-failed] to become visible. ``` For HID waiting I've added the state and HID as well - so something like this: ``` TimeoutException: Message: Failed waiting on history item 1 state to change to [ok] current state [failed]. Timeout waiting on CSS selector [#dataset-adb5f5c93f827949.state-failed] to become visible. ``` Commit: 9ccb0953ad63aa46464a0ef8ec3bb6d5d1944539 https://github.com/galaxyproject/galaxy/commit/9ccb0953ad63aa46464a0ef8ec3b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-07 (Tue, 07 Mar 2017) Changed paths: M test/galaxy_selenium/has_driver.py M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation-data.yml A test/selenium_tests/test_collection_builders.py Log Message: ----------- Merge pull request #3716 from jmchilton/selenium_uploads_0 Selenium Testing Improvements Compare: https://github.com/galaxyproject/galaxy/compare/656a0f396ed6...9ccb0953ad63

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[galaxyproject/galaxy] 006801: Escape FTP filename. Thanks @yhoogstrate
by GitHub 07 Mar '17

07 Mar '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 006801ba1aace0a58f0ae90ba6a6777dfb834b58 https://github.com/galaxyproject/galaxy/commit/006801ba1aace0a58f0ae90ba6a6… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-07 (Tue, 07 Mar 2017) Changed paths: M client/galaxy/scripts/mvc/upload/upload-ftp.js M static/maps/mvc/upload/upload-ftp.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/upload/upload-ftp.js Log Message: ----------- Escape FTP filename. Thanks @yhoogstrate Commit: 656a0f396ed6d64a8010d9a6a32f138539f0b296 https://github.com/galaxyproject/galaxy/commit/656a0f396ed6d64a8010d9a6a32f… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2017-03-07 (Tue, 07 Mar 2017) Changed paths: M client/galaxy/scripts/mvc/upload/upload-ftp.js M static/maps/mvc/upload/upload-ftp.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/upload/upload-ftp.js Log Message: ----------- Merge pull request #3722 from dannon/escape_ftp_filename Filename handling for FTP upload Compare: https://github.com/galaxyproject/galaxy/compare/b8b773929267...656a0f396ed6

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[galaxyproject/galaxy] 4c4f78: Swap to using tag values to store name instead of ...
by GitHub 07 Mar '17

07 Mar '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4c4f78857b7141227e6ac320c36aad7c3429b7b5 https://github.com/galaxyproject/galaxy/commit/4c4f78857b7141227e6ac320c36a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-06 (Mon, 06 Mar 2017) Changed paths: M lib/galaxy/managers/hdas.py Log Message: ----------- Swap to using tag values to store name instead of child values. Commit: 2e5e6bb028165a735908543a063396f03bed375e https://github.com/galaxyproject/galaxy/commit/2e5e6bb028165a735908543a0633… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-06 (Mon, 06 Mar 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/style/less/ui.less M static/maps/mvc/ui/ui-select-content.js.map M static/maps/mvc/ui/ui-select-default.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 M static/scripts/mvc/ui/ui-select-default.js M static/style/blue/base.css Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into nametags_to_value Commit: d20e19e85a11ab8cf7eaff4fd0b3ee3dee337ff2 https://github.com/galaxyproject/galaxy/commit/d20e19e85a11ab8cf7eaff4fd0b3… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-06 (Mon, 06 Mar 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-default.js M lib/galaxy/tools/parameters/basic.py M static/maps/mvc/ui/ui-select-content.js.map M static/maps/mvc/ui/ui-select-default.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 M static/scripts/mvc/ui/ui-select-default.js Log Message: ----------- Include values in tags and tag selection lgoic Commit: 942f0d98d912196e95cfbb6f390c321676c28bce https://github.com/galaxyproject/galaxy/commit/942f0d98d912196e95cfbb6f390c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-06 (Mon, 06 Mar 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-default.js M static/maps/mvc/ui/ui-select-default.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-default.js Log Message: ----------- Only compose tag:value one time on the client. Commit: 278da1b35653aa1ad5835b74206bb46bb4d6373a https://github.com/galaxyproject/galaxy/commit/278da1b35653aa1ad5835b74206b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-06 (Mon, 06 Mar 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-default.js M static/maps/mvc/ui/ui-select-default.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-default.js Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into nametags_to_value Commit: f8e6b84998ab13cc99037c5eda3425f81329cbe5 https://github.com/galaxyproject/galaxy/commit/f8e6b84998ab13cc99037c5eda34… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-06 (Mon, 06 Mar 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-default.js M lib/galaxy/tools/parameters/basic.py M static/maps/mvc/ui/ui-select-default.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-default.js Log Message: ----------- Compose tag:value serverside -- we don't benefit from having them split when shipped (yet) Commit: 477626385c14e3df00aa654194dd8502c064c5d7 https://github.com/galaxyproject/galaxy/commit/477626385c14e3df00aa654194dd… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-03-06 (Mon, 06 Mar 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-default.js M static/maps/mvc/ui/ui-select-default.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-default.js Log Message: ----------- Filter tags by query term Commit: 192d75a4654411ad242819536a7968703697f524 https://github.com/galaxyproject/galaxy/commit/192d75a4654411ad242819536a79… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-06 (Mon, 06 Mar 2017) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Strip hanging extra comma. Commit: b8b7739292676ba928664417be771bd6e3f8f087 https://github.com/galaxyproject/galaxy/commit/b8b7739292676ba928664417be77… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2017-03-06 (Mon, 06 Mar 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-default.js M lib/galaxy/managers/hdas.py M lib/galaxy/tools/parameters/basic.py M static/maps/mvc/ui/ui-select-content.js.map M static/maps/mvc/ui/ui-select-default.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 M static/scripts/mvc/ui/ui-select-default.js Log Message: ----------- Merge pull request #3719 from dannon/nametags_to_value Use values for 'name'tags instead of child tags. Compare: https://github.com/galaxyproject/galaxy/compare/e54792f4263e...b8b773929267

