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

[galaxyproject/galaxy] 8c126a: Update contributors, diff of 17.01->17.05.
by GitHub 19 May '17

19 May '17

Branch: refs/heads/release_17.05 Home: https://github.com/galaxyproject/galaxy Commit: 8c126a87579f89a3689cdcacf467ee01bbe6793a https://github.com/galaxyproject/galaxy/commit/8c126a87579f89a3689cdcacf467… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-05-16 (Tue, 16 May 2017) Changed paths: M CONTRIBUTORS.md Log Message: ----------- Update contributors, diff of 17.01->17.05. Commit: 3807b5d3037d569138366c44659d9ee955a5590f https://github.com/galaxyproject/galaxy/commit/3807b5d3037d569138366c44659d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-05-16 (Tue, 16 May 2017) Changed paths: M CONTRIBUTORS.md Log Message: ----------- 16.10 -> 17.01 contributor diff. Commit: b88097ae395968d562c1847189fae0b129f6ce4b https://github.com/galaxyproject/galaxy/commit/b88097ae395968d562c1847189fa… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-05-16 (Tue, 16 May 2017) Changed paths: M CONTRIBUTORS.md Log Message: ----------- 16.07 -> 16.10 contributors update. Commit: 5b27ad4cb47b5b250db3cf0cf2624b09a05b40ed https://github.com/galaxyproject/galaxy/commit/5b27ad4cb47b5b250db3cf0cf262… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-05-16 (Tue, 16 May 2017) Changed paths: M CONTRIBUTORS.md Log Message: ----------- CONTRIBUTORS update 16.04 -> 16.07 Commit: 3d6dfa4f60741743507c259da6d5610ab6fa14ff https://github.com/galaxyproject/galaxy/commit/3d6dfa4f60741743507c259da6d5… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-05-19 (Fri, 19 May 2017) Changed paths: M CONTRIBUTORS.md Log Message: ----------- For people without a commit-signing email, just use the github username (for now -- they can of course change this via PR) Commit: b1e9552e1b13c36c8d9ec7343e2f4cd11817cbef https://github.com/galaxyproject/galaxy/commit/b1e9552e1b13c36c8d9ec7343e2f… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-05-19 (Fri, 19 May 2017) Changed paths: M CONTRIBUTORS.md Log Message: ----------- Merge pull request #4070 from dannon/contrib_update [17.05] CONTRIBUTORS update Compare: https://github.com/galaxyproject/galaxy/compare/4125f79161e5...b1e9552e1b13

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[galaxyproject/galaxy] 238e2a: remove the content alert from TS response
by GitHub 19 May '17

19 May '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 238e2a7e5f333daf83ffba4b0dfaf1a1c3737268 https://github.com/galaxyproject/galaxy/commit/238e2a7e5f333daf83ffba4b0dfa… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-05-18 (Thu, 18 May 2017) Changed paths: M lib/galaxy/webapps/tool_shed/api/repositories.py Log Message: ----------- remove the content alert from TS response Commit: 50bb430b1a80d201c58a6933f6d0194068b2e41e https://github.com/galaxyproject/galaxy/commit/50bb430b1a80d201c58a6933f6d0… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-05-19 (Fri, 19 May 2017) Changed paths: M lib/galaxy/webapps/tool_shed/api/repositories.py Log Message: ----------- Merge pull request #4082 from martenson/remove-alert-response remove the content alert from TS response Compare: https://github.com/galaxyproject/galaxy/compare/e826ded26415...50bb430b1a80

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[galaxyproject/infrastructure-playbook] bfb0cc: Set $HOME for Pulsar so that ~/.condarc can be wri...
by GitHub 18 May '17

18 May '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: bfb0cc017d25e0989e64b0d2e46741aa56289d89 https://github.com/galaxyproject/infrastructure-playbook/commit/bfb0cc017d2… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-05-18 (Thu, 18 May 2017) Changed paths: M jetstream_common/templates/supervisor/pulsar.j2 Log Message: ----------- Set $HOME for Pulsar so that ~/.condarc can be written

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[galaxyproject/galaxy] aa8576: Rebuild to provide new localization.
by GitHub 18 May '17

18 May '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: aa85760996fa6d6dd9b94a38cf7220d39b8770bc https://github.com/galaxyproject/galaxy/commit/aa85760996fa6d6dd9b94a38cf72… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-05-18 (Thu, 18 May 2017) Changed paths: M static/maps/nls/fr/locale.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map M static/scripts/nls/fr/locale.js Log Message: ----------- Rebuild to provide new localization. Commit: e826ded26415ef29257acce776d02d272994a25c https://github.com/galaxyproject/galaxy/commit/e826ded26415ef29257acce776d0… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-05-18 (Thu, 18 May 2017) Changed paths: M static/maps/nls/fr/locale.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map M static/scripts/nls/fr/locale.js Log Message: ----------- Merge pull request #4081 from dannon/locale_rebuild Rebuild to provide new localization. Compare: https://github.com/galaxyproject/galaxy/compare/e09aabe1d504...e826ded26415

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[galaxyproject/galaxy] dac779: Fix French translation errors
by GitHub 18 May '17

18 May '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: dac779858fcf3a5673fac4e1fb4ae12777e56c99 https://github.com/galaxyproject/galaxy/commit/dac779858fcf3a5673fac4e1fb4a… Author: Yvan Le Bras <yvan.le_bras(a)irisa.fr> Date: 2017-05-18 (Thu, 18 May 2017) Changed paths: M client/galaxy/scripts/nls/fr/locale.js Log Message: ----------- Fix French translation errors Commit: e09aabe1d504057bcd463bd385f932a93724e4fd https://github.com/galaxyproject/galaxy/commit/e09aabe1d504057bcd463bd385f9… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-05-18 (Thu, 18 May 2017) Changed paths: M client/galaxy/scripts/nls/fr/locale.js Log Message: ----------- Merge pull request #4080 from yvanlebras/patch-2 Fix French translation errors Compare: https://github.com/galaxyproject/galaxy/compare/7028ca04c755...e09aabe1d504

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[galaxyproject/galaxy] 2099c0: Add job runner for Chronos
by GitHub 18 May '17

18 May '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 2099c09f6ab5a8f5951d01cd6fa67681618e2dda https://github.com/galaxyproject/galaxy/commit/2099c09f6ab5a8f5951d01cd6fa6… Author: Thodoris Sotiropoulos <theosot(a)grnet.gr> Date: 2017-04-20 (Thu, 20 Apr 2017) Changed paths: M config/job_conf.xml.sample_advanced M lib/galaxy/dependencies/conditional-requirements.txt A lib/galaxy/jobs/runners/chronos.py Log Message: ----------- Add job runner for Chronos Chronos is a framework for the Apache Mesos; a software which manages computer clusters. Specifically, Chronos is a batch processing scheduler that runs on top of Mesos and it is used for job orchestration. Commit: 339c3724fb94d7d85732c7ef7f8f48e822f83c7d https://github.com/galaxyproject/galaxy/commit/339c3724fb94d7d85732c7ef7f8f… Author: Thodoris Sotiropoulos <theosot(a)dmst.aueb.gr> Date: 2017-04-26 (Wed, 26 Apr 2017) Changed paths: M lib/galaxy/dependencies/conditional-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt Log Message: ----------- Add chronos client to the pinned-requirements.txt Commit: 05ee848cd327ab293e20300d22dae94fc0e0473e https://github.com/galaxyproject/galaxy/commit/05ee848cd327ab293e20300d22da… Author: Thodoris Sotiropoulos <theosot(a)dmst.aueb.gr> Date: 2017-05-05 (Fri, 05 May 2017) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt Log Message: ----------- Pin version of chronos-python to 0.38 Commit: c01c9bbe616c9524883db148df38e770ea25547e https://github.com/galaxyproject/galaxy/commit/c01c9bbe616c9524883db148df38… Author: Thodoris Sotiropoulos <theosot(a)dmst.aueb.gr> Date: 2017-05-05 (Fri, 05 May 2017) Changed paths: M config/job_conf.xml.sample_advanced Log Message: ----------- Add an explanatory comment about job_conf of chronos Commit: 7028ca04c7554e87ca7ad63a547d962476810080 https://github.com/galaxyproject/galaxy/commit/7028ca04c7554e87ca7ad63a547d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-05-18 (Thu, 18 May 2017) Changed paths: M config/job_conf.xml.sample_advanced M lib/galaxy/dependencies/pinned-requirements.txt A lib/galaxy/jobs/runners/chronos.py Log Message: ----------- Merge pull request #3946 from theosotr/feature-chronos Add job runner for Chronos Compare: https://github.com/galaxyproject/galaxy/compare/b9fb2de42b53...7028ca04c755

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[galaxyproject/galaxy] be7dea: Sanitize container names sending to Kubernetes.
by GitHub 17 May '17

17 May '17

Branch: refs/heads/release_17.05 Home: https://github.com/galaxyproject/galaxy Commit: be7dea47d556823abfab7a369b3ac466f6dea494 https://github.com/galaxyproject/galaxy/commit/be7dea47d556823abfab7a369b3a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-05-05 (Fri, 05 May 2017) Changed paths: M lib/galaxy/jobs/runners/kubernetes.py Log Message: ----------- Sanitize container names sending to Kubernetes. Commit: 4125f79161e584aa98098016e6a540111c7b5e2a https://github.com/galaxyproject/galaxy/commit/4125f79161e584aa98098016e6a5… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-05-17 (Wed, 17 May 2017) Changed paths: M lib/galaxy/jobs/runners/kubernetes.py Log Message: ----------- Merge pull request #4034 from jmchilton/k8_name_fixed [17.05] Sanitize container names sending to Kubernetes. Compare: https://github.com/galaxyproject/galaxy/compare/6614e94a4953...4125f79161e5

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[galaxyproject/usegalaxy-playbook] 376b8c: Update Test Tool Shed
by GitHub 17 May '17

