galaxy-commits June 2017

galaxy-commits@lists.galaxyproject.org

1 participants
76 discussions

[galaxyproject/galaxy] 0b1eaf: fix - remove extra slash
by GitHub 06 Jun '17

06 Jun '17

Branch: refs/heads/release_17.05 Home: https://github.com/galaxyproject/galaxy Commit: 0b1eaf3269ed5ccbfba7807826e822b38f57778e https://github.com/galaxyproject/galaxy/commit/0b1eaf3269ed5ccbfba7807826e8… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-06-06 (Tue, 06 Jun 2017) Changed paths: M config/plugins/webhooks/demo/search/config/searchover.yaml M config/plugins/webhooks/demo/tool_list/config/tool_list.yml M test/functional/webhooks/trans_object/config/trans_object.yaml Log Message: ----------- fix - remove extra slash Commit: d39b955e8a5d6c54852d3b32cd9cd1e7e2d3e519 https://github.com/galaxyproject/galaxy/commit/d39b955e8a5d6c54852d3b32cd9c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-06-06 (Tue, 06 Jun 2017) Changed paths: M config/plugins/webhooks/demo/search/config/searchover.yaml M config/plugins/webhooks/demo/tool_list/config/tool_list.yml M test/functional/webhooks/trans_object/config/trans_object.yaml Log Message: ----------- Merge pull request #4158 from martenson/webhooks-fix-prefix [17.05] fix webhooks loading url Compare: https://github.com/galaxyproject/galaxy/compare/cbe9944815d0...d39b955e8a5d

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[galaxyproject/galaxy]
by GitHub 06 Jun '17

06 Jun '17

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

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[galaxyproject/galaxy] 4db996: Move galaxy.tools.toolbox.cache to galaxy.tools.ca...
by GitHub 06 Jun '17

06 Jun '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4db996a4de91f9ed816b3abce16e9db2f9ffefcf https://github.com/galaxyproject/galaxy/commit/4db996a4de91f9ed816b3abce16e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-06-06 (Tue, 06 Jun 2017) Changed paths: M lib/galaxy/app.py A lib/galaxy/tools/cache.py R lib/galaxy/tools/toolbox/cache.py M test/unit/tools/test_toolbox.py Log Message: ----------- Move galaxy.tools.toolbox.cache to galaxy.tools.cache. galaxy.tools.toolbox is shared with galaxy-lib and so should have no dependencies on sqlalchemy. Also this really seems to be caching tools and tool shed repositories and fairly independent of the toolbox abstraction so I think it is solid refactoring independent of the sqlalchemy/galaxy-lib constraints. Commit: fae508b48f403db3edaed3207fa6bf65fcded8bb https://github.com/galaxyproject/galaxy/commit/fae508b48f403db3edaed3207fa6… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-06-06 (Tue, 06 Jun 2017) Changed paths: M lib/galaxy/app.py A lib/galaxy/tools/cache.py R lib/galaxy/tools/toolbox/cache.py M test/unit/tools/test_toolbox.py Log Message: ----------- Merge pull request #4155 from jmchilton/tool_cache_move Move galaxy.tools.toolbox.cache to galaxy.tools.cache. Compare: https://github.com/galaxyproject/galaxy/compare/5da6cb70cc14...fae508b48f40

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[galaxyproject/galaxy] 7467bc: More reporting in new transiently failing collecti...
by GitHub 06 Jun '17

06 Jun '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 7467bcf10192a1bda3e4edec5afe86a8b7b5b882 https://github.com/galaxyproject/galaxy/commit/7467bcf10192a1bda3e4edec5afe… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-06-06 (Tue, 06 Jun 2017) Changed paths: M test/api/test_dataset_collections.py Log Message: ----------- More reporting in new transiently failing collection download test. Commit: 5da6cb70cc14885ad703d4035fc4c86b67f3b2ab https://github.com/galaxyproject/galaxy/commit/5da6cb70cc14885ad703d4035fc4… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-06-06 (Tue, 06 Jun 2017) Changed paths: M test/api/test_dataset_collections.py Log Message: ----------- Merge pull request #4156 from jmchilton/new_api_test_improvement More reporting in new transiently failing collection download test. Compare: https://github.com/galaxyproject/galaxy/compare/9d1a382f8642...5da6cb70cc14

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[galaxyproject/galaxy] a0dc50: fix plugin access path
by GitHub 05 Jun '17

05 Jun '17

Branch: refs/heads/example_fix Home: https://github.com/galaxyproject/galaxy Commit: a0dc50b2a1f878ac9567a4a60b491b14897db9d9 https://github.com/galaxyproject/galaxy/commit/a0dc50b2a1f878ac9567a4a60b49… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-06-05 (Mon, 05 Jun 2017) Changed paths: M config/plugins/webhooks/demo/search/config/searchover.yaml Log Message: ----------- fix plugin access path

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[galaxyproject/galaxy] 3084e1: Add API route for downloading entire collections
by GitHub 05 Jun '17