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[galaxyproject/galaxy] 496f47: Fix tag escaping
by GitHub 06 Mar '17

06 Mar '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 496f476b300733d818062fcace7e8d1a61517abc https://github.com/galaxyproject/galaxy/commit/496f476b300733d818062fcace7e… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-03-06 (Mon, 06 Mar 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-default.js M static/maps/mvc/ui/ui-select-default.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-default.js Log Message: ----------- Fix tag escaping Commit: a52695dee6b179ed6cb24eaeb7146c946b28ccc9 https://github.com/galaxyproject/galaxy/commit/a52695dee6b179ed6cb24eaeb714… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-03-06 (Mon, 06 Mar 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-default.js M static/maps/mvc/ui/ui-select-default.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-default.js Log Message: ----------- Escape title for select labels Commit: e54792f4263ed5ddacc1044fe0b2182735732fdb https://github.com/galaxyproject/galaxy/commit/e54792f4263ed5ddacc1044fe0b2… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-06 (Mon, 06 Mar 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-default.js M static/maps/mvc/ui/ui-select-default.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-default.js Log Message: ----------- Merge pull request #3720 from guerler/escape_tags Fix tag escaping Compare: https://github.com/galaxyproject/galaxy/compare/0d95bf43ad84...e54792f4263e

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[galaxyproject/galaxy] ecaf1b: Show tags in select search field
by GitHub 06 Mar '17

06 Mar '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ecaf1be02f2364a2494e7adabd3b8733e194baf7 https://github.com/galaxyproject/galaxy/commit/ecaf1be02f2364a2494e7adabd3b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-03-06 (Mon, 06 Mar 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/style/less/ui.less M static/maps/mvc/ui/ui-select-content.js.map M static/maps/mvc/ui/ui-select-default.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 M static/scripts/mvc/ui/ui-select-default.js M static/style/blue/base.css Log Message: ----------- Show tags in select search field Commit: e606dbdacbbad0b604f5395c1140571d9a219984 https://github.com/galaxyproject/galaxy/commit/e606dbdacbbad0b604f5395c1140… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-03-06 (Mon, 06 Mar 2017) Changed paths: M client/galaxy/style/less/ui.less M static/style/blue/base.css Log Message: ----------- Fix style Commit: 0d95bf43ad84f014b404624a8e41f69f55b2a132 https://github.com/galaxyproject/galaxy/commit/0d95bf43ad84f014b404624a8e41… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-06 (Mon, 06 Mar 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/style/less/ui.less M static/maps/mvc/ui/ui-select-content.js.map M static/maps/mvc/ui/ui-select-default.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 M static/scripts/mvc/ui/ui-select-default.js M static/style/blue/base.css Log Message: ----------- Merge pull request #3718 from guerler/add_tags_to_label_000 Show tags in select search field Compare: https://github.com/galaxyproject/galaxy/compare/5055283f49d7...0d95bf43ad84