17 May '17

Branch: refs/heads/reorg Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 376b8c62fac4419299ec0c85cf2921c8aa47da70 https://github.com/galaxyproject/usegalaxy-playbook/commit/376b8c62fac44192… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-05-17 (Wed, 17 May 2017) Changed paths: M env/testtoolshed/group_vars/toolshedservers/vars.yml Log Message: ----------- Update Test Tool Shed

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[galaxyproject/galaxy] f8e92f: Add parameter to workflows API to list workflows w...
by GitHub 17 May '17

17 May '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f8e92fe011b17c8a2f3b249453043854a1cff305 https://github.com/galaxyproject/galaxy/commit/f8e92fe011b17c8a2f3b24945304… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-08-17 (Wed, 17 Aug 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Add parameter to workflows API to list workflows with missing tools. Commit: ddbbe76c0a8266d4c49694ef43d43ecefb2ac943 https://github.com/galaxyproject/galaxy/commit/ddbbe76c0a8266d4c49694ef43d4… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-08-18 (Thu, 18 Aug 2016) Changed paths: M config/datatypes_conf.xml.sample M config/galaxy.ini.sample M lib/galaxy/app.py M lib/galaxy/config.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/triples.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/actions/post.py M lib/galaxy/jobs/runners/slurm.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/toolbox/watcher.py M lib/galaxy/util/template.py M lib/galaxy/web/framework/middleware/sentry.py M lib/galaxy/webapps/galaxy/api/history_contents.py M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/app.py M lib/galaxy/webapps/tool_shed/buildapp.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy_ext/metadata/set_metadata.py 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 test/base/interactor.py A test/functional/tools/dbkey_output_action.xml M test/functional/tools/samples_tool_conf.xml A test/functional/tools/tool_provided_metadata_1.xml A test/functional/tools/tool_provided_metadata_2.xml A test/functional/tools/tool_provided_metadata_3.xml Log Message: ----------- Merge branch 'dev' of git://github.com/galaxyproject/galaxy into repo_queue_sharing Commit: 24bc782259786c03b0279e5e33b2eb96c1933c89 https://github.com/galaxyproject/galaxy/commit/24bc782259786c03b0279e5e33b2… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-08-18 (Thu, 18 Aug 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/tool_shed/api/repositories.py M templates/admin/tool_shed_repository/browse_toolsheds.mako Log Message: ----------- Implement display of workflows missing tools and the repository that contains those tools. Commit: e8255841573b551c36e444e1559f8665687d3b9d https://github.com/galaxyproject/galaxy/commit/e8255841573b551c36e444e1559f… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-08-19 (Fri, 19 Aug 2016) Changed paths: M config/galaxy.ini.sample M lib/galaxy/model/migrate/check.py Log Message: ----------- Merge branch 'dev' of git://github.com/galaxyproject/galaxy into repo_queue_sharing Commit: ec153e30627ad46a091a1a24a494cc2314ce22b1 https://github.com/galaxyproject/galaxy/commit/ec153e30627ad46a091a1a24a494… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-08-19 (Fri, 19 Aug 2016) Changed paths: M templates/admin/tool_shed_repository/browse_toolsheds.mako Log Message: ----------- Allow adding a repository to the queue from a workflow. Commit: f72f1f106c161d3d4d87dc0670b92a7f42b0207c https://github.com/galaxyproject/galaxy/commit/f72f1f106c161d3d4d87dc0670b9… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-08-22 (Mon, 22 Aug 2016) Changed paths: M config/galaxy.ini.sample M lib/galaxy/web/proxy/__init__.py M lib/galaxy/web/proxy/js/lib/main.js M lib/galaxy/web/proxy/js/lib/proxy.js M lib/galaxy/web/proxy/js/package.json Log Message: ----------- Merge branch 'dev' of git://github.com/galaxyproject/galaxy into repo_queue_sharing Commit: 4a02d0516ff7c661ad9b46dcd428ccdc8cba3717 https://github.com/galaxyproject/galaxy/commit/4a02d0516ff7c661ad9b46dcd428… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-08-22 (Mon, 22 Aug 2016) Changed paths: M lib/galaxy/tools/toolbox/base.py M lib/galaxy/webapps/galaxy/api/workflows.py M templates/admin/tool_shed_repository/browse_toolsheds.mako Log Message: ----------- Move the method that checks for missing tools into the toolbox, where it belongs. Commit: ca987e706fb0a128fc3d68ea6f07f3fd44e83d74 https://github.com/galaxyproject/galaxy/commit/ca987e706fb0a128fc3d68ea6f07… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-08-25 (Thu, 25 Aug 2016) Changed paths: M .ci/flake8_lint_include_list.txt M client/galaxy/scripts/mvc/dataset/data.js M config/galaxy.ini.sample M config/reports.ini.sample M config/tool_shed.ini.sample A doc/source/admin/chat-0.png A doc/source/admin/chat-1.png A doc/source/admin/chat-2.png A doc/source/admin/chat-3.png A doc/source/admin/chat-4.png A doc/source/admin/chat.rst A doc/source/admin/communication_server.png A doc/source/admin/communication_server_rooms.png A doc/source/admin/conda_faq.rst M doc/source/admin/index.rst A doc/source/releases/16.07.rst M doc/source/releases/16.07_announce.rst A doc/source/releases/16.10_announce.rst M lib/galaxy/auth/providers/ldap_ad.py M lib/galaxy/config.py M lib/galaxy/jobs/__init__.py M lib/galaxy/security/validate_user_input.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/util/postfork.py M lib/galaxy/web/framework/base.py A lib/galaxy/web/framework/middleware/batch.py M lib/galaxy/webapps/galaxy/api/jobs.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/tool_shed/config.py M static/maps/mvc/dataset/data.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/dataset/data.js M templates/webapps/tool_shed/index.mako A test/api/test_api_batch.py A test/casperjs/api-batch-tests.js Log Message: ----------- Merge branch 'dev' of git://github.com/galaxyproject/galaxy into repo_queue_sharing Commit: 73cdfc716bba938921d1fd9262b25a6778cc7f10 https://github.com/galaxyproject/galaxy/commit/73cdfc716bba938921d1fd9262b2… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-08-25 (Thu, 25 Aug 2016) Changed paths: M lib/galaxy/tools/toolbox/base.py M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py Log Message: ----------- Rework the return value of /api/workflows?missing_tools=True Commit: 57c01f11af470e62164566af2b4af609d1cbebb9 https://github.com/galaxyproject/galaxy/commit/57c01f11af470e62164566af2b4a… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-08-25 (Thu, 25 Aug 2016) Changed paths: M templates/admin/tool_shed_repository/browse_toolsheds.mako Log Message: ----------- Update the display of workflows missing tools. Thus accomodating the API changes made in the previous commit. Commit: 4d85eec0c9b8dda5d971aaf8714e65886f7e2f41 https://github.com/galaxyproject/galaxy/commit/4d85eec0c9b8dda5d971aaf8714e… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-08-29 (Mon, 29 Aug 2016) Changed paths: M Makefile M client/galaxy/scripts/mvc/form/form-data.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/ui/ui-color-picker.js M client/galaxy/scripts/mvc/ui/ui-tabs.js M client/galaxy/scripts/utils/utils.js M config/plugins/visualizations/charts/static/app.css M config/plugins/visualizations/charts/static/app.js R config/plugins/visualizations/charts/static/charts/forms/default.js M config/plugins/visualizations/charts/static/charts/jqplot/bar/config.js M config/plugins/visualizations/charts/static/charts/jqplot/bar/wrapper.js M config/plugins/visualizations/charts/static/charts/jqplot/boxplot/config.js M config/plugins/visualizations/charts/static/charts/jqplot/boxplot/wrapper.js M 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Commit: d9d3f259944b640f2844745c895224f8bb9ea6bd https://github.com/galaxyproject/galaxy/commit/d9d3f259944b640f2844745c8952… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-08-30 (Tue, 30 Aug 2016) Changed paths: M doc/source/admin/chat.rst M doc/source/admin/conda_faq.rst M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M templates/webapps/galaxy/workflow/display.mako Log Message: ----------- Merge branch 'dev' of git://github.com/galaxyproject/galaxy into repo_queue_sharing Commit: de1510f3cc367c036bf6c19bcd15e95f5dc46b30 https://github.com/galaxyproject/galaxy/commit/de1510f3cc367c036bf6c19bcd15… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-08-30 (Tue, 30 Aug 2016) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Fix the imports I broke in an earlier commit. Commit: 6e40fe957a777c6b64218844bc521da946f65279 https://github.com/galaxyproject/galaxy/commit/6e40fe957a777c6b64218844bc52… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-09-02 (Fri, 02 Sep 2016) Changed paths: M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/scratchbook.js M doc/source/admin/conda_faq.rst M lib/galaxy/tools/cwl/parser.py M lib/galaxy/tools/deps/resolvers/conda.py R lib/galaxy/tools/toolbox/requirements.py A lib/galaxy/util/filelock.py M lib/galaxy/web/proxy/__init__.py R lib/galaxy/web/proxy/filelock.py M static/maps/layout/menu.js.map M static/maps/layout/scratchbook.