05 Jun '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 3084e192cb9553f82910aa2cac1187d793b2c5f1 https://github.com/galaxyproject/galaxy/commit/3084e192cb9553f82910aa2cac11… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-05-22 (Mon, 22 May 2017) Changed paths: M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/data.py M lib/galaxy/managers/collections_util.py M lib/galaxy/webapps/galaxy/api/history_contents.py M lib/galaxy/webapps/galaxy/buildapp.py M test/api/test_dataset_collections.py Log Message: ----------- Add API route for downloading entire collections Entire collections can now be downloaded as tarballs. I have used the StreamBall class from galaxy.utils, so archives start downloading immediately. The collection structure is mapped onto a directory struture, where each level of a collection is a directory in the archive. Collections of BAM files are included alongside their .bai indices, and composite datatype are supported as well. API tests for downloading list, paired and list:paired collections are included. Currently collection elements that are not in the OK status will be skipped, so we should probably hide the download button if not all collection elements are in a final state. Commit: 1093b614427f21986068e3fc609099e1573b6c4f https://github.com/galaxyproject/galaxy/commit/1093b614427f21986068e3fc6090… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-05-22 (Mon, 22 May 2017) Changed paths: M client/galaxy/scripts/mvc/collection/collection-view.js M static/maps/mvc/collection/collection-view.js.map M static/scripts/bundled/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.map M static/scripts/mvc/collection/collection-view.js Log Message: ----------- Add download button for collections Commit: 9db1cc455d48e0b74e3db6b1f39b623297f9b453 https://github.com/galaxyproject/galaxy/commit/9db1cc455d48e0b74e3db6b1f39b… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-05-22 (Mon, 22 May 2017) Changed paths: M test/api/test_dataset_collections.py M test/base/populators.py Log Message: ----------- Fix the API tests for collection downloads by waiting for the datasets to become ready. Commit: 7527609e60a7775b705262a1562c969910b65a91 https://github.com/galaxyproject/galaxy/commit/7527609e60a7775b705262a1562c… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-05-23 (Tue, 23 May 2017) Changed paths: M test/api/test_dataset_collections.py Log Message: ----------- Set assert_ok to true when wiaiting for datasets to become ready Commit: 00de5b9f9a129805636760f0e0a88cd6cdfc9108 https://github.com/galaxyproject/galaxy/commit/00de5b9f9a129805636760f0e0a8… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-06-05 (Mon, 05 Jun 2017) Changed paths: M .ci/flake8_lint_include_list.txt M CONTRIBUTORS.md M README.rst M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/grid/grid-template.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/hdca-li.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js A client/galaxy/scripts/mvc/workflow/workflow-configure-menu.js M client/galaxy/scripts/mvc/workflow/workflow.js M client/galaxy/style/less/base.less M client/webpack.config.js M config/job_conf.xml.sample_advanced M contrib/galaxy.debian-init M contrib/galaxy_supervisor.conf M doc/Makefile R doc/patch.py M doc/source/admin/authentication.md M doc/source/admin/special_topics/mulled_containers.rst R doc/source/api/api.rst R doc/source/api/ts_api.rst M doc/source/dev/build_a_job_runner.rst M doc/source/lib/galaxy.actions.rst M doc/source/lib/galaxy.auth.providers.rst M doc/source/lib/galaxy.auth.rst A doc/source/lib/galaxy.containers.rst M doc/source/lib/galaxy.dataset_collections.rst M doc/source/lib/galaxy.dataset_collections.types.rst M doc/source/lib/galaxy.datatypes.converters.rst M doc/source/lib/galaxy.datatypes.dataproviders.rst M doc/source/lib/galaxy.datatypes.display_applications.rst M doc/source/lib/galaxy.datatypes.rst M doc/source/lib/galaxy.datatypes.util.rst M doc/source/lib/galaxy.dependencies.rst M doc/source/lib/galaxy.eggs.rst M doc/source/lib/galaxy.exceptions.rst M doc/source/lib/galaxy.external_services.result_handlers.rst M doc/source/lib/galaxy.external_services.rst M doc/source/lib/galaxy.forms.rst M doc/source/lib/galaxy.jobs.actions.rst M doc/source/lib/galaxy.jobs.deferred.rst M doc/source/lib/galaxy.jobs.metrics.collectl.rst M doc/source/lib/galaxy.jobs.metrics.instrumenters.rst M doc/source/lib/galaxy.jobs.metrics.rst M doc/source/lib/galaxy.jobs.rst M doc/source/lib/galaxy.jobs.runners.rst M doc/source/lib/galaxy.jobs.runners.state_handlers.rst M doc/source/lib/galaxy.jobs.runners.util.cli.job.rst M doc/source/lib/galaxy.jobs.runners.util.cli.rst M doc/source/lib/galaxy.jobs.runners.util.cli.shell.rst M doc/source/lib/galaxy.jobs.runners.util.condor.rst A doc/source/lib/galaxy.jobs.runners.util.drmaa.rst M doc/source/lib/galaxy.jobs.runners.util.job_script.rst M doc/source/lib/galaxy.jobs.runners.util.rst M doc/source/lib/galaxy.jobs.splitters.rst M doc/source/lib/galaxy.managers.rst M doc/source/lib/galaxy.model.migrate.rst M doc/source/lib/galaxy.model.orm.rst M doc/source/lib/galaxy.model.rst M doc/source/lib/galaxy.model.tool_shed_install.migrate.rst M doc/source/lib/galaxy.model.tool_shed_install.rst M doc/source/lib/galaxy.objectstore.rst M doc/source/lib/galaxy.openid.rst M doc/source/lib/galaxy.quota.rst M doc/source/lib/galaxy.rst M doc/source/lib/galaxy.sample_tracking.rst M doc/source/lib/galaxy.security.rst R doc/source/lib/galaxy.tags.rst M doc/source/lib/galaxy.tools.actions.rst A doc/source/lib/galaxy.tools.cwl.rst M doc/source/lib/galaxy.tools.data.rst M doc/source/lib/galaxy.tools.data_manager.rst A doc/source/lib/galaxy.tools.deps.container_resolvers.rst A doc/source/lib/galaxy.tools.deps.mulled.rst M doc/source/lib/galaxy.tools.deps.resolvers.rst M doc/source/lib/galaxy.tools.deps.rst M doc/source/lib/galaxy.tools.filters.rst M doc/source/lib/galaxy.tools.imp_exp.rst M doc/source/lib/galaxy.tools.linters.rst A doc/source/lib/galaxy.tools.locations.rst M doc/source/lib/galaxy.tools.parameters.rst M doc/source/lib/galaxy.tools.parser.rst M doc/source/lib/galaxy.tools.rst M doc/source/lib/galaxy.tools.search.rst M doc/source/lib/galaxy.tools.toolbox.filters.rst M doc/source/lib/galaxy.tools.toolbox.lineages.rst M doc/source/lib/galaxy.tools.toolbox.rst M doc/source/lib/galaxy.tools.util.galaxyops.rst M doc/source/lib/galaxy.tools.util.rst A doc/source/lib/galaxy.tools.verify.asserts.rst A doc/source/lib/galaxy.tools.verify.rst A doc/source/lib/galaxy.tours.rst M doc/source/lib/galaxy.util.backports.rst M doc/source/lib/galaxy.util.log.rst M doc/source/lib/galaxy.util.pastescript.rst M doc/source/lib/galaxy.util.rst M doc/source/lib/galaxy.visualization.data_providers.phyloviz.rst M doc/source/lib/galaxy.visualization.data_providers.rst M doc/source/lib/galaxy.visualization.genome.rst M doc/source/lib/galaxy.visualization.plugins.rst M doc/source/lib/galaxy.visualization.rst M doc/source/lib/galaxy.visualization.tracks.rst M doc/source/lib/galaxy.web.base.controllers.rst M doc/source/lib/galaxy.web.base.rst M doc/source/lib/galaxy.web.framework.helpers.rst M doc/source/lib/galaxy.web.framework.middleware.rst M doc/source/lib/galaxy.web.framework.rst M doc/source/lib/galaxy.web.proxy.rst M doc/source/lib/galaxy.web.rst M doc/source/lib/galaxy.web.security.rst A doc/source/lib/galaxy.web.stack.rst A doc/source/lib/galaxy.webapps.galaxy.api.rst M doc/source/lib/galaxy.webapps.galaxy.controllers.rst M doc/source/lib/galaxy.webapps.galaxy.rst M doc/source/lib/galaxy.webapps.reports.controllers.rst M