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[galaxyproject/galaxy] 9f4764: Preserve tags (ignoring collection handling for no...
by GitHub 06 Mar '17

06 Mar '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 9f4764f22cc63f7a734b9ea98707bfcb842aed14 https://github.com/galaxyproject/galaxy/commit/9f4764f22cc63f7a734b9ea98707… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-02 (Thu, 02 Mar 2017) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Preserve tags (ignoring collection handling for now) when running tools. Commit: 31d222c91031775629896feb027e00ea535ef7d9 https://github.com/galaxyproject/galaxy/commit/31d222c91031775629896feb027e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-02 (Thu, 02 Mar 2017) Changed paths: M client/galaxy/scripts/mvc/history/hda-li.js M client/galaxy/style/less/history.less 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 M static/style/blue/base.css Log Message: ----------- 'name' tag rendering, very basic, needs styling and loading fixes Commit: f6353c28f6f3a7012daf1eb95a7f7bcfd1d58d7c https://github.com/galaxyproject/galaxy/commit/f6353c28f6f3a7012daf1eb95a7f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-02 (Thu, 02 Mar 2017) Changed paths: M client/galaxy/style/less/history.less M static/style/blue/base.css Log Message: ----------- Fix underlines in nametags Commit: 9e5008984fc3ce1fd8359acfe502b3010ca76c1f https://github.com/galaxyproject/galaxy/commit/9e5008984fc3ce1fd8359acfe502… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-02 (Thu, 02 Mar 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: ----------- nametags first, then hid+title Commit: ef1344f03f291468b87c89d90b3a0f06ec9b0a79 https://github.com/galaxyproject/galaxy/commit/ef1344f03f291468b87c89d90b3a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-02 (Thu, 02 Mar 2017) Changed paths: M client/galaxy/style/less/history.less M static/style/blue/base.css Log Message: ----------- Adjust margins on labels Commit: a144ce58939b122cc1bfb0575081a2082942e773 https://github.com/galaxyproject/galaxy/commit/a144ce58939b122cc1bfb0575081… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-02 (Thu, 02 Mar 2017) Changed paths: M lib/galaxy/managers/hdas.py Log Message: ----------- Swap tags to default view for hdas -- may need to revisit this if it proves too expensive. Commit: 4b7fea8d3fe0afa062213f81a75003cac593ad74 https://github.com/galaxyproject/galaxy/commit/4b7fea8d3fe0afa062213f81a750… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-02 (Thu, 02 Mar 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: ----------- Adjust positioning again for nametags, below the standard title but still visible above the fold. Commit: a3ab46ef26031ba4c1fb22ebd0232bdb930651e5 https://github.com/galaxyproject/galaxy/commit/a3ab46ef26031ba4c1fb22ebd023… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-03 (Fri, 03 Mar 2017) Changed paths: M client/galaxy/scripts/mvc/history/hda-li.js M lib/galaxy/managers/hdas.py 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: ----------- Swap to a 'nametags' field in the high level view instead of returning all tags. TODO: Optimize this Commit: 861368ae1c7fa21f4ee7b55fbb682f78e07ece9d https://github.com/galaxyproject/galaxy/commit/861368ae1c7fa21f4ee7b55fbb68… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-03 (Fri, 03 Mar 2017) Changed paths: M lib/galaxy/managers/hdas.py Log Message: ----------- Remove dead code from prior work in nametag collection, change to user_tname usage. Commit: 5055283f49d73b7eb3b420875dfe8ccc1adb85de https://github.com/galaxyproject/galaxy/commit/5055283f49d73b7eb3b420875dfe… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-03-06 (Mon, 06 Mar 2017) Changed paths: M client/galaxy/scripts/mvc/history/hda-li.js M client/galaxy/style/less/history.less M lib/galaxy/managers/hdas.py M lib/galaxy/tools/actions/__init__.py A static/maps/analysis.js.map A static/maps/app.js.map A static/maps/app/analysis.js.map M static/maps/mvc/history/hda-li.js.map A static/scripts/analysis.js A static/scripts/app.js A static/scripts/app/analysis.js 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/style/blue/base.css Log Message: ----------- Merge branch 'tags_in_history' into dev Compare: https://github.com/galaxyproject/galaxy/compare/179e58c8b3a7...5055283f49d7