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/layout/scratchbook.js M templates/admin/tool_shed_repository/common.mako Log Message: ----------- Merge branch 'dev' of git://github.com/galaxyproject/galaxy into repo_queue_sharing Commit: 6998d338cfa22644d1fdc2cec819ee504147e784 https://github.com/galaxyproject/galaxy/commit/6998d338cfa22644d1fdc2cec819… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-09-12 (Mon, 12 Sep 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/tool_shed/api/categories.py M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/tool_shed/util/repository_util.py M templates/admin/tool_shed_repository/browse_toolsheds.mako Log Message: ----------- Integrate whoosh with the API installation's search boxes. Commit: aae40ca9064a67e57b12b30837f96de14bd5a4a9 https://github.com/galaxyproject/galaxy/commit/aae40ca9064a67e57b12b30837f9… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-09-12 (Mon, 12 Sep 2016) Changed paths: M .ci/flake8_lint_include_list.txt M .gitignore M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/exceptions/error_codes.py M lib/galaxy/jobs/metrics/__init__.py M lib/galaxy/jobs/metrics/collectl/cli.py M lib/galaxy/jobs/metrics/collectl/processes.py M lib/galaxy/jobs/metrics/instrumenters/__init__.py M lib/galaxy/jobs/metrics/instrumenters/collectl.py M lib/galaxy/jobs/metrics/instrumenters/core.py M lib/galaxy/jobs/metrics/instrumenters/cpuinfo.py M lib/galaxy/jobs/metrics/instrumenters/env.py M lib/galaxy/jobs/metrics/instrumenters/meminfo.py M lib/galaxy/model/tool_shed_install/__init__.py M lib/galaxy/objectstore/__init__.py M lib/galaxy/objectstore/azure_blob.py M lib/galaxy/objectstore/rods.py M lib/galaxy/objectstore/s3.py M 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M test/functional/tools/multi_output.xml M test/functional/tools/multi_output_assign_primary.xml M test/functional/tools/multi_output_configured.xml M test/functional/tools/tool_directory.xml M test/functional/tools/validation_repeat.xml M test/shed_functional/functional/test_1040_install_repository_basic_circular_dependencies.py M test/shed_functional/functional/test_1080_advanced_circular_dependency_installation.py M test/unit/shed_unit/test_tool_panel_manager.py M test/unit/test_objectstore.py M test/unit/tools/test_parsing.py M test/unit/tools/test_tool_deps.py M test/unit/tools/test_tool_loader.py M test/unit/tools/test_toolbox.py M test/unit/tools/test_toolbox_filters.py M test/unit/tools/test_watcher.py M test/unit/tools/test_wrappers.py M test/unit/tools_support.py M tools/data_source/upload.xml Log Message: ----------- Merge branch 'dev' of git://github.com/galaxyproject/galaxy into repo_queue_sharing Commit: 0baf22ca6f891497a265fcefd3141a0796e1fd5d 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M static/maps/viz/trackster/tracks.js.map A static/scripts/libs/bbi/bigwig.js A static/scripts/libs/bbi/jquery-ajax-native.js A static/scripts/libs/bbi/jszlib.js A static/scripts/libs/bbi/spans.js A static/scripts/viz/bbi-data-manager.js M static/scripts/viz/trackster/painters.js M static/scripts/viz/trackster/tracks.js M templates/webapps/galaxy/workflow/run.mako R test/functional/tools/multi_page.xml M test/functional/tools/samples_tool_conf.xml M test/unit/managers/test_DatasetManager.py M tox.ini Log Message: ----------- Merge branch 'dev' of git://github.com/galaxyproject/galaxy into repo_queue_sharing Commit: 4106d975fa5b8767d72b13671ce183d9a8bd98ad https://github.com/galaxyproject/galaxy/commit/4106d975fa5b8767d72b13671ce1… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-09-19 (Mon, 19 Sep 2016) Changed paths: M templates/admin/tool_shed_repository/browse_toolsheds.mako Log Message: ----------- Some cleanup, initial url hash navigation. Commit: cdea4b3cee3024618e99b6b1f498d2f25fa53295 https://github.com/galaxyproject/galaxy/commit/cdea4b3cee3024618e99b6b1f498… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-09-20 (Tue, 20 Sep 2016) Changed paths: A lib/galaxy/datatypes/converters/tabular_to_dbnsfp.py Log Message: ----------- Merge branch 'dev' of git://github.com/galaxyproject/galaxy into repo_queue_sharing Commit: 8d15670a5d4709cf9043ffd0d3b296494fc252fb https://github.com/galaxyproject/galaxy/commit/8d15670a5d4709cf9043ffd0d3b2… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-09-20 (Tue, 20 Sep 2016) Changed paths: M templates/admin/tool_shed_repository/browse_toolsheds.mako Log Message: ----------- Remove debugging. Commit: 22240074c30a98c541c36b6dab4fb0947112b6be https://github.com/galaxyproject/galaxy/commit/22240074c30a98c541c36b6dab4f… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-09-20 (Tue, 20 Sep 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/tool_shed/api/tools.py M lib/galaxy/webapps/tool_shed/buildapp.py M templates/admin/tool_shed_repository/browse_toolsheds.mako Log Message: ----------- Initial work to show tool form preview on repository preview page. Commit: ca7fb1db62e6c1f03bfc0836f1bd7aeacb1f0294 https://github.com/galaxyproject/galaxy/commit/ca7fb1db62e6c1f03bfc0836f1bd… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-09-20 (Tue, 20 Sep 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/webapps/tool_shed/api/tools.py Log Message: ----------- Make request_context (trans) the first argument to populate_model. Commit: 18b93014572c04d597b9ea6f0750686e9cba39b4 https://github.com/galaxyproject/galaxy/commit/18b93014572c04d597b9ea6f0750… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-09-20 (Tue, 20 Sep 2016) Changed paths: M lib/galaxy/web/framework/decorators.py Log Message: ----------- Merge branch 'dev' of git://github.com/galaxyproject/galaxy into repo_queue_sharing Commit: 07cc3a9462db302478ab4aacd378b6128282e52b https://github.com/galaxyproject/galaxy/commit/07cc3a9462db302478ab4aacd378… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-09-21 (Wed, 21 Sep 2016) Changed paths: M lib/galaxy/security/validate_user_input.py M lib/galaxy/webapps/galaxy/controllers/mobile.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/workflow/extract.py M templates/user/info.mako M templates/user/register.mako M templates/user/username.mako M templates/webapps/galaxy/workflow/build_from_current_history.mako M test/unit/managers/test_UserManager.py Log Message: ----------- Merge branch 'dev' of git://github.com/galaxyproject/galaxy into repo_queue_sharing Commit: 5309c8eeb782140fa7f729d7933a388cf29f6505 https://github.com/galaxyproject/galaxy/commit/5309c8eeb782140fa7f729d7933a… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-09-21 (Wed, 21 Sep 2016) Changed paths: M templates/admin/tool_shed_repository/browse_toolsheds.mako Log Message: ----------- Show a modal with the tool form when clicking on the button. Commit: dd783f418e3fb33a169766235febffa575e0696a https://github.com/galaxyproject/galaxy/commit/dd783f418e3fb33a169766235feb… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-09-21 (Wed, 21 Sep 2016) Changed paths: M templates/admin/tool_shed_repository/browse_toolsheds.mako Log Message: ----------- A bit of styling. Commit: 6da7ce304e34db2cb0495cdd88c553514514573b https://github.com/galaxyproject/galaxy/commit/6da7ce304e34db2cb0495cdd88c5… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-09-21 (Wed, 21 Sep 2016) Changed paths: M templates/admin/tool_shed_repository/browse_toolsheds.mako Log Message: ----------- Additional styling. Commit: d60bc8a97b5f229bbf9416e4e5a0f92e028aad01 https://github.com/galaxyproject/galaxy/commit/d60bc8a97b5f229bbf9416e4e5a0… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-09-21 (Wed, 21 Sep 2016) Changed paths: M lib/galaxy/webapps/tool_shed/api/tools.py Log Message: ----------- Improve travis' demeanor. Commit: b29d6f55d8546aac4354d4293ee585d08645c790 https://github.com/galaxyproject/galaxy/commit/b29d6f55d8546aac4354d4293ee5… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-09-23 (Fri, 23 Sep 2016) Changed paths: M lib/galaxy/webapps/tool_shed/api/tools.py Log Message: ----------- Remove unused import. Commit: adbcc26286909bae7bd0a9c4587ea4815137a8e3 https://github.com/galaxyproject/galaxy/commit/adbcc26286909bae7bd0a9c4587e… Author: Dave B <dave(a)bx.psu.edu> Date: 2016-09-26 (Mon, 26 Sep 2016) Changed paths: M templates/admin/tool_shed_repository/browse_toolsheds.mako Log Message: ----------- Fix the per-tool panel selection features. 