doc/source/lib/galaxy.webapps.reports.rst M doc/source/lib/galaxy.webapps.rst A doc/source/lib/galaxy.webapps.tool_shed.api.rst M doc/source/lib/galaxy.webapps.tool_shed.controllers.rst M doc/source/lib/galaxy.webapps.tool_shed.framework.middleware.rst M doc/source/lib/galaxy.webapps.tool_shed.framework.rst M doc/source/lib/galaxy.webapps.tool_shed.model.migrate.rst M doc/source/lib/galaxy.webapps.tool_shed.model.rst M doc/source/lib/galaxy.webapps.tool_shed.rst M doc/source/lib/galaxy.webapps.tool_shed.search.rst M doc/source/lib/galaxy.webapps.tool_shed.security.rst M doc/source/lib/galaxy.webapps.tool_shed.util.rst A doc/source/lib/galaxy.webhooks.rst M doc/source/lib/galaxy.work.rst M doc/source/lib/galaxy.workflow.rst M doc/source/lib/galaxy.workflow.schedulers.rst M doc/source/lib/galaxy_ext.metadata.rst M doc/source/lib/galaxy_ext.rst M doc/source/lib/log_tempfile.rst M doc/source/lib/psyco_full.rst M doc/source/lib/tool_shed.capsule.rst M doc/source/lib/tool_shed.dependencies.repository.rst M doc/source/lib/tool_shed.dependencies.rst M doc/source/lib/tool_shed.dependencies.tool.rst M doc/source/lib/tool_shed.galaxy_install.datatypes.rst M doc/source/lib/tool_shed.galaxy_install.grids.rst M doc/source/lib/tool_shed.galaxy_install.metadata.rst M doc/source/lib/tool_shed.galaxy_install.migrate.rst M doc/source/lib/tool_shed.galaxy_install.repository_dependencies.rst M doc/source/lib/tool_shed.galaxy_install.rst M doc/source/lib/tool_shed.galaxy_install.tool_dependencies.recipe.rst M doc/source/lib/tool_shed.galaxy_install.tool_dependencies.rst M doc/source/lib/tool_shed.galaxy_install.tools.rst M doc/source/lib/tool_shed.galaxy_install.utility_containers.rst M doc/source/lib/tool_shed.grids.rst M doc/source/lib/tool_shed.managers.rst M doc/source/lib/tool_shed.metadata.rst M doc/source/lib/tool_shed.repository_types.rst M doc/source/lib/tool_shed.rst M doc/source/lib/tool_shed.tools.rst M doc/source/lib/tool_shed.util.rst M doc/source/lib/tool_shed.utility_containers.rst M doc/source/releases/13.01_announce.rst M doc/source/releases/13.02_announce.rst M doc/source/releases/13.04_announce.rst M doc/source/releases/13.06_announce.rst M doc/source/releases/13.08_announce.rst M doc/source/releases/13.11_announce.rst M doc/source/releases/14.02_announce.rst M doc/source/releases/14.04_announce.rst M doc/source/releases/14.06_announce.rst M doc/source/releases/14.08_announce.rst M doc/source/releases/14.10_announce.rst M doc/source/releases/15.01_announce.rst M doc/source/releases/15.03_announce.rst M doc/source/releases/15.05.rst M doc/source/releases/15.05_announce.rst M doc/source/releases/15.07_announce.rst M doc/source/releases/15.10_announce.rst M doc/source/releases/16.01_announce.rst M doc/source/releases/16.04_announce.rst M doc/source/releases/16.07_announce.rst M doc/source/releases/16.10_announce.rst M doc/source/releases/17.01_announce.rst A doc/source/releases/17.05.rst M doc/source/releases/17.05_announce.rst A doc/source/releases/17.09_announce.rst M doc/source/releases/_thanks.rst M doc/source/releases/index.rst M doc/source/releases/older_releases.rst M doc/source/slideshow/architecture/galaxy_architecture.md M lib/galaxy/datatypes/converters/cml_to_inchi_converter.xml M lib/galaxy/datatypes/converters/cml_to_mol2_converter.xml M lib/galaxy/datatypes/converters/cml_to_sdf_converter.xml M lib/galaxy/datatypes/converters/cml_to_smi_converter.xml M lib/galaxy/datatypes/converters/inchi_to_cml_converter.xml M lib/galaxy/datatypes/converters/inchi_to_mol2_converter.xml M lib/galaxy/datatypes/converters/inchi_to_mol_converter.xml M lib/galaxy/datatypes/converters/inchi_to_sdf_converter.xml M lib/galaxy/datatypes/converters/inchi_to_smi_converter.xml M lib/galaxy/datatypes/converters/mol2_to_cml_converter.xml M lib/galaxy/datatypes/converters/mol2_to_inchi_converter.xml M lib/galaxy/datatypes/converters/mol2_to_mol_converter.xml M lib/galaxy/datatypes/converters/mol2_to_sdf_converter.xml M lib/galaxy/datatypes/converters/mol2_to_smi_converter.xml M lib/galaxy/datatypes/converters/mol_to_cml_converter.xml M lib/galaxy/datatypes/converters/mol_to_inchi_converter.xml M lib/galaxy/datatypes/converters/mol_to_mol2_converter.xml M lib/galaxy/datatypes/converters/mol_to_smi_converter.xml M lib/galaxy/datatypes/converters/sdf_to_cml_converter.xml M lib/galaxy/datatypes/converters/sdf_to_inchi_converter.xml M lib/galaxy/datatypes/converters/sdf_to_mol2_converter.xml M lib/galaxy/datatypes/converters/sdf_to_smi_converter.xml M lib/galaxy/datatypes/converters/smi_to_cml_converter.xml M lib/galaxy/datatypes/converters/smi_to_inchi_converter.xml M lib/galaxy/datatypes/converters/smi_to_mol2_converter.xml M lib/galaxy/datatypes/converters/smi_to_mol_converter.xml M lib/galaxy/datatypes/converters/smi_to_sdf_converter.xml M lib/galaxy/datatypes/converters/smi_to_smi_converter.xml M lib/galaxy/jobs/actions/post.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/drmaa.py M lib/galaxy/managers/collections.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/parameters/__init__.py M lib/galaxy/tools/xsd/README.md M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/util/compression_utils.py M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/page.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/env_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py M lib/tool_shed/metadata/metadata_generator.py M scripts/bootstrap_history.py M static/maps/layout/menu.js.map M static/maps/mvc/dataset/dataset-li.js.map M static/maps/mvc/form/form-input.js.map M static/maps/mvc/grid/grid-template.js.map M static/maps/mvc/grid/grid-view.js.map M static/maps/mvc/history/hda-li.js.map M static/maps/mvc/history/hdca-li.js.map M static/maps/mvc/tool/tool-form-composite.js.map A static/maps/mvc/workflow/workflow-configure-menu.js.map M static/maps/mvc/workflow/workflow.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/dataset/dataset-li.js M static/scripts/mvc/form/form-input.js M static/scripts/mvc/grid/grid-template.js M static/scripts/mvc/grid/grid-view.js M static/scripts/mvc/history/hda-li.js M static/scripts/mvc/history/hdca-li.js M static/scripts/mvc/tool/tool-form-composite.js A static/scripts/mvc/workflow/workflow-configure-menu.js M static/scripts/mvc/workflow/workflow.js M static/style/blue/base.css M static/welcome.html.sample M templates/grid_base.mako R templates/webapps/galaxy/page/list_published.mako R templates/webapps/galaxy/workflow/configure_menu.mako M test/functional/tools/sample_datatypes_conf.xml M test/qunit/test-data/bootstrapped.js M test/qunit/tests/galaxy-app-base.js Log Message: ----------- Merge remote-tracking branch 'jmchilton/dev' into download_collection Commit: 9d1a382f8642959fd157b9695cca52ac056d2d81 https://github.com/galaxyproject/galaxy/commit/9d1a382f8642959fd157b9695cca… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-06-05 (Mon, 05 Jun 2017) Changed paths: M client/galaxy/scripts/mvc/collection/collection-view.js M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/data.py M lib/galaxy/managers/collections_util.py M lib/galaxy/webapps/galaxy/api/history_contents.py M lib/galaxy/webapps/galaxy/buildapp.py M static/maps/mvc/collection/collection-view.js.map 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.map M static/scripts/mvc/collection/collection-view.js M test/api/test_dataset_collections.py M test/base/populators.py Log Message: ----------- Merge pull request #4098 from mvdbeek/download_collection Add possibility for downloading entire collections Compare: https://github.com/galaxyproject/galaxy/compare/294c1d115413...9d1a382f8642