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[galaxyproject/galaxy] ad3025: Touch up Galaxy testing documentation.
by GitHub 06 Mar '17

06 Mar '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ad3025f46a00190674bbc4dbc3bfab16983f9cb4 https://github.com/galaxyproject/galaxy/commit/ad3025f46a00190674bbc4dbc3bf… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-03-06 (Mon, 06 Mar 2017) Changed paths: M run_tests.sh M test/TESTING.md Log Message: ----------- Touch up Galaxy testing documentation. Commit: 179e58c8b3a7d10fa15e238ec7d2f982aa3fed00 https://github.com/galaxyproject/galaxy/commit/179e58c8b3a7d10fa15e238ec7d2… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-03-06 (Mon, 06 Mar 2017) Changed paths: M run_tests.sh M test/TESTING.md Log Message: ----------- Merge pull request #3715 from jmchilton/test_docs_0 Touch up Galaxy testing documentation. Compare: https://github.com/galaxyproject/galaxy/compare/97d6e1b6c1ca...179e58c8b3a7

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[galaxyproject/galaxy] 7cc25c: Parse tags with datatoolparameter options
by GitHub 06 Mar '17

06 Mar '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 7cc25c9082de5df6ff4ed89365f34f39dbbec545 https://github.com/galaxyproject/galaxy/commit/7cc25c9082de5df6ff4ed89365f3… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-03-01 (Wed, 01 Mar 2017) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Parse tags with datatoolparameter options Commit: a02c1cfda10e2b600e5209db7f7be8dfb0069467 https://github.com/galaxyproject/galaxy/commit/a02c1cfda10e2b600e5209db7f7b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-03-01 (Wed, 01 Mar 2017) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Add tags to name Commit: 4d5a03ba55eeb1a1f3884999f3399fb47503cbcc https://github.com/galaxyproject/galaxy/commit/4d5a03ba55eeb1a1f3884999f339… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-03-01 (Wed, 01 Mar 2017) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Remove brackets Commit: ca238c4323a9d8efd8bb6fca06da5dd87d86032f https://github.com/galaxyproject/galaxy/commit/ca238c4323a9d8efd8bb6fca06da… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-03-02 (Thu, 02 Mar 2017) Changed paths: M test/unit/tools/test_data_parameters.py M test/unit/tools/test_evaluation.py Log Message: ----------- Add tags to mock hda Commit: 2135e63f8e144e21c926c8ea593acb5ce9615069 https://github.com/galaxyproject/galaxy/commit/2135e63f8e144e21c926c8ea593a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-03-02 (Thu, 02 Mar 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-content.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M lib/galaxy/tools/parameters/basic.py M static/maps/mvc/ui/ui-select-content.js.map M static/maps/mvc/ui/ui-select-default.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 M static/scripts/mvc/ui/ui-select-default.js Log Message: ----------- Filter tags regardless of given select field label Commit: 7e19245c8af5b203c0a76f2ab5eee5a1856fdded https://github.com/galaxyproject/galaxy/commit/7e19245c8af5b203c0a76f2ab5ee… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-03-02 (Thu, 02 Mar 2017) Changed paths: M test/unit/tools/test_evaluation.py Log Message: ----------- Fix spacing Commit: a93c29fa4a438b93016cb5e31d0e4ef88ca88029 https://github.com/galaxyproject/galaxy/commit/a93c29fa4a438b93016cb5e31d0e… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-03-02 (Thu, 02 Mar 2017) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Add tag filtering for collections Commit: 82137b433cf00f2b83a00e08b71bdea2bfebf9bd https://github.com/galaxyproject/galaxy/commit/82137b433cf00f2b83a00e08b71b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-03-02 (Thu, 02 Mar 2017) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Fix append calling for collections Commit: 735f56ec95dba7d58d8d1dad922a01c3074af1ce https://github.com/galaxyproject/galaxy/commit/735f56ec95dba7d58d8d1dad922a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-03-03 (Fri, 03 Mar 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-default.js M static/maps/mvc/ui/ui-select-default.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-default.js Log Message: ----------- Concat all tags to improve front-end performance Commit: 83df8d5c9653c8e213eed63aecb9377503eb42f2 https://github.com/galaxyproject/galaxy/commit/83df8d5c9653c8e213eed63aecb9… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-03-03 (Fri, 03 Mar 2017) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Attempt to prefetch tags when building active datasets list Commit: 6b2f9be75ab16e69a8fb1c72d10d169d20ab7854 https://github.com/galaxyproject/galaxy/commit/6b2f9be75ab16e69a8fb1c72d10d… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-03-03 (Fri, 03 Mar 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-default.js 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-default.js Log Message: ----------- Use space instead of comma when concatenating tags Commit: 97d6e1b6c1ca56575c1297649fd0484c85e15a7a https://github.com/galaxyproject/galaxy/commit/97d6e1b6c1ca56575c1297649fd0… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-06 (Mon, 06 Mar 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-content.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M lib/galaxy/model/__init__.py M lib/galaxy/tools/parameters/basic.py M static/maps/mvc/ui/ui-select-content.js.map M static/maps/mvc/ui/ui-select-default.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 M static/scripts/mvc/ui/ui-select-default.js M test/unit/tools/test_data_parameters.py Log Message: ----------- Merge branch 'filter_dataset_tags' into dev Compare: https://github.com/galaxyproject/galaxy/compare/6e3a9661d45c...97d6e1b6c1ca