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tools/maf/maf_to_fasta_concat.py M tools/maf/maf_to_fasta_multiple_sets.py M tools/maf/vcf_to_maf_customtrack.py M tools/metag_tools/shrimp_color_wrapper.py M tools/metag_tools/shrimp_wrapper.py M tools/next_gen_conversion/solid2fastq.py M tools/next_gen_conversion/solid_to_fastq.py M tools/ngs_simulation/ngs_simulation.py M tools/phenotype_association/pagetag.py M tools/phenotype_association/senatag.py M tools/solid_tools/maq_cs_wrapper.py M tools/solid_tools/solid_qual_stats.py M tools/sr_assembly/velvetg_wrapper.py M tools/sr_mapping/bfast_wrapper.py M tools/stats/filtering.py M tools/stats/grouping.py M tools/stats/gsummary.py M tools/visualization/LAJ_code.py Log Message: ----------- Merge branch 'dev' of git://github.com/galaxyproject/galaxy into repo_queue_sharing Commit: 92724347feedac97f319af6c8ab6f2c703ef9811 https://github.com/galaxyproject/galaxy/commit/92724347feedac97f319af6c8ab6… Author: Dave B <dave(a)bx.psu.edu> Date: 2016-10-04 (Tue, 04 Oct 2016) Changed paths: M templates/admin/tool_shed_repository/browse_toolsheds.mako Log Message: ----------- Fix repository installation. Commit: 84545674af6fc81e0f5a2dd87448aaee176106eb https://github.com/galaxyproject/galaxy/commit/84545674af6fc81e0f5a2dd87448… Author: Dave B <dave(a)bx.psu.edu> Date: 2016-10-04 (Tue, 04 Oct 2016) Changed paths: M templates/admin/tool_shed_repository/browse_toolsheds.mako Log Message: ----------- Fix the 'Add from workflow' button. 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static/scripts/mvc/ui/ui-tabs.js A static/scripts/mvc/ui/ui-thumbnails.js A static/scripts/mvc/webhooks.js M static/scripts/mvc/workflow/workflow-view.js M static/scripts/utils/utils.js M static/style/blue/base.css M templates/user/index.mako M templates/webapps/galaxy/workflow/editor.mako R templates/webapps/galaxy/workflow/index.mako R templates/webapps/galaxy/workflow/missing_tools.mako R templates/webapps/galaxy/workflow/myexp_export_content.mako R templates/webapps/galaxy/workflow/rename.mako M test/api/helpers.py M test/api/test_api_batch.py M test/api/test_authenticate.py M test/api/test_dataset_collections.py M test/api/test_histories.py M test/api/test_history_contents.py M test/api/test_libraries.py M test/api/test_page_revisions.py M test/api/test_pages.py M test/api/test_tool_data.py M test/api/test_tools.py M test/api/test_users.py M test/api/test_workflow_extraction.py M test/api/test_workflows.py M test/api/workflows_format_2/__init__.py M test/api/workflows_format_2/converter.py M test/api/workflows_format_2/main.py M test/base/api.py M test/base/driver_util.py M test/base/integration_util.py M test/base/interactor.py M test/base/test_logging.py M test/base/twilltestcase.py M test/functional/test_data_managers.py M test/functional/test_library_templates.py M test/functional/test_toolbox.py A test/functional/tools/color_param.xml A test/functional/tools/mulled_example_multi_1.xml A test/functional/tools/multi_data_optional.xml M test/functional/tools/samples_tool_conf.xml A test/functional/tools/version_command.py A test/functional/tools/version_command_interpreter.xml A test/functional/tools/version_command_plain.xml A test/functional/tools/version_command_tool_dir.xml M test/functional/workflow.py M test/integration/test_resolvers.py M test/manual/workflows_scaling.py M test/qunit/package.json M test/qunit/tests/ui_tests.js M test/shed_functional/base/test_db_util.py M test/shed_functional/functional/test_0300_reset_all_metadata.py M test/shed_functional/functional/test_1140_simple_repository_dependency_multiple_owners.py M test/shed_functional/functional/test_1300_reset_all_metadata.py M test/shed_functional/functional_tests.py M test/unit/jobs/test_job_wrapper.py M test/unit/jobs/test_runner_local.py M test/unit/tools/test_tool_dependency_description.py M test/unit/tools/test_toolbox.py M test/unit/tools_support.py M test/unit/unittest_utils/utility.py A tool-data/blastdb.loc.sample A tool-data/blastdb_d.loc.sample A tool-data/blastdb_p.loc.sample M tools/data_source/upload.py M tools/filters/gff/gff_filter_by_attribute.py M tools/stats/filtering.py Log Message: ----------- Merge branch 'dev' of git://github.com/galaxyproject/galaxy into repo_queue_sharing Commit: 9e37adb93251ea72e6592966e6b5e810a756f9d8 https://github.com/galaxyproject/galaxy/commit/9e37adb93251ea72e6592966e6b5… Author: Dave B <dave(a)bx.psu.edu> Date: 2016-11-09 (Wed, 09 Nov 2016) Changed paths: A client/galaxy/scripts/admin.toolshed.js A client/galaxy/scripts/mvc/toolshed/categories-view.js A client/galaxy/scripts/mvc/toolshed/repo-queue-view.js A client/galaxy/scripts/mvc/toolshed/repositories-view.js A client/galaxy/scripts/mvc/toolshed/repository-view.js A client/galaxy/scripts/mvc/toolshed/shed-list-view.js A client/galaxy/scripts/mvc/toolshed/toolshed-model.js M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py A static/maps/admin.toolshed.js.map A static/maps/mvc/toolshed/repo-queue-view.js.map A static/maps/mvc/toolshed/shed-category-view.js.map A static/maps/mvc/toolshed/shed-repo-details-view.js.map A static/maps/mvc/toolshed/shed-repo-list-view.js.map A static/maps/mvc/toolshed/sheds-list-view.js.map A static/maps/mvc/toolshed/toolshed-model.js.map A static/scripts/admin.toolshed.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map A static/scripts/mvc/toolshed/categories-view.js A static/scripts/mvc/toolshed/repo-queue-view.js A static/scripts/mvc/toolshed/repositories-view.js A static/scripts/mvc/toolshed/repository-view.js A static/scripts/mvc/toolshed/shed-category-view.js A static/scripts/mvc/toolshed/shed-list-view.js A static/scripts/mvc/toolshed/shed-repo-details-view.js A static/scripts/mvc/toolshed/shed-repo-list-view.js A static/scripts/mvc/toolshed/sheds-list-view.js A static/scripts/mvc/toolshed/toolshed-model.js M static/scripts/mvc/ui/ui-thumbnails.js M static/scripts/mvc/webhooks.js R templates/admin/tool_shed_repository/browse_toolsheds.mako Log Message: ----------- Initial backbonification of API repo installation. Commit: 1700b1f3a5ebf72fdacafcf067cba23e3a88db1a https://github.com/galaxyproject/galaxy/commit/1700b1f3a5ebf72fdacafcf067cb… Author: Dave B <dave(a)bx.psu.edu> Date: 2016-11-10 (Thu, 10 Nov 2016) Changed paths: M client/galaxy/scripts/admin.toolshed.js M client/galaxy/scripts/mvc/toolshed/categories-view.js M client/galaxy/scripts/mvc/toolshed/repositories-view.js M client/galaxy/scripts/mvc/toolshed/repository-view.js M lib/galaxy/webapps/galaxy/buildapp.py M static/scripts/admin.toolshed.js M static/scripts/mvc/toolshed/categories-view.js M static/scripts/mvc/toolshed/repositories-view.js M static/scripts/mvc/toolshed/repository-view.js Log Message: ----------- Fix forward navigation. Commit: 1e8965f1e4f68c4bec8c9bc832bb55330e3942a5 https://github.com/galaxyproject/galaxy/commit/1e8965f1e4f68c4bec8c9bc832bb… Author: Dave B <dave(a)bx.psu.edu> Date: 2016-11-11 (Fri, 11 Nov 2016) Changed paths: M client/galaxy/scripts/mvc/toolshed/repository-view.js M static/scripts/mvc/toolshed/repository-view.js Log Message: ----------- Fix installation. Commit: 476df39fe2163a00bbcd441e66f49b14325bf3af https://github.com/galaxyproject/galaxy/commit/476df39fe2163a00bbcd441e66f4… Author: Dave B <dave(a)bx.psu.edu> Date: 2016-11-11 (Fri, 11 Nov 2016) Changed paths: M lib/galaxy/model/mapping.py M lib/galaxy/tools/toolbox/integrated_panel.py M lib/tool_shed/tools/tool_validator.py M scripts/api/filter_failed_datasets_from_collection.py Log Message: ----------- Merge branch 'dev' of git://github.com/galaxyproject/galaxy into ts_api_backbone Commit: 104aee5114880d744f427dcd96515d193d3798f0 https://github.com/galaxyproject/galaxy/commit/104aee5114880d744f427dcd9651… Author: Dave B <dave(a)bx.psu.edu> Date: 2016-11-14 (Mon, 14 Nov 2016) Changed paths: M client/galaxy/scripts/mvc/toolshed/repository-view.js M static/scripts/mvc/toolshed/repository-view.js Log Message: ----------- Some cleanup, improved the jstree. Commit: 529c7c5b74470f8a1dfb8a913ca0e84d55f8610d https://github.com/galaxyproject/galaxy/commit/529c7c5b74470f8a1dfb8a913ca0… Author: Dave B <dave(a)bx.psu.edu> Date: 2016-11-14 (Mon, 14 Nov 2016) Changed paths: M client/galaxy/scripts/mvc/toolshed/repository-view.js M static/scripts/mvc/toolshed/repository-view.js Log Message: ----------- Fix tool form modal. Commit: edd7417102e51bde3ae199365b05c519cd0d6f3b https://github.com/galaxyproject/galaxy/commit/edd7417102e51bde3ae199365b05… Author: Dave B <dave(a)bx.psu.edu> Date: 2016-11-14 (Mon, 14 Nov 2016) Changed paths: M .ci/flake8_lint_include_list.txt M Makefile M config/galaxy.ini.sample M doc/source/admin/interactive_environments.rst M lib/galaxy/datatypes/converters/bed_to_fli_converter.xml M lib/galaxy/datatypes/converters/bed_to_gff_converter.xml M lib/galaxy/datatypes/converters/bed_to_tabix_converter.xml M lib/galaxy/datatypes/converters/bedgraph_to_array_tree_converter.xml M lib/galaxy/datatypes/converters/bedgraph_to_bigwig_converter.xml 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/encodepeak_to_bgzip_converter.xml M lib/galaxy/datatypes/converters/encodepeak_to_tabix_converter.xml M lib/galaxy/datatypes/converters/fasta_to_2bit.xml M lib/galaxy/datatypes/converters/fasta_to_bowtie_base_index_converter.xml M lib/galaxy/datatypes/converters/fasta_to_bowtie_color_index_converter.xml M lib/galaxy/datatypes/converters/fasta_to_len.xml M lib/galaxy/datatypes/converters/fasta_to_tabular_converter.xml M lib/galaxy/datatypes/converters/fastq_to_fqtoc.xml M lib/galaxy/datatypes/converters/fastqsolexa_to_fasta_converter.xml M lib/galaxy/datatypes/converters/fastqsolexa_to_qual_converter.xml M lib/galaxy/datatypes/converters/gff_to_bed_converter.xml M lib/galaxy/datatypes/converters/gff_to_bgzip_converter.xml M