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[galaxyproject/galaxy] bd361d: Fix chronos client initialization
by GitHub 05 Jun '17

05 Jun '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: bd361d550c03340a3880716c9a6aa405a6058a6a https://github.com/galaxyproject/galaxy/commit/bd361d550c03340a3880716c9a6a… Author: Thodoris Sotiropoulos <theosot(a)dmst.aueb.gr> Date: 2017-05-29 (Mon, 29 May 2017) Changed paths: M lib/galaxy/jobs/runners/chronos.py Log Message: ----------- Fix chronos client initialization Provide the missing keyword arguments during chronos client initialization based on the runner parameters. Commit: 4c888be5abe563a77c7df57e0a5fb5263edfd0bd https://github.com/galaxyproject/galaxy/commit/4c888be5abe563a77c7df57e0a5f… Author: Thodoris Sotiropoulos <theosot(a)dmst.aueb.gr> Date: 2017-05-30 (Tue, 30 May 2017) Changed paths: M lib/galaxy/jobs/runners/chronos.py Log Message: ----------- minor fix: make expession be in one line Commit: f2f1fba10ea5f49398abddce575565062d353fc7 https://github.com/galaxyproject/galaxy/commit/f2f1fba10ea5f49398abddce5755… Author: Thodoris Sotiropoulos <theosot(a)dmst.aueb.gr> Date: 2017-06-01 (Thu, 01 Jun 2017) Changed paths: M config/job_conf.xml.sample_advanced Log Message: ----------- chronos-runner: Mention about insecure option at job_conf Commit: 294c1d115413e96ae0f5daaa27a50076b200ff66 https://github.com/galaxyproject/galaxy/commit/294c1d115413e96ae0f5daaa27a5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-06-05 (Mon, 05 Jun 2017) Changed paths: M config/job_conf.xml.sample_advanced M lib/galaxy/jobs/runners/chronos.py Log Message: ----------- Merge pull request #4120 from theosotr/fix-client-initialization Fix chronos client initialization Compare: https://github.com/galaxyproject/galaxy/compare/c269041b61c0...294c1d115413