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[galaxyproject/galaxy] 075d53: Fix for transiently failing workflow test.
by GitHub 06 Mar '17

06 Mar '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 075d53af92ea2640ba3005f36354712b966ea98e https://github.com/galaxyproject/galaxy/commit/075d53af92ea2640ba3005f36354… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-02-24 (Fri, 24 Feb 2017) Changed paths: M test/api/test_workflows.py Log Message: ----------- Fix for transiently failing workflow test. The history can be complete before a workflow has fully scheduled if the workflow still has more jobs to schedule but all the current ones are complete. Commit: 6e3a9661d45cb239e116660888834ea8037b726b https://github.com/galaxyproject/galaxy/commit/6e3a9661d45cb239e11666088883… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-03-06 (Mon, 06 Mar 2017) Changed paths: M test/api/test_workflows.py Log Message: ----------- Merge pull request #3668 from jmchilton/workflow_transient_failing_test Fix for transiently failing workflow test. Compare: https://github.com/galaxyproject/galaxy/compare/b769da1b3d67...6e3a9661d45c

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[galaxyproject/galaxy] 0914c0: fix metadata failure for large count tables
by GitHub 06 Mar '17

06 Mar '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 0914c05f8823759af21b37ff0ea8a7e757c4ba3a https://github.com/galaxyproject/galaxy/commit/0914c05f8823759af21b37ff0ea8… Author: shiltemann <zazkia(a)gmail.com> Date: 2017-03-03 (Fri, 03 Mar 2017) Changed paths: M lib/galaxy/datatypes/mothur.py Log Message: ----------- fix metadata failure for large count tables Commit: fe41ec185f85cdca4e0eb4a5705b511d20f699aa https://github.com/galaxyproject/galaxy/commit/fe41ec185f85cdca4e0eb4a5705b… Author: Saskia Hiltemann <shiltemann(a)users.noreply.github.com> Date: 2017-03-03 (Fri, 03 Mar 2017) Changed paths: M lib/galaxy/datatypes/mothur.py Log Message: ----------- fix typos Commit: b769da1b3d67195d3a2cd908321f0f200dc2a8b0 https://github.com/galaxyproject/galaxy/commit/b769da1b3d67195d3a2cd908321f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-03-06 (Mon, 06 Mar 2017) Changed paths: M lib/galaxy/datatypes/mothur.py Log Message: ----------- Merge pull request #3706 from shiltemann/mothur-dataype-fix Mothur datatypes: fix metadata failure for large count tables Compare: https://github.com/galaxyproject/galaxy/compare/4aec70cae28f...b769da1b3d67

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[galaxyproject/galaxy] 293726: Support Docker Engine swarm mode
by GitHub 03 Mar '17