lib/galaxy/datatypes/converters/gff_to_fli_converter.xml M lib/galaxy/datatypes/converters/gff_to_interval_index_converter.xml M lib/galaxy/datatypes/converters/gff_to_tabix_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/interval_to_bed12_converter.xml M lib/galaxy/datatypes/converters/interval_to_bed6_converter.xml M lib/galaxy/datatypes/converters/interval_to_bed_converter.xml M lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.xml M lib/galaxy/datatypes/converters/interval_to_bgzip_converter.xml M lib/galaxy/datatypes/converters/interval_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/interval_to_coverage.xml M lib/galaxy/datatypes/converters/interval_to_interval_index_converter.xml M lib/galaxy/datatypes/converters/interval_to_tabix_converter.xml M lib/galaxy/datatypes/converters/len_to_linecount.xml M lib/galaxy/datatypes/converters/maf_to_fasta_converter.xml M lib/galaxy/datatypes/converters/maf_to_interval_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/picard_interval_list_to_bed6_converter.xml M lib/galaxy/datatypes/converters/pileup_to_interval_index_converter.xml M lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.xml M lib/galaxy/datatypes/converters/sam_to_bam.xml M lib/galaxy/datatypes/converters/sam_to_bigwig_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/datatypes/converters/tabular_to_dbnsfp.xml M lib/galaxy/datatypes/converters/vcf_to_bgzip_converter.xml M lib/galaxy/datatypes/converters/vcf_to_interval_index_converter.xml M lib/galaxy/datatypes/converters/vcf_to_tabix_converter.xml M lib/galaxy/datatypes/converters/wig_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/wiggle_to_array_tree_converter.xml M lib/galaxy/datatypes/converters/wiggle_to_simple_converter.xml M lib/galaxy/datatypes/data.py M lib/galaxy/exceptions/error_codes.py M lib/galaxy/jobs/metrics/__init__.py M lib/galaxy/jobs/metrics/collectl/cli.py M lib/galaxy/jobs/metrics/collectl/subsystems.py M lib/galaxy/jobs/metrics/instrumenters/core.py M lib/galaxy/jobs/metrics/instrumenters/cpuinfo.py M lib/galaxy/jobs/metrics/instrumenters/env.py M lib/galaxy/jobs/metrics/instrumenters/meminfo.py M lib/galaxy/jobs/runners/cli.py M lib/galaxy/model/__init__.py M lib/galaxy/objectstore/rods.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/cwl/runtime_actions.py M lib/galaxy/tools/cwl/schema.py M lib/galaxy/tools/deps/commands.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/deps/mulled/_cli.py M lib/galaxy/tools/deps/mulled/mulled_build.py M lib/galaxy/tools/deps/mulled/mulled_build_channel.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/deps/resolvers/modules.py M lib/galaxy/tools/imp_exp/exp_history_to_archive.xml M lib/galaxy/tools/parser/output_actions.py M lib/galaxy/tools/parser/output_collection_def.py M lib/galaxy/tools/toolbox/lineages/tool_shed.py M lib/galaxy/tools/toolbox/parser.py M lib/galaxy/util/__init__.py M lib/galaxy/util/hash_util.py M lib/galaxy/util/object_wrapper.py Log Message: ----------- Merge branch 'dev' of git://github.com/galaxyproject/galaxy into ts_api_backbone Commit: 419fb3bde91d792bbda6f2a291c99371cad96d29 https://github.com/galaxyproject/galaxy/commit/419fb3bde91d792bbda6f2a291c9… Author: Dave B <dave(a)bx.psu.edu> Date: 2016-11-14 (Mon, 14 Nov 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py A lib/galaxy/webapps/galaxy/api/toolshed.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Refactor API endpoints. Commit: d00f89707f591b226b1d501959e648a45f62431b https://github.com/galaxyproject/galaxy/commit/d00f89707f591b226b1d501959e6… Author: Dave B <dave(a)bx.psu.edu> Date: 2016-11-15 (Tue, 15 Nov 2016) Changed paths: M client/galaxy/scripts/admin.toolshed.js M client/galaxy/scripts/mvc/toolshed/categories-view.js M client/galaxy/scripts/mvc/toolshed/repositories-view.js M client/galaxy/scripts/mvc/toolshed/repository-view.js M client/galaxy/scripts/mvc/toolshed/shed-list-view.js M client/galaxy/scripts/mvc/toolshed/toolshed-model.js M lib/galaxy/webapps/galaxy/api/toolshed.py M static/scripts/admin.toolshed.js M static/scripts/mvc/toolshed/categories-view.js M static/scripts/mvc/toolshed/repositories-view.js M static/scripts/mvc/toolshed/repository-view.js M static/scripts/mvc/toolshed/shed-list-view.js M static/scripts/mvc/toolshed/toolshed-model.js Log Message: ----------- Fix navigation, update API calls. Commit: 3e83e5ba811bbac19864b39f632f294956c7587e https://github.com/galaxyproject/galaxy/commit/3e83e5ba811bbac19864b39f632f… Author: Dave B <dave(a)bx.psu.edu> Date: 2016-11-16 (Wed, 16 Nov 2016) Changed paths: M client/galaxy/scripts/mvc/toolshed/repository-view.js M static/scripts/mvc/toolshed/repository-view.js Log Message: ----------- Fix disabling button when changeset is installed. Commit: 8ead327a46b0dfcde163e4591895f41575fac21f https://github.com/galaxyproject/galaxy/commit/8ead327a46b0dfcde163e4591895… Author: Dave B <dave(a)bx.psu.edu> Date: 2016-11-16 (Wed, 16 Nov 2016) Changed paths: M client/galaxy/scripts/mvc/toolshed/categories-view.js M client/galaxy/scripts/mvc/toolshed/repositories-view.js M client/galaxy/scripts/mvc/toolshed/repository-view.js M client/galaxy/scripts/mvc/toolshed/shed-list-view.js M static/scripts/mvc/toolshed/categories-view.js M static/scripts/mvc/toolshed/repositories-view.js M static/scripts/mvc/toolshed/repository-view.js M static/scripts/mvc/toolshed/shed-list-view.js Log Message: ----------- Tweaked the UI a bit. Commit: 9463d94a2aa4d30140d18094db55bb4e58e9ebc7 https://github.com/galaxyproject/galaxy/commit/9463d94a2aa4d30140d18094db55… Author: Dave B <dave(a)bx.psu.edu> Date: 2017-01-06 (Fri, 06 Jan 2017) Changed paths: M .ci/flake8_lint_include_list.txt A .ci/jenkins/api/run_tests.sh A .ci/jenkins/framework/run_tests.sh A .ci/jenkins/integration/run_tests.sh A .ci/jenkins/selenium/Dockerfile A .ci/jenkins/selenium/docker-compose.yml A .ci/jenkins/selenium/galaxy.ini A .ci/jenkins/selenium/run_galaxy.bash A .ci/jenkins/selenium/run_tests.sh A .ci/jenkins/toolshed/run_tests.sh M .ci/py3_sources.txt M Makefile M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/tool-panel.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/tool/tool-form-workflow.js M client/galaxy/scripts/mvc/tool/tools.js M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/mvc/upload/composite/composite-row.js M client/galaxy/scripts/mvc/upload/default/default-row.js A client/galaxy/scripts/mvc/user/user-preferences.js M client/galaxy/style/less/base.less M client/galaxy/style/less/dataset.less M client/galaxy/style/less/ui.less M client/galaxy/style/source_material/circle.py M config/datatypes_conf.xml.sample M config/galaxy.ini.sample M config/job_conf.xml.sample_advanced M config/plugins/interactive_environments/jupyter/config/jupyter.ini.sample M config/plugins/interactive_environments/jupyter/config/jupyter.xml M config/plugins/interactive_environments/rstudio/config/allowed_images.yml.sample M config/plugins/interactive_environments/rstudio/config/rstudio.xml M 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tools/stats/aggregate_scores_in_intervals.py M tools/stats/filtering.py M tools/stats/grouping.py M tools/stats/gsummary.py Log Message: ----------- Merge in -dev. Commit: 6954c082fded87b9ab71f97675aa7bc94a975770 https://github.com/galaxyproject/galaxy/commit/6954c082fded87b9ab71f97675aa… Author: Dave B <dave(a)bx.psu.edu> Date: 2017-01-06 (Fri, 06 Jan 2017) Changed paths: M client/galaxy/scripts/mvc/toolshed/categories-view.js M client/galaxy/scripts/mvc/toolshed/repositories-view.js A client/galaxy/scripts/mvc/toolshed/repository-queue-view.js A client/galaxy/scripts/mvc/toolshed/util.js M lib/galaxy/webapps/galaxy/api/toolshed.py M static/scripts/mvc/toolshed/categories-view.js M static/scripts/mvc/toolshed/repositories-view.js Log Message: ----------- Preliminary commit before fixing the search autocomplete. Commit: c955e6fd979a9a402b57f083930108146b21f24a https://github.com/galaxyproject/galaxy/commit/c955e6fd979a9a402b57f0839301… Author: Dave B <dave(a)bx.psu.edu> Date: 2017-01-12 (Thu, 12 Jan 2017) Changed paths: M client/galaxy/scripts/mvc/toolshed/categories-view.js M client/galaxy/scripts/mvc/toolshed/repositories-view.js M client/galaxy/scripts/mvc/toolshed/repository-view.js M client/galaxy/scripts/mvc/toolshed/shed-list-view.js M client/galaxy/scripts/mvc/toolshed/util.js M lib/galaxy/webapps/galaxy/buildapp.py M static/scripts/mvc/toolshed/categories-view.js M static/scripts/mvc/toolshed/repositories-view.js M static/scripts/mvc/toolshed/repository-view.js M static/scripts/mvc/toolshed/shed-list-view.js Log Message: ----------- Fix searching. Commit: de8e43fd65d001a2a076ea4044d192199ae3c446 https://github.com/galaxyproject/galaxy/commit/de8e43fd65d001a2a076ea4044d1… Author: Dave B <dave(a)bx.psu.edu> Date: 2017-01-19 (Thu, 19 Jan 2017) Changed paths: M client/galaxy/scripts/mvc/toolshed/repository-view.js M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/api/toolshed.py M static/scripts/mvc/toolshed/repository-view.js Log Message: ----------- Fix tool form modal. Commit: 8d5b154ef0d25e4b8cbbba7128d14c26e2c4a758 