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[galaxyproject/galaxy] fdc712: Hide error highlighting if user interacts with hig...
by GitHub 04 Jun '17

04 Jun '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: fdc712fb8884ada20373eab548144d4179aa0461 https://github.com/galaxyproject/galaxy/commit/fdc712fb8884ada20373eab54814… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-06-02 (Fri, 02 Jun 2017) Changed paths: M client/galaxy/scripts/mvc/form/form-input.js M static/maps/mvc/form/form-input.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.map M static/scripts/mvc/form/form-input.js Log Message: ----------- Hide error highlighting if user interacts with highlighted field Commit: 9d0f9efbbaf52b81baed355e9b88afd9b29a7472 https://github.com/galaxyproject/galaxy/commit/9d0f9efbbaf52b81baed355e9b88… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-06-02 (Fri, 02 Jun 2017) Changed paths: M client/galaxy/scripts/mvc/form/form-input.js M static/maps/mvc/form/form-input.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/form/form-input.js Log Message: ----------- Disable feature for forms which auto refresh with a server validation Commit: cbe9944815d0e543247824969b2c6aa5212b971b https://github.com/galaxyproject/galaxy/commit/cbe9944815d0e543247824969b2c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-06-04 (Sun, 04 Jun 2017) Changed paths: M client/galaxy/scripts/mvc/form/form-input.js M static/maps/mvc/form/form-input.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.map M static/scripts/mvc/form/form-input.js Log Message: ----------- Merge pull request #4147 from martenson/fix_hide_error [17.05] Hide error highlighting if user interacts with highlighted field Commit: c269041b61c0224ccfcc715701dbc75f1f304e47 https://github.com/galaxyproject/galaxy/commit/c269041b61c0224ccfcc715701db… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-06-04 (Sun, 04 Jun 2017) Changed paths: M client/galaxy/scripts/mvc/form/form-input.js M static/maps/mvc/form/form-input.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/form/form-input.js Log Message: ----------- Merge remote-tracking branch 'upstream/release_17.05' into dev Compare: https://github.com/galaxyproject/galaxy/compare/1fc12ebf1c4a...c269041b61c0

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[galaxyproject/galaxy] fdc712: Hide error highlighting if user interacts with hig...
by GitHub 04 Jun '17

04 Jun '17

Branch: refs/heads/release_17.05 Home: https://github.com/galaxyproject/galaxy Commit: fdc712fb8884ada20373eab548144d4179aa0461 https://github.com/galaxyproject/galaxy/commit/fdc712fb8884ada20373eab54814… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-06-02 (Fri, 02 Jun 2017) Changed paths: M client/galaxy/scripts/mvc/form/form-input.js M static/maps/mvc/form/form-input.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.map M static/scripts/mvc/form/form-input.js Log Message: ----------- Hide error highlighting if user interacts with highlighted field Commit: 9d0f9efbbaf52b81baed355e9b88afd9b29a7472 https://github.com/galaxyproject/galaxy/commit/9d0f9efbbaf52b81baed355e9b88… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-06-02 (Fri, 02 Jun 2017) Changed paths: M client/galaxy/scripts/mvc/form/form-input.js M static/maps/mvc/form/form-input.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/form/form-input.js Log Message: ----------- Disable feature for forms which auto refresh with a server validation Commit: cbe9944815d0e543247824969b2c6aa5212b971b https://github.com/galaxyproject/galaxy/commit/cbe9944815d0e543247824969b2c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-06-04 (Sun, 04 Jun 2017) Changed paths: M client/galaxy/scripts/mvc/form/form-input.js M static/maps/mvc/form/form-input.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.map M static/scripts/mvc/form/form-input.js Log Message: ----------- Merge pull request #4147 from martenson/fix_hide_error [17.05] Hide error highlighting if user interacts with highlighted field Compare: https://github.com/galaxyproject/galaxy/compare/0272e188a81b...cbe9944815d0

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[galaxyproject/galaxy] 5ab560: Update lib documentation
by GitHub 02 Jun '17