03 Mar '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 293726c57933cb2465a650d005332241eac0f912 https://github.com/galaxyproject/galaxy/commit/293726c57933cb2465a650d00533… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-03-03 (Fri, 03 Mar 2017) Changed paths: M config/galaxy.ini.sample M config/plugins/interactive_environments/bam_iobio/config/bam_iobio.ini.sample M config/plugins/interactive_environments/jupyter/config/jupyter.ini.sample M config/plugins/interactive_environments/neo/config/neo.ini.sample M config/plugins/interactive_environments/phinch/config/phinch.ini.sample M config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample A cron/clean_docker_swarm_mode_services.sh M doc/source/admin/interactive_environments.rst M lib/galaxy/config.py M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Support Docker Engine swarm mode Commit: 4aec70cae28f336212a6bc8f5d24a325cb851bab https://github.com/galaxyproject/galaxy/commit/4aec70cae28f336212a6bc8f5d24… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-03-03 (Fri, 03 Mar 2017) Changed paths: M config/galaxy.ini.sample M config/plugins/interactive_environments/bam_iobio/config/bam_iobio.ini.sample M config/plugins/interactive_environments/jupyter/config/jupyter.ini.sample M config/plugins/interactive_environments/neo/config/neo.ini.sample M config/plugins/interactive_environments/phinch/config/phinch.ini.sample M config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample A cron/clean_docker_swarm_mode_services.sh M doc/source/admin/interactive_environments.rst M lib/galaxy/config.py M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Merge pull request #3666 from natefoo/docker-swarm-mode Support Docker Engine swarm mode for Interactive Environments Compare: https://github.com/galaxyproject/galaxy/compare/bb604e65ee0f...4aec70cae28f

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[galaxyproject/usegalaxy-playbook] 217776: Update Test (it was already updated once before ma...
by GitHub 03 Mar '17

03 Mar '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 21777674694404bcb7ff18f8036487a90133e46d https://github.com/galaxyproject/usegalaxy-playbook/commit/21777674694404bc… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-03-03 (Fri, 03 Mar 2017) Changed paths: M files/galaxy/test.galaxyproject.org/var/integrated_tool_panel.xml M stage/galaxy_version.yml Log Message: ----------- Update Test (it was already updated once before manually to d3840c5.

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[galaxyproject/galaxy] 4fa76c: Set $HOME to a temp directory rather than conda_pr...
by GitHub 03 Mar '17

03 Mar '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4fa76caf67e33ce38f2e45325d504e2f1ff824a7 https://github.com/galaxyproject/galaxy/commit/4fa76caf67e33ce38f2e45325d50… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-03-02 (Thu, 02 Mar 2017) Changed paths: M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- Set $HOME to a temp directory rather than conda_prefix because conda_prefix may not be writable either. Commit: bb604e65ee0f34ccce664f5798c55adbcedc9e5e https://github.com/galaxyproject/galaxy/commit/bb604e65ee0f34ccce664f5798c5… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2017-03-03 (Fri, 03 Mar 2017) Changed paths: M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- Merge pull request #3701 from natefoo/conda_home_temp Set $HOME to a temp directory rather than conda_prefix because conda_prefix may not be writable either. Compare: https://github.com/galaxyproject/galaxy/compare/d3840c5c4140...bb604e65ee0f

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[galaxyproject/usegalaxy-playbook] dbaff9: Set conda_prefix so conda uses /cvmfs for shebangs...
by GitHub 02 Mar '17

02 Mar '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: dbaff915e1bd2c4ddf4d66c84959a2f45d3e3ee7 https://github.com/galaxyproject/usegalaxy-playbook/commit/dbaff915e1bd2c4d… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-03-02 (Thu, 02 Mar 2017) Changed paths: M stage/group_vars/galaxyservers.yml Log Message: ----------- Set conda_prefix so conda uses /cvmfs for shebangs and whatnot, instead of /galaxy/test/deps, which is a symlink to /cvmfs/test.galaxyproject.org/deps

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[galaxyproject/galaxy] ce7f9e: Annotate converters that appear to need galaxy on ...
by GitHub 02 Mar '17

02 Mar '17

Branch: refs/heads/release_17.01 Home: https://github.com/galaxyproject/galaxy Commit: ce7f9e91ca8893ce290aeeac4836e18db07af3a5 https://github.com/galaxyproject/galaxy/commit/ce7f9e91ca8893ce290aeeac4836… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-03-01 (Wed, 01 Mar 2017) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Annotate converters that appear to need galaxy on PYTHONPATH. Should fix #3499 (thanks for the explicit heads up @mvdbeek). Commit: 93a802bd450658f0c66d4226c626112e8163d5a6 https://github.com/galaxyproject/galaxy/commit/93a802bd450658f0c66d4226c626… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-03-02 (Thu, 02 Mar 2017) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge pull request #3690 from jmchilton/converter_galaxy_lib_fixes [17.01] Annotate converters that appear to need galaxy on PYTHONPATH. Compare: https://github.com/galaxyproject/galaxy/compare/ca5bb99ee043...93a802bd4506

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