https://github.com/galaxyproject/galaxy/commit/8d5b154ef0d25e4b8cbbba7128d1… Author: Dave B <dave(a)bx.psu.edu> Date: 2017-02-02 (Thu, 02 Feb 2017) Changed paths: M client/galaxy/scripts/admin.toolshed.js M client/galaxy/scripts/mvc/toolshed/categories-view.js M client/galaxy/scripts/mvc/toolshed/repositories-view.js M client/galaxy/scripts/mvc/toolshed/repository-queue-view.js M client/galaxy/scripts/mvc/toolshed/repository-view.js M client/galaxy/scripts/mvc/toolshed/shed-list-view.js M client/galaxy/scripts/mvc/toolshed/toolshed-model.js M static/maps/admin.toolshed.js.map M static/maps/mvc/toolshed/toolshed-model.js.map M static/scripts/admin.toolshed.js M static/scripts/mvc/toolshed/categories-view.js M static/scripts/mvc/toolshed/repositories-view.js M static/scripts/mvc/toolshed/repository-view.js M static/scripts/mvc/toolshed/shed-list-view.js M static/scripts/mvc/toolshed/toolshed-model.js Log Message: ----------- Finally got the repository queue rendering semi-properly. Commit: e92fcf1457e0396e3173b1b7541c53b26a33a47b https://github.com/galaxyproject/galaxy/commit/e92fcf1457e0396e3173b1b7541c… Author: Dave B <dave(a)bx.psu.edu> Date: 2017-02-03 (Fri, 03 Feb 2017) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/jenkins/selenium/run_galaxy.bash M .ci/py3_sources.txt M README.rst 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/tool/tool-form-composite.js M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/mvc/workflow/workflow-canvas.js A client/galaxy/scripts/mvc/workflow/workflow-icons.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/viz/trackster/tracks.js M client/galaxy/style/less/base.less A 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Message: ----------- Merge -dev. Commit: 03ae0d5d6f5c278e0d1d501f68aef49e4f63ff7c https://github.com/galaxyproject/galaxy/commit/03ae0d5d6f5c278e0d1d501f68ae… Author: Dave B <dave(a)bx.psu.edu> Date: 2017-02-09 (Thu, 09 Feb 2017) Changed paths: M client/galaxy/scripts/admin.toolshed.js A client/galaxy/scripts/mvc/toolshed/repo-status-view.js M client/galaxy/scripts/mvc/toolshed/repositories-view.js M client/galaxy/scripts/mvc/toolshed/repository-queue-view.js M client/galaxy/scripts/mvc/toolshed/repository-view.js M client/galaxy/scripts/mvc/toolshed/toolshed-model.js M client/galaxy/scripts/mvc/toolshed/util.js M lib/galaxy/webapps/galaxy/api/toolshed.py M lib/galaxy/webapps/galaxy/buildapp.py A static/maps/mvc/toolshed/categories-view.js.map A static/maps/mvc/toolshed/repositories-view.js.map A static/maps/mvc/toolshed/repository-queue-view.js.map A static/maps/mvc/toolshed/repository-view.js.map A static/maps/mvc/toolshed/shed-list-view.js.map A static/maps/mvc/toolshed/util.js.map M static/scripts/admin.toolshed.js A static/scripts/mvc/toolshed/repo-status-view.js M static/scripts/mvc/toolshed/repositories-view.js A static/scripts/mvc/toolshed/repository-queue-view.js M static/scripts/mvc/toolshed/repository-view.js M static/scripts/mvc/toolshed/toolshed-model.js A static/scripts/mvc/toolshed/util.js Log Message: ----------- Fix installation from queue, add repository installation status view. 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static/maps/mvc/tool/tool-form-workflow.js.map M static/maps/mvc/tool/tool-form.js.map M static/maps/mvc/ui/ui-misc.js.map M static/maps/mvc/ui/ui-portlet.js.map M static/maps/mvc/workflow/workflow-manager.js.map M static/maps/mvc/workflow/workflow-node.js.map M static/maps/mvc/workflow/workflow-view.js.map M static/maps/ui/autocom_tagging.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/libs/jquery/jquery.autocomplete.js M static/scripts/mvc/form/form-input.js M static/scripts/mvc/form/form-section.js M static/scripts/mvc/form/form-view.js M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/tool/tool-form-composite.js M static/scripts/mvc/tool/tool-form-workflow.js M static/scripts/mvc/tool/tool-form.js M static/scripts/mvc/ui/ui-misc.js M static/scripts/mvc/ui/ui-portlet.js M static/scripts/mvc/workflow/workflow-manager.js M static/scripts/mvc/workflow/workflow-node.js M static/scripts/mvc/workflow/workflow-view.js M static/scripts/ui/autocom_tagging.js M templates/webapps/tool_shed/repository/tool_form.mako M test/api/test_histories.py M test/api/test_history_contents.py M test/qunit/tests/form_tests.js M test/unit/managers/test_HDAManager.py M test/unit/managers/test_HistoryManager.py Log Message: ----------- Merge with -dev. Commit: b15fdf080ad86e157829e312da056829710dae12 https://github.com/galaxyproject/galaxy/commit/b15fdf080ad86e157829e312da05… Author: Dave B <dave(a)bx.psu.edu> Date: 2017-02-14 (Tue, 14 Feb 2017) Changed paths: M client/galaxy/scripts/admin.toolshed.js M client/galaxy/scripts/mvc/toolshed/repository-queue-view.js M client/galaxy/scripts/mvc/toolshed/toolshed-model.js A client/galaxy/scripts/mvc/toolshed/workflows-view.js M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/tool_shed/api/repositories.py M static/scripts/admin.toolshed.js M static/scripts/mvc/toolshed/repository-queue-view.js M static/scripts/mvc/toolshed/toolshed-model.js A static/scripts/mvc/toolshed/workflows-view.js Log Message: ----------- Enable preview of repository from workflows missing tools. Commit: dbbcdee9abb88e2479574c9d410fa50cd29b2b41 https://github.com/galaxyproject/galaxy/commit/dbbcdee9abb88e2479574c9d410f… Author: Dave B <dave(a)bx.psu.edu> Date: 2017-02-14 (Tue, 14 Feb 2017) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/jenkins/selenium/run_tests.sh M .ci/py3_sources.txt M CONTRIBUTING.md M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/user/user-quotameter.js M config/datatypes_conf.xml.sample M config/plugins/tours/core.galaxy_ui.yaml M doc/source/slideshow/architecture/galaxy_architecture.md M doc/source/slideshow/architecture/images/hda_dataset.plantuml.svg M doc/source/slideshow/architecture/images/hda_hdca.plantuml.svg M doc/source/slideshow/architecture/images/objectstore.plantuml.svg M doc/source/slideshow/architecture/images/plantuml_options.txt M doc/source/slideshow/architecture/images/server_client.plantuml.svg M doc/source/slideshow/architecture/images/server_client_old.plantuml.svg M doc/source/slideshow/architecture/images/webapp.plantuml.svg M doc/source/slideshow/architecture/style.css M lib/galaxy/datatypes/genetics.py M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/proteomics.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/web/base/controllers/admin.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/workflow/steps.py M scripts/slideshow/slideshow_template.html M static/maps/mvc/tool/tool-form-base.js.map M static/maps/mvc/user/user-quotameter.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/user/user-quotameter.js M templates/admin/reload_tool.mako M test/api/test_tools.py M test/api/test_workflow_extraction.py M test/base/populators.py A test/functional/tools/output_format_deprecated_when.xml M test/functional/tools/samples_tool_conf.xml M test/selenium_tests/framework.py M test/selenium_tests/test_stock_tours.py M test/selenium_tests/test_uploads.py Log Message: ----------- Merge branch 'dev' of git://github.com/galaxyproject/galaxy into ts_api_backbone Commit: e3eecfc0ec7994aa0385a7d3a4e38ebde0c9125e https://github.com/galaxyproject/galaxy/commit/e3eecfc0ec7994aa0385a7d3a4e3… Author: Dave B <dave(a)bx.psu.edu> Date: 2017-02-14 (Tue, 14 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/toolshed/repository-queue-view.js M static/scripts/mvc/toolshed/repository-queue-view.js Log Message: ----------- Fix repository queue view. Commit: 64ad2fcf084218e9dea63dc0ade49314b650a721 https://github.com/galaxyproject/galaxy/commit/64ad2fcf084218e9dea63dc0ade4… Author: Dave B <dave(a)bx.psu.edu> Date: 2017-02-15 (Wed, 15 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/toolshed/repository-queue-view.js M client/galaxy/scripts/mvc/toolshed/repository-view.js M client/galaxy/scripts/mvc/toolshed/toolshed-model.js M client/galaxy/scripts/mvc/toolshed/util.js M client/galaxy/scripts/mvc/toolshed/workflows-view.js M lib/galaxy/webapps/galaxy/api/toolshed.py M static/scripts/mvc/toolshed/repository-view.js M static/scripts/mvc/toolshed/toolshed-model.js M static/scripts/mvc/toolshed/util.js M static/scripts/mvc/toolshed/workflows-view.js Log Message: ----------- Implement adding a workflow repository to the installation queue. Commit: da9c57d3656a61c8da31322d54702e509bb69232 https://github.com/galaxyproject/galaxy/commit/da9c57d3656a61c8da31322d5470… Author: Dave B <dave(a)bx.psu.edu> Date: 2017-02-15 (Wed, 15 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/user/user-quotameter.