02 Jun '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 5ab560068d521266d1bb655948deb58b457a66cf https://github.com/galaxyproject/galaxy/commit/5ab560068d521266d1bb655948de… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-06-02 (Fri, 02 Jun 2017) Changed paths: M .ci/flake8_lint_include_list.txt M doc/Makefile R doc/patch.py M doc/source/api/api.rst M doc/source/api/ts_api.rst M doc/source/lib/galaxy.actions.rst M doc/source/lib/galaxy.auth.providers.rst M doc/source/lib/galaxy.auth.rst A doc/source/lib/galaxy.containers.rst M doc/source/lib/galaxy.dataset_collections.rst M doc/source/lib/galaxy.dataset_collections.types.rst M doc/source/lib/galaxy.datatypes.converters.rst M doc/source/lib/galaxy.datatypes.dataproviders.rst M doc/source/lib/galaxy.datatypes.display_applications.rst M doc/source/lib/galaxy.datatypes.rst M doc/source/lib/galaxy.datatypes.util.rst M doc/source/lib/galaxy.dependencies.rst M doc/source/lib/galaxy.eggs.rst M doc/source/lib/galaxy.exceptions.rst M doc/source/lib/galaxy.external_services.result_handlers.rst M doc/source/lib/galaxy.external_services.rst M doc/source/lib/galaxy.forms.rst M doc/source/lib/galaxy.jobs.actions.rst M doc/source/lib/galaxy.jobs.deferred.rst M doc/source/lib/galaxy.jobs.metrics.collectl.rst M doc/source/lib/galaxy.jobs.metrics.instrumenters.rst M doc/source/lib/galaxy.jobs.metrics.rst M doc/source/lib/galaxy.jobs.rst M doc/source/lib/galaxy.jobs.runners.rst M doc/source/lib/galaxy.jobs.runners.state_handlers.rst M doc/source/lib/galaxy.jobs.runners.util.cli.job.rst M doc/source/lib/galaxy.jobs.runners.util.cli.rst M doc/source/lib/galaxy.jobs.runners.util.cli.shell.rst M doc/source/lib/galaxy.jobs.runners.util.condor.rst A doc/source/lib/galaxy.jobs.runners.util.drmaa.rst M doc/source/lib/galaxy.jobs.runners.util.job_script.rst M doc/source/lib/galaxy.jobs.runners.util.rst M doc/source/lib/galaxy.jobs.splitters.rst M doc/source/lib/galaxy.managers.rst M doc/source/lib/galaxy.model.migrate.rst M doc/source/lib/galaxy.model.orm.rst M doc/source/lib/galaxy.model.rst M doc/source/lib/galaxy.model.tool_shed_install.migrate.rst M doc/source/lib/galaxy.model.tool_shed_install.rst M doc/source/lib/galaxy.objectstore.rst M doc/source/lib/galaxy.openid.rst M doc/source/lib/galaxy.quota.rst M doc/source/lib/galaxy.rst M doc/source/lib/galaxy.sample_tracking.rst M doc/source/lib/galaxy.security.rst R doc/source/lib/galaxy.tags.rst M doc/source/lib/galaxy.tools.actions.rst A doc/source/lib/galaxy.tools.cwl.rst M doc/source/lib/galaxy.tools.data.rst M doc/source/lib/galaxy.tools.data_manager.rst A doc/source/lib/galaxy.tools.deps.container_resolvers.rst A doc/source/lib/galaxy.tools.deps.mulled.rst M doc/source/lib/galaxy.tools.deps.resolvers.rst M doc/source/lib/galaxy.tools.deps.rst M doc/source/lib/galaxy.tools.filters.rst M doc/source/lib/galaxy.tools.imp_exp.rst M doc/source/lib/galaxy.tools.linters.rst A doc/source/lib/galaxy.tools.locations.rst M doc/source/lib/galaxy.tools.parameters.rst M doc/source/lib/galaxy.tools.parser.rst M doc/source/lib/galaxy.tools.rst M doc/source/lib/galaxy.tools.search.rst M doc/source/lib/galaxy.tools.toolbox.filters.rst M doc/source/lib/galaxy.tools.toolbox.lineages.rst M doc/source/lib/galaxy.tools.toolbox.rst M doc/source/lib/galaxy.tools.util.galaxyops.rst M doc/source/lib/galaxy.tools.util.rst A doc/source/lib/galaxy.tools.verify.asserts.rst A doc/source/lib/galaxy.tools.verify.rst A doc/source/lib/galaxy.tours.rst M doc/source/lib/galaxy.util.backports.rst M doc/source/lib/galaxy.util.log.rst M doc/source/lib/galaxy.util.pastescript.rst M doc/source/lib/galaxy.util.rst M doc/source/lib/galaxy.visualization.data_providers.phyloviz.rst M doc/source/lib/galaxy.visualization.data_providers.rst M doc/source/lib/galaxy.visualization.genome.rst M doc/source/lib/galaxy.visualization.plugins.rst M doc/source/lib/galaxy.visualization.rst M doc/source/lib/galaxy.visualization.tracks.rst M doc/source/lib/galaxy.web.base.controllers.rst M doc/source/lib/galaxy.web.base.rst M doc/source/lib/galaxy.web.framework.helpers.rst M doc/source/lib/galaxy.web.framework.middleware.rst M doc/source/lib/galaxy.web.framework.rst M doc/source/lib/galaxy.web.proxy.rst M doc/source/lib/galaxy.web.rst M doc/source/lib/galaxy.web.security.rst A doc/source/lib/galaxy.web.stack.rst A doc/source/lib/galaxy.webapps.galaxy.api.rst M doc/source/lib/galaxy.webapps.galaxy.controllers.rst M doc/source/lib/galaxy.webapps.galaxy.rst M doc/source/lib/galaxy.webapps.reports.controllers.rst M doc/source/lib/galaxy.webapps.reports.rst M doc/source/lib/galaxy.webapps.rst A doc/source/lib/galaxy.webapps.tool_shed.api.rst M doc/source/lib/galaxy.webapps.tool_shed.controllers.rst M doc/source/lib/galaxy.webapps.tool_shed.framework.middleware.rst M doc/source/lib/galaxy.webapps.tool_shed.framework.rst M doc/source/lib/galaxy.webapps.tool_shed.model.migrate.rst M doc/source/lib/galaxy.webapps.tool_shed.model.rst