- galaxy-commits - lists.galaxyproject.org

[galaxyproject/infrastructure-playbook] 629aee: nventory documentation improvements and fixes for ...
by GitHub 30 Oct '17

30 Oct '17

Branch: refs/heads/galaxyenv Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 629aee142143ce08dbd781688d22126a4351bfaf https://github.com/galaxyproject/infrastructure-playbook/commit/629aee14214… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-30 (Mon, 30 Oct 2017) Changed paths: M env/galaxy/inventory Log Message: ----------- nventory documentation improvements and fixes for authorized keys Commit: b5b266f439840b839f1394ee497f8864c9fc4960 https://github.com/galaxyproject/infrastructure-playbook/commit/b5b266f4398… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-30 (Mon, 30 Oct 2017) Changed paths: M env/galaxy/inventory M env/galaxy/playbook.yml Log Message: ----------- Add a "fullenv" group to the Galaxy env ("liteenv" + AFS) Commit: b6c8a7134dfd9cf3ebc57ca756ef3ef24d5bd85a https://github.com/galaxyproject/infrastructure-playbook/commit/b6c8a7134df… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-30 (Mon, 30 Oct 2017) Changed paths: M env/galaxy/inventory M env/galaxy/playbook.yml A roles/kerberos_kdc/defaults/main.yml A roles/kerberos_kdc/handlers/main.yml A roles/kerberos_kdc/meta/main.yml A roles/kerberos_kdc/tasks/debian.yml A roles/kerberos_kdc/tasks/heimdal.yml A roles/kerberos_kdc/tasks/main.yml A roles/kerberos_kdc/templates/kadmind.acl.j2 A roles/kerberos_kdc/templates/kdc.conf.j2 A roles/kerberos_kdc/vars/debian.yml A roles/kerberos_kdc/vars/heimdal.yml Log Message: ----------- Add the Kerberos KDC role from the pre-vault playbook and update it. Compare: https://github.com/galaxyproject/infrastructure-playbook/compare/46d754c2b7…

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[galaxyproject/galaxy] 59e5b1: Fix path to example conda mapping
by GitHub 30 Oct '17

30 Oct '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 59e5b17ac704e1c45cf693187174225d3eefe994 https://github.com/galaxyproject/galaxy/commit/59e5b17ac704e1c45cf693187174… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-10-04 (Wed, 04 Oct 2017) Changed paths: M config/local_conda_mapping.yml.sample Log Message: ----------- Fix path to example conda mapping Commit: aef5f4fa95c56362029dba6cf636103cf235fd13 https://github.com/galaxyproject/galaxy/commit/aef5f4fa95c56362029dba6cf636… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-26 (Thu, 26 Oct 2017) Changed paths: M lib/galaxy/dependencies/dev-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt Log Message: ----------- [16.10] Fix test fixtures dependency. It should have never been in the pinned requirements and has disappeared from PyPI. Commit: 7bf2bbfa405029898a65f1ea092d8cacd2903483 https://github.com/galaxyproject/galaxy/commit/7bf2bbfa405029898a65f1ea092d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-27 (Fri, 27 Oct 2017) Changed paths: M lib/galaxy/dependencies/dev-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt Log Message: ----------- Merge pull request #4873 from jmchilton/fix_test_fixtures [16.10] Fix test fixtures dependency. Commit: 676f6a5960a185c80d7400b9cb8c92d5217bfae4 https://github.com/galaxyproject/galaxy/commit/676f6a5960a185c80d7400b9cb8c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-10-30 (Mon, 30 Oct 2017) Changed paths: M client/galaxy/style/less/upload.less M static/style/blue/base.css Log Message: ----------- Fix uploadbox text content formatting. Commit: 09fdac513d59ca6dad440616a53daa97751ff905 https://github.com/galaxyproject/galaxy/commit/09fdac513d59ca6dad440616a53d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-30 (Mon, 30 Oct 2017) Changed paths: M scripts/common_startup.sh Log Message: ----------- Fix extra index URL call in common startup. - Use it for dev requirements also. - Use more correct API target that supports older versions of dependencies on PyPI. xref https://gist.github.com/jmchilton/ad8f180f5ac1eb5f689f815b04f603fa Commit: 45d4fefe63d59627063cbacaf6cdd797ee81d158 https://github.com/galaxyproject/galaxy/commit/45d4fefe63d59627063cbacaf6cd… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-10-30 (Mon, 30 Oct 2017) Changed paths: M scripts/common_startup.sh Log Message: ----------- Merge pull request #4898 from jmchilton/fix_extra_index [17.09] Fix extra index URL call in common startup. Commit: a537aa4ca4f7622bafe20da7339d5652e263d78f https://github.com/galaxyproject/galaxy/commit/a537aa4ca4f7622bafe20da7339d… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-10-30 (Mon, 30 Oct 2017) Changed paths: M config/local_conda_mapping.yml.sample Log Message: ----------- Merge pull request #4749 from mvdbeek/conda_mapping_path_fix [17.05] Fix path to example conda mapping Commit: 1664a2c7e644ee12a3bd599bfd08c5a618443ef0 https://github.com/galaxyproject/galaxy/commit/1664a2c7e644ee12a3bd599bfd08… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-10-30 (Mon, 30 Oct 2017) Changed paths: M client/galaxy/style/less/upload.less M static/style/blue/base.css Log Message: ----------- Merge pull request #4897 from dannon/uploadbox_wrap_fix [17.09] Fix uploadbox text content formatting. Commit: c7b09f870d31b93dab87a2eaaa95ace7f6f503b4 https://github.com/galaxyproject/galaxy/commit/c7b09f870d31b93dab87a2eaaa95… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-10-30 (Mon, 30 Oct 2017) Changed paths: M lib/galaxy/dependencies/dev-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt Log Message: ----------- Merge branch 'release_16.10' into release_17.01 Conflicts: lib/galaxy/dependencies/pinned-requirements.txt Commit: 7688b057e604f4e6e38a21fca3e47ce65c16c413 https://github.com/galaxyproject/galaxy/commit/7688b057e604f4e6e38a21fca3e4… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-10-30 (Mon, 30 Oct 2017) Changed paths: M lib/galaxy/dependencies/dev-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt Log Message: ----------- Merge branch 'release_17.01' into release_17.05 Commit: be30d6824d4975f6cb15fdd9519f4edf3e9e3079 https://github.com/galaxyproject/galaxy/commit/be30d6824d4975f6cb15fdd9519f… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-10-30 (Mon, 30 Oct 2017) Changed paths: M config/local_conda_mapping.yml.sample M lib/galaxy/dependencies/dev-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt Log Message: ----------- Merge branch 'release_17.05' into release_17.09 Commit: aacdf8d939e554ef9dca9fea3075813f1c0862d3 https://github.com/galaxyproject/galaxy/commit/aacdf8d939e554ef9dca9fea3075… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-10-30 (Mon, 30 Oct 2017) Changed paths: M client/galaxy/style/less/upload.less M config/local_conda_mapping.yml.sample M lib/galaxy/dependencies/dev-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt M scripts/common_startup.sh M static/style/blue/base.css Log Message: ----------- Merge branch 'release_17.09' into dev Conflicts: static/style/blue/base.css Compare: https://github.com/galaxyproject/galaxy/compare/c2f4b5ac8f8d...aacdf8d939e5