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/model/mapping.py M lib/galaxy/model/orm/engine_factory.py M lib/galaxy/webapps/galaxy/api/history_contents.py M lib/galaxy/webapps/galaxy/controllers/user.py M static/maps/mvc/user/user-quotameter.js.map M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/user/user-quotameter.js M static/scripts/mvc/workflow/workflow-view.js M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Merge branch 'dev' of git://github.com/galaxyproject/galaxy into ts_api_backbone Commit: 9688b7ba4d08b63033ddd407b9944cf96e4f4032 https://github.com/galaxyproject/galaxy/commit/9688b7ba4d08b63033ddd407b994… Author: Dave B <dave(a)bx.psu.edu> Date: 2017-02-15 (Wed, 15 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/toolshed/repository-queue-view.js M client/galaxy/scripts/mvc/toolshed/util.js M client/galaxy/scripts/mvc/toolshed/workflows-view.js M static/scripts/mvc/toolshed/repository-queue-view.js M static/scripts/mvc/toolshed/util.js M static/scripts/mvc/toolshed/workflows-view.js Log Message: ----------- Fix discovering a repository for workflows. Commit: afc7b1c2cd0641d2b57821c5c1a8e0e245a2ad54 https://github.com/galaxyproject/galaxy/commit/afc7b1c2cd0641d2b57821c5c1a8… Author: Dave B <dave(a)bx.psu.edu> Date: 2017-02-16 (Thu, 16 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/toolshed/repo-status-view.js M static/scripts/mvc/toolshed/repo-status-view.js Log Message: ----------- Fix styling for repository installation status. Commit: 233b90c610b8ed3d8067da7a4b4944ab6d322000 https://github.com/galaxyproject/galaxy/commit/233b90c610b8ed3d8067da7a4b49… Author: Dave B <dave(a)bx.psu.edu> Date: 2017-02-16 (Thu, 16 Feb 2017) Changed paths: M client/galaxy/scripts/admin.toolshed.js M client/galaxy/scripts/mvc/toolshed/categories-view.js M client/galaxy/scripts/mvc/toolshed/repo-status-view.js M client/galaxy/scripts/mvc/toolshed/repositories-view.js M client/galaxy/scripts/mvc/toolshed/repository-queue-view.js M client/galaxy/scripts/mvc/toolshed/repository-view.js M client/galaxy/scripts/mvc/toolshed/shed-list-view.js M client/galaxy/scripts/mvc/toolshed/util.js M client/galaxy/scripts/mvc/toolshed/workflows-view.js M static/scripts/admin.toolshed.js M static/scripts/mvc/toolshed/categories-view.js M static/scripts/mvc/toolshed/repo-status-view.js M static/scripts/mvc/toolshed/repositories-view.js M static/scripts/mvc/toolshed/repository-queue-view.js M static/scripts/mvc/toolshed/repository-view.js M static/scripts/mvc/toolshed/shed-list-view.js M static/scripts/mvc/toolshed/util.js M static/scripts/mvc/toolshed/workflows-view.js Log Message: ----------- Style the repository queue properly. Commit: 661e93a139ba5189856d8189886dcce8ac06d7d6 https://github.com/galaxyproject/galaxy/commit/661e93a139ba5189856d8189886d… Author: Dave B <dave(a)bx.psu.edu> Date: 2017-02-16 (Thu, 16 Feb 2017) Changed paths: 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 config/plugins/visualizations/charts/static/repository/visualizations/ngl/viewer/config.js A config/plugins/visualizations/charts/static/repository/visualizations/ngl/viewer/logo.png A config/plugins/visualizations/charts/static/repository/visualizations/ngl/viewer/wrapper.js A scripts/secret_decoder_ring.py Log Message: ----------- Merge branch 'dev' of git://github.com/galaxyproject/galaxy into ts_api_backbone Commit: ba1ccce10af37ebd84b83a77ad7b764ab4d9efe5 https://github.com/galaxyproject/galaxy/commit/ba1ccce10af37ebd84b83a77ad7b… Author: Dave B <dave(a)bx.psu.edu> Date: 2017-02-16 (Thu, 16 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/toolshed/categories-view.js M client/galaxy/scripts/mvc/toolshed/repository-queue-view.js M client/galaxy/scripts/mvc/toolshed/workflows-view.js M static/scripts/mvc/toolshed/workflows-view.js Log Message: ----------- Remove superfluous commands. Commit: 6aa167ba50c3f4f31a7b0c637f88b1d7400dc501 https://github.com/galaxyproject/galaxy/commit/6aa167ba50c3f4f31a7b0c637f88… Author: Dave B <dave(a)bx.psu.edu> Date: 2017-02-16 (Thu, 16 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/toolshed/categories-view.js M client/galaxy/scripts/mvc/toolshed/repositories-view.js M static/scripts/mvc/toolshed/categories-view.js M static/scripts/mvc/toolshed/repositories-view.js Log Message: ----------- Made search results more readable. Commit: 73773d269ba4bb014f99d5230fd8ecdc811ede52 https://github.com/galaxyproject/galaxy/commit/73773d269ba4bb014f99d5230fd8… Author: Dave B <dave(a)bx.psu.edu> Date: 2017-02-16 (Thu, 16 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/toolshed/repo-status-view.js M client/galaxy/scripts/mvc/toolshed/repository-view.js M static/scripts/mvc/toolshed/repo-status-view.js M static/scripts/mvc/toolshed/repository-view.js Log Message: ----------- Remove queue button from installed repos. Commit: e0bb34cdf5e4ffa6927c758ba03823f1160966c3 https://github.com/galaxyproject/galaxy/commit/e0bb34cdf5e4ffa6927c758ba038… Author: Dave B <dave(a)bx.psu.edu> Date: 2017-02-17 (Fri, 17 Feb 2017) Changed paths: M doc/source/releases/17.01_announce.rst M lib/galaxy/model/__init__.py M lib/galaxy/tools/parameters/basic.py M test/unit/tools/test_data_parameters.py M test/unit/tools/test_execution.py Log Message: ----------- Merge branch 'dev' of git://github.com/galaxyproject/galaxy into ts_api_backbone Commit: 68a51acc5395d5a2af0c5a68bf756fe41b14c9f2 https://github.com/galaxyproject/galaxy/commit/68a51acc5395d5a2af0c5a68bf75… Author: Dave B <dave(a)bx.psu.edu> Date: 2017-02-17 (Fri, 17 Feb 2017) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/api/toolshed.py Log Message: ----------- Correct errors revealed by travis. Commit: 5dc9728d29bc4c0c8b587dc30cd492a87193065a https://github.com/galaxyproject/galaxy/commit/5dc9728d29bc4c0c8b587dc30cd4… Author: Dave B <dave(a)bx.psu.edu> Date: 2017-02-21 (Tue, 21 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/toolshed/repository-queue-view.js M client/galaxy/scripts/mvc/toolshed/repository-view.js M static/scripts/mvc/toolshed/repository-queue-view.js M static/scripts/mvc/toolshed/repository-view.js Log Message: ----------- Mostly fixed repository dependency jstree. Commit: fdf95d3702118cfee16dd904dc461898316b7bf9 https://github.com/galaxyproject/galaxy/commit/fdf95d3702118cfee16dd904dc46… Author: Dave B <dave(a)bx.psu.edu> Date: 2017-02-21 (Tue, 21 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/tool/tool-form-workflow.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M config/galaxy.ini.sample M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run_request.py M lib/tool_shed/util/workflow_util.py M static/maps/mvc/tool/tool-form-base.js.map M static/maps/mvc/tool/tool-form-composite.js.map M static/maps/mvc/tool/tool-form-workflow.js.map M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/tool/tool-form-composite.js M static/scripts/mvc/tool/tool-form-workflow.js M static/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Merge dev. Commit: fbe557f09b86c97700043a5bd4222b62d9d0d49a https://github.com/galaxyproject/galaxy/commit/fbe557f09b86c97700043a5bd422… Author: Dave B <dave(a)bx.psu.edu> Date: 2017-03-06 (Mon, 06 Mar 2017) Changed paths: M .ci/flake8_blacklist.txt M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/grid/grid-view.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-composite.js R client/galaxy/scripts/mvc/tool/tool-form-workflow.js A client/galaxy/scripts/mvc/workflow/workflow-forms.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M config/datatypes_conf.xml.sample M config/galaxy.ini.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/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 doc/source/releases/17.01_announce.rst M lib/galaxy/auth/providers/ldap_ad.py M lib/galaxy/config.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/mothur.py M lib/galaxy/datatypes/proteomics.py M lib/galaxy/exceptions/error_codes.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/dynamic_tool_destination.py M lib/galaxy/managers/workflows.py M lib/galaxy/model/orm/engine_factory.py M lib/galaxy/queue_worker.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/mulled/invfile.lua M lib/galaxy/tools/deps/mulled/mulled_build.py M lib/galaxy/tools/linters/general.py M lib/galaxy/tools/linters/outputs.py M lib/galaxy/tools/linters/stdio.py M lib/galaxy/tools/linters/tests.py M lib/galaxy/tools/search/__init__.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/visualization/plugins/plugin.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/web/framework/middleware/remoteuser.