M doc/source/lib/galaxy.webapps.tool_shed.rst M doc/source/lib/galaxy.webapps.tool_shed.search.rst M doc/source/lib/galaxy.webapps.tool_shed.security.rst M doc/source/lib/galaxy.webapps.tool_shed.util.rst A doc/source/lib/galaxy.webhooks.rst M doc/source/lib/galaxy.work.rst M doc/source/lib/galaxy.workflow.rst M doc/source/lib/galaxy.workflow.schedulers.rst M doc/source/lib/galaxy_ext.metadata.rst M doc/source/lib/galaxy_ext.rst M doc/source/lib/log_tempfile.rst M doc/source/lib/psyco_full.rst M doc/source/lib/tool_shed.capsule.rst M doc/source/lib/tool_shed.dependencies.repository.rst M doc/source/lib/tool_shed.dependencies.rst M doc/source/lib/tool_shed.dependencies.tool.rst M doc/source/lib/tool_shed.galaxy_install.datatypes.rst M doc/source/lib/tool_shed.galaxy_install.grids.rst M doc/source/lib/tool_shed.galaxy_install.metadata.rst M doc/source/lib/tool_shed.galaxy_install.migrate.rst M doc/source/lib/tool_shed.galaxy_install.repository_dependencies.rst M doc/source/lib/tool_shed.galaxy_install.rst M doc/source/lib/tool_shed.galaxy_install.tool_dependencies.recipe.rst M doc/source/lib/tool_shed.galaxy_install.tool_dependencies.rst M doc/source/lib/tool_shed.galaxy_install.tools.rst M doc/source/lib/tool_shed.galaxy_install.utility_containers.rst M doc/source/lib/tool_shed.grids.rst M doc/source/lib/tool_shed.managers.rst M doc/source/lib/tool_shed.metadata.rst M doc/source/lib/tool_shed.repository_types.rst M doc/source/lib/tool_shed.rst M doc/source/lib/tool_shed.tools.rst M doc/source/lib/tool_shed.util.rst M doc/source/lib/tool_shed.utility_containers.rst Log Message: ----------- Update lib documentation Also simplify updaterst target in doc/Makefile Partially revert commit b4feb85f11280935b0ce13ea5d3693122f4319e8 : re-add doc/source/lib/galaxy.webapps.galaxy.api.rst and doc/source/lib/galaxy.webapps.tool_shed.api.rst and include them in doc/source/api/api.rst and doc/source/api/ts_api.rst respectively to simplify doc maintenance. Commit: 92952882d26303f83a100d73b1cb04d36a4abd34 https://github.com/galaxyproject/galaxy/commit/92952882d26303f83a100d73b1cb… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-06-02 (Fri, 02 Jun 2017) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Fix some links and syntax errors in tool XML doc Commit: 71df810ddb293faffc4c2c8711bef600e698cfd9 https://github.com/galaxyproject/galaxy/commit/71df810ddb293faffc4c2c8711be… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-06-02 (Fri, 02 Jun 2017) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Document <hook> sub-element of <code> This is deprecated and used only by: - https://toolshed.g2.bx.psu.edu/view/devteam/cluster/ - https://toolshed.g2.bx.psu.edu/view/devteam/merge/ Fix https://github.com/galaxyproject/galaxy/issues/3516 . Commit: fc9b3ad4a985dc7ce1d7ebb62bd307e09e9f9ccb https://github.com/galaxyproject/galaxy/commit/fc9b3ad4a985dc7ce1d7ebb62bd3… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-06-02 (Fri, 02 Jun 2017) Changed paths: M doc/Makefile R doc/source/api/api.rst R doc/source/api/ts_api.rst Log Message: ----------- Generate api.rst and ts_api.rst during make Commit: 1fc12ebf1c4a02716c39814c460e67a3ab120f71 https://github.com/galaxyproject/galaxy/commit/1fc12ebf1c4a02716c39814c460e… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-06-02 (Fri, 02 Jun 2017) Changed paths: M .ci/flake8_lint_include_list.txt M doc/Makefile R doc/patch.py R doc/source/api/api.rst R doc/source/api/ts_api.rst M doc/source/lib/galaxy.actions.rst M doc/source/lib/galaxy.auth.providers.rst M doc/source/lib/galaxy.auth.rst A doc/source/lib/galaxy.containers.rst M doc/source/lib/galaxy.dataset_collections.rst M doc/source/lib/galaxy.dataset_collections.types.rst M doc/source/lib/galaxy.datatypes.converters.rst M doc/source/lib/galaxy.datatypes.dataproviders.rst M doc/source/lib/galaxy.datatypes.display_applications.rst M doc/source/lib/galaxy.datatypes.rst M doc/source/lib/galaxy.datatypes.util.rst M doc/source/lib/galaxy.dependencies.rst M doc/source/lib/galaxy.eggs.rst M doc/source/lib/galaxy.exceptions.rst M doc/source/lib/galaxy.external_services.result_handlers.rst M doc/source/lib/galaxy.external_services.rst M doc/source/lib/galaxy.forms.rst M doc/source/lib/galaxy.jobs.actions.rst M doc/source/lib/galaxy.jobs.deferred.rst M doc/source/lib/galaxy.jobs.metrics.collectl.rst M doc/source/lib/galaxy.jobs.metrics.instrumenters.rst M doc/source/lib/galaxy.jobs.metrics.rst M doc/source/lib/galaxy.jobs.rst M doc/source/lib/galaxy.jobs.runners.rst M doc/source/lib/galaxy.jobs.runners.state_handlers.rst M doc/source/lib/galaxy.jobs.runners.util.cli.job.rst M doc/source/lib/galaxy.jobs.runners.util.cli.rst M doc/source/lib/galaxy.jobs.runners.util.cli.shell.rst M doc/source/lib/galaxy.jobs.runners.util.condor.rst A doc/source/lib/galaxy.jobs.runners.util.drmaa.rst M doc/source/lib/galaxy.jobs.runners.util.job_script.rst M doc/source/lib/galaxy.jobs.runners.util.rst M