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/workflow/modules.py M scripts/bootstrap_history.py M static/maps/mvc/form/form-input.js.map M static/maps/mvc/form/form-section.js.map M static/maps/mvc/grid/grid-view.js.map M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/history-view.js.map M static/maps/mvc/history/options-menu.js.map M static/maps/mvc/tool/tool-form-composite.js.map R static/maps/mvc/tool/tool-form-workflow.js.map A static/maps/mvc/workflow/workflow-forms.js.map M static/maps/mvc/workflow/workflow-view.js.map R 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.map M static/scripts/mvc/form/form-input.js M static/scripts/mvc/form/form-section.js M static/scripts/mvc/grid/grid-view.js M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/history-view.js M static/scripts/mvc/history/options-menu.js M static/scripts/mvc/tool/tool-form-composite.js R static/scripts/mvc/tool/tool-form-workflow.js A static/scripts/mvc/workflow/workflow-forms.js M static/scripts/mvc/workflow/workflow-view.js M templates/grid_base.mako A templates/webapps/galaxy/user/manage_info.mako M test/api/test_workflows.py A test/functional/tools/mulled_example_multi_incomplete.xml M test/functional/tools/samples_tool_conf.xml M test/unit/workflows/test_modules.py M tools/data_source/upload.py Log Message: ----------- Merge branch 'dev' of git://github.com/galaxyproject/galaxy into ts_api_backbone Commit: fb5005bba40d1d1b53b826ab620686662d42c39e https://github.com/galaxyproject/galaxy/commit/fb5005bba40d1d1b53b826ab6206… Author: Dave B <dave(a)bx.psu.edu> Date: 2017-03-06 (Mon, 06 Mar 2017) Changed paths: M client/galaxy/scripts/mvc/toolshed/repository-view.js M lib/galaxy/tools/__init__.py M static/scripts/mvc/toolshed/repository-view.js M static/scripts/mvc/webhooks.js Log Message: ----------- Fix incorrect merge. Commit: 9309cecef039e6a00eb944c6b6d445e8e935c1cf https://github.com/galaxyproject/galaxy/commit/9309cecef039e6a00eb944c6b6d4… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-03-21 (Tue, 21 Mar 2017) Changed paths: M client/galaxy/scripts/mvc/toolshed/shed-list-view.js M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py Log Message: ----------- add small stylystic changes Commit: 0ba78254e57b8f0fd2c8c64a36c4385f3a8bda87 https://github.com/galaxyproject/galaxy/commit/0ba78254e57b8f0fd2c8c64a36c4… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-03-21 (Tue, 21 Mar 2017) Changed paths: M static/maps/admin.toolshed.js.map M static/maps/mvc/toolshed/categories-view.js.map A static/maps/mvc/toolshed/repo-status-view.js.map M static/maps/mvc/toolshed/repositories-view.js.map M static/maps/mvc/toolshed/repository-queue-view.js.map M static/maps/mvc/toolshed/repository-view.js.map M static/maps/mvc/toolshed/shed-list-view.js.map M static/maps/mvc/toolshed/toolshed-model.js.map M static/maps/mvc/toolshed/util.js.map A static/maps/mvc/toolshed/workflows-view.js.map M static/scripts/admin.toolshed.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/toolshed/categories-view.js M static/scripts/mvc/toolshed/repo-status-view.js M static/scripts/mvc/toolshed/repositories-view.js M static/scripts/mvc/toolshed/repository-queue-view.js M static/scripts/mvc/toolshed/repository-view.js M static/scripts/mvc/toolshed/shed-list-view.js M static/scripts/mvc/toolshed/toolshed-model.js M static/scripts/mvc/toolshed/util.js M static/scripts/mvc/toolshed/workflows-view.js M static/scripts/mvc/ui/ui-thumbnails.js Log Message: ----------- repack client (seems to not be done in a while) Commit: 6ba72513e492609e81095cd6c7a75c9c4eb908c6 https://github.com/galaxyproject/galaxy/commit/6ba72513e492609e81095cd6c7a7… Author: Dave B <dave(a)bx.psu.edu> Date: 2017-03-21 (Tue, 21 Mar 2017) Changed paths: M .ci/py3_sources.txt M README.rst M 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static/scripts/mvc/upload/upload-ftp.js M static/scripts/mvc/user/user-preferences.js M static/style/blue/base.css M templates/grid_base.mako M templates/webapps/galaxy/admin/index.mako A templates/webapps/galaxy/admin/manage_dependencies.mako R templates/webapps/galaxy/user/manage_info.mako M templates/webapps/tool_shed/repository/common.mako M test/TESTING.md M test/docker/base/run_test_wrapper.sh M test/galaxy_selenium/has_driver.py M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation-data.yml M test/integration/test_resolvers.py A test/selenium_tests/test_collection_builders.py M test/unit/tools/test_data_parameters.py Log Message: ----------- Merge with -dev. Commit: 0d87bb58805cb1ec1ee45f5c9c6557e56154a2cf https://github.com/galaxyproject/galaxy/commit/0d87bb58805cb1ec1ee45f5c9c65… Author: Dave B <dave(a)bx.psu.edu> Date: 2017-03-21 (Tue, 21 Mar 2017) Changed paths: M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Remove duplicate import. 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Commit: 88a3ee1073b939bb161980389f5d55abc483439f https://github.com/galaxyproject/galaxy/commit/88a3ee1073b939bb161980389f5d… Author: Dave B <dave(a)bx.psu.edu> Date: 2017-04-24 (Mon, 24 Apr 2017) Changed paths: M config/openid_conf.xml.sample M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/text.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/deferred/__init__.py M lib/galaxy/jobs/handler.py M lib/galaxy/jobs/metrics/__init__.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/local.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/jobs/runners/tasks.py M lib/galaxy/managers/citations.py M lib/galaxy/model/migrate/versions/0048_dataset_instance_state_column.py M lib/galaxy/model/migrate/versions/0062_user_openid_table.py M lib/galaxy/model/migrate/versions/0068_rename_sequencer_to_external_services.py M lib/galaxy/model/migrate/versions/0089_add_object_store_id_columns.py M 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lib/tool_shed/metadata/repository_metadata_manager.py M lib/tool_shed/repository_registry.py M lib/tool_shed/util/commit_util.py M lib/tool_shed/util/common_util.py M lib/tool_shed/util/readme_util.py M lib/tool_shed/util/repository_util.py M lib/tool_shed/util/workflow_util.py M lib/tool_shed/utility_containers/__init__.py R openid/google.xml Log Message: ----------- Merge branch 'dev' of git://github.com/galaxyproject/galaxy into ts_api_backbone Commit: 1d620ef260297affe8947fa57d5f542ce418e769 https://github.com/galaxyproject/galaxy/commit/1d620ef260297affe8947fa57d5f… Author: Dave B <dave(a)bx.psu.edu> Date: 2017-04-24 (Mon, 24 Apr 2017) Changed paths: M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/nls/fr/locale.js M client/galaxy/scripts/nls/locale.js M static/maps/layout/menu.js.map M static/maps/nls/fr/locale.js.map M static/maps/nls/locale.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/nls/fr/locale.js M static/scripts/nls/locale.js Log Message: ----------- Merge branch 'dev' of git://github.com/galaxyproject/galaxy into ts_api_backbone Commit: 272fbd2235aeaa9ea9d9b257958c8a14301d8e7b https://github.com/galaxyproject/galaxy/commit/272fbd2235aeaa9ea9d9b257958c… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-05-17 (Wed, 17 May 2017) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py Log Message: ----------- enable TS beta isntallation interface by default Commit: b9fb2de42b53fcb1516422cdd3d40177d507529a https://github.com/galaxyproject/galaxy/commit/b9fb2de42b53fcb1516422cdd3d4… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-05-17 (Wed, 17 May 2017) Changed paths: A client/galaxy/scripts/admin.toolshed.js A client/galaxy/scripts/mvc/toolshed/categories-view.js A client/galaxy/scripts/mvc/toolshed/repo-queue-view.js A client/galaxy/scripts/mvc/toolshed/repo-status-view.js A 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static/maps/admin.toolshed.js.map A static/maps/mvc/toolshed/categories-view.js.map A static/maps/mvc/toolshed/repo-queue-view.js.map A static/maps/mvc/toolshed/repo-status-view.js.map A static/maps/mvc/toolshed/repositories-view.js.map A static/maps/mvc/toolshed/repository-queue-view.js.map A static/maps/mvc/toolshed/repository-view.js.map A static/maps/mvc/toolshed/shed-category-view.js.map A static/maps/mvc/toolshed/shed-list-view.js.map A static/maps/mvc/toolshed/shed-repo-details-view.js.map A static/maps/mvc/toolshed/shed-repo-list-view.js.map A static/maps/mvc/toolshed/sheds-list-view.js.map A static/maps/mvc/toolshed/toolshed-model.js.map A static/maps/mvc/toolshed/util.js.map A static/maps/mvc/toolshed/workflows-view.js.map A static/scripts/admin.toolshed.js A static/scripts/mvc/toolshed/categories-view.js A static/scripts/mvc/toolshed/repo-queue-view.js A static/scripts/mvc/toolshed/repo-status-view.js A static/scripts/mvc/toolshed/repositories-view.js A static/scripts/mvc/toolshed/repository-queue-view.js A static/scripts/mvc/toolshed/repository-view.js A static/scripts/mvc/toolshed/shed-category-view.js A static/scripts/mvc/toolshed/shed-list-view.js A static/scripts/mvc/toolshed/shed-repo-details-view.js A static/scripts/mvc/toolshed/shed-repo-list-view.js A static/scripts/mvc/toolshed/sheds-list-view.js A static/scripts/mvc/toolshed/toolshed-model.js A static/scripts/mvc/toolshed/util.js A static/scripts/mvc/toolshed/workflows-view.js R templates/admin/tool_shed_repository/browse_toolsheds.mako Log Message: ----------- Merge pull request #3626 from davebx/ts_api_backbone API installation of toolshed repositories. Compare: https://github.com/galaxyproject/galaxy/compare/5eadd4842dcd...b9fb2de42b53

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[galaxyproject/usegalaxy-playbook] 890912: Fixed conda env generation on Jetstream: Manually ...
by GitHub 17 May '17

17 May '17

Branch: refs/heads/reorg Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 890912424aae8cc959f25fe88d70d82a5c0e5102 https://github.com/galaxyproject/usegalaxy-playbook/commit/890912424aae8cc9… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-05-17 (Wed, 17 May 2017) Log Message: ----------- Fixed conda env generation on Jetstream: Manually upgraded galaxy-lib from 16.7.10 to 17.5.9. No committable changes.

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