doc/source/lib/galaxy.jobs.splitters.rst M doc/source/lib/galaxy.managers.rst M doc/source/lib/galaxy.model.migrate.rst M doc/source/lib/galaxy.model.orm.rst M doc/source/lib/galaxy.model.rst M doc/source/lib/galaxy.model.tool_shed_install.migrate.rst M doc/source/lib/galaxy.model.tool_shed_install.rst M doc/source/lib/galaxy.objectstore.rst M doc/source/lib/galaxy.openid.rst M doc/source/lib/galaxy.quota.rst M doc/source/lib/galaxy.rst M doc/source/lib/galaxy.sample_tracking.rst M doc/source/lib/galaxy.security.rst R doc/source/lib/galaxy.tags.rst M doc/source/lib/galaxy.tools.actions.rst A doc/source/lib/galaxy.tools.cwl.rst M doc/source/lib/galaxy.tools.data.rst M doc/source/lib/galaxy.tools.data_manager.rst A doc/source/lib/galaxy.tools.deps.container_resolvers.rst A doc/source/lib/galaxy.tools.deps.mulled.rst M doc/source/lib/galaxy.tools.deps.resolvers.rst M doc/source/lib/galaxy.tools.deps.rst M doc/source/lib/galaxy.tools.filters.rst M doc/source/lib/galaxy.tools.imp_exp.rst M doc/source/lib/galaxy.tools.linters.rst A doc/source/lib/galaxy.tools.locations.rst M doc/source/lib/galaxy.tools.parameters.rst M doc/source/lib/galaxy.tools.parser.rst M doc/source/lib/galaxy.tools.rst M doc/source/lib/galaxy.tools.search.rst M doc/source/lib/galaxy.tools.toolbox.filters.rst M doc/source/lib/galaxy.tools.toolbox.lineages.rst M doc/source/lib/galaxy.tools.toolbox.rst M doc/source/lib/galaxy.tools.util.galaxyops.rst M doc/source/lib/galaxy.tools.util.rst A doc/source/lib/galaxy.tools.verify.asserts.rst A doc/source/lib/galaxy.tools.verify.rst A doc/source/lib/galaxy.tours.rst M doc/source/lib/galaxy.util.backports.rst M doc/source/lib/galaxy.util.log.rst M doc/source/lib/galaxy.util.pastescript.rst M doc/source/lib/galaxy.util.rst M doc/source/lib/galaxy.visualization.data_providers.phyloviz.rst M doc/source/lib/galaxy.visualization.data_providers.rst M doc/source/lib/galaxy.visualization.genome.rst M doc/source/lib/galaxy.visualization.plugins.rst M doc/source/lib/galaxy.visualization.rst M doc/source/lib/galaxy.visualization.tracks.rst M doc/source/lib/galaxy.web.base.controllers.rst M doc/source/lib/galaxy.web.base.rst M doc/source/lib/galaxy.web.framework.helpers.rst M doc/source/lib/galaxy.web.framework.middleware.rst M doc/source/lib/galaxy.web.framework.rst M doc/source/lib/galaxy.web.proxy.rst M doc/source/lib/galaxy.web.rst M doc/source/lib/galaxy.web.security.rst A doc/source/lib/galaxy.web.stack.rst A doc/source/lib/galaxy.webapps.galaxy.api.rst M doc/source/lib/galaxy.webapps.galaxy.controllers.rst M doc/source/lib/galaxy.webapps.galaxy.rst M doc/source/lib/galaxy.webapps.reports.controllers.rst M doc/source/lib/galaxy.webapps.reports.rst M doc/source/lib/galaxy.webapps.rst A doc/source/lib/galaxy.webapps.tool_shed.api.rst M doc/source/lib/galaxy.webapps.tool_shed.controllers.rst M doc/source/lib/galaxy.webapps.tool_shed.framework.middleware.rst M doc/source/lib/galaxy.webapps.tool_shed.framework.rst M doc/source/lib/galaxy.webapps.tool_shed.model.migrate.rst M doc/source/lib/galaxy.webapps.tool_shed.model.rst M doc/source/lib/galaxy.webapps.tool_shed.rst M doc/source/lib/galaxy.webapps.tool_shed.search.rst M doc/source/lib/galaxy.webapps.tool_shed.security.rst M doc/source/lib/galaxy.webapps.tool_shed.util.rst A doc/source/lib/galaxy.webhooks.rst M doc/source/lib/galaxy.work.rst M doc/source/lib/galaxy.workflow.rst M doc/source/lib/galaxy.workflow.schedulers.rst M doc/source/lib/galaxy_ext.metadata.rst M doc/source/lib/galaxy_ext.rst M doc/source/lib/log_tempfile.rst M doc/source/lib/psyco_full.rst M doc/source/lib/tool_shed.capsule.rst M doc/source/lib/tool_shed.dependencies.repository.rst M doc/source/lib/tool_shed.dependencies.rst M doc/source/lib/tool_shed.dependencies.tool.rst M doc/source/lib/tool_shed.galaxy_install.datatypes.rst M doc/source/lib/tool_shed.galaxy_install.grids.rst M doc/source/lib/tool_shed.galaxy_install.metadata.rst M doc/source/lib/tool_shed.galaxy_install.migrate.rst M doc/source/lib/tool_shed.galaxy_install.repository_dependencies.rst M doc/source/lib/tool_shed.galaxy_install.rst M doc/source/lib/tool_shed.galaxy_install.tool_dependencies.recipe.rst M doc/source/lib/tool_shed.galaxy_install.tool_dependencies.rst M doc/source/lib/tool_shed.galaxy_install.tools.rst M doc/source/lib/tool_shed.galaxy_install.utility_containers.rst M doc/source/lib/tool_shed.grids.rst M doc/source/lib/tool_shed.managers.rst M doc/source/lib/tool_shed.metadata.rst M doc/source/lib/tool_shed.repository_types.rst M doc/source/lib/tool_shed.rst M doc/source/lib/tool_shed.tools.rst M doc/source/lib/tool_shed.util.rst M doc/source/lib/tool_shed.utility_containers.rst M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Merge pull request #4146 from nsoranzo/doc_fixes Documentation fixes and improvements Compare: https://github.com/galaxyproject/galaxy/compare/e8f730895c34...1fc12ebf1c4a

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