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[galaxyproject/galaxy] 59e5b1: Fix path to example conda mapping
by GitHub 30 Oct '17

30 Oct '17

Branch: refs/heads/release_17.09 Home: https://github.com/galaxyproject/galaxy Commit: 59e5b17ac704e1c45cf693187174225d3eefe994 https://github.com/galaxyproject/galaxy/commit/59e5b17ac704e1c45cf693187174… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-10-04 (Wed, 04 Oct 2017) Changed paths: M config/local_conda_mapping.yml.sample Log Message: ----------- Fix path to example conda mapping Commit: aef5f4fa95c56362029dba6cf636103cf235fd13 https://github.com/galaxyproject/galaxy/commit/aef5f4fa95c56362029dba6cf636… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-26 (Thu, 26 Oct 2017) Changed paths: M lib/galaxy/dependencies/dev-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt Log Message: ----------- [16.10] Fix test fixtures dependency. It should have never been in the pinned requirements and has disappeared from PyPI. Commit: 7bf2bbfa405029898a65f1ea092d8cacd2903483 https://github.com/galaxyproject/galaxy/commit/7bf2bbfa405029898a65f1ea092d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-27 (Fri, 27 Oct 2017) Changed paths: M lib/galaxy/dependencies/dev-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt Log Message: ----------- Merge pull request #4873 from jmchilton/fix_test_fixtures [16.10] Fix test fixtures dependency. Commit: a537aa4ca4f7622bafe20da7339d5652e263d78f https://github.com/galaxyproject/galaxy/commit/a537aa4ca4f7622bafe20da7339d… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-10-30 (Mon, 30 Oct 2017) Changed paths: M config/local_conda_mapping.yml.sample Log Message: ----------- Merge pull request #4749 from mvdbeek/conda_mapping_path_fix [17.05] Fix path to example conda mapping Commit: c7b09f870d31b93dab87a2eaaa95ace7f6f503b4 https://github.com/galaxyproject/galaxy/commit/c7b09f870d31b93dab87a2eaaa95… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-10-30 (Mon, 30 Oct 2017) Changed paths: M lib/galaxy/dependencies/dev-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt Log Message: ----------- Merge branch 'release_16.10' into release_17.01 Conflicts: lib/galaxy/dependencies/pinned-requirements.txt Commit: 7688b057e604f4e6e38a21fca3e47ce65c16c413 https://github.com/galaxyproject/galaxy/commit/7688b057e604f4e6e38a21fca3e4… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-10-30 (Mon, 30 Oct 2017) Changed paths: M lib/galaxy/dependencies/dev-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt Log Message: ----------- Merge branch 'release_17.01' into release_17.05 Commit: be30d6824d4975f6cb15fdd9519f4edf3e9e3079 https://github.com/galaxyproject/galaxy/commit/be30d6824d4975f6cb15fdd9519f… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-10-30 (Mon, 30 Oct 2017) Changed paths: M config/local_conda_mapping.yml.sample M lib/galaxy/dependencies/dev-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt Log Message: ----------- Merge branch 'release_17.05' into release_17.09 Compare: https://github.com/galaxyproject/galaxy/compare/1664a2c7e644...be30d6824d49

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[galaxyproject/galaxy] aef5f4: [16.10] Fix test fixtures dependency.
by GitHub 30 Oct '17

30 Oct '17

Branch: refs/heads/release_17.05 Home: https://github.com/galaxyproject/galaxy Commit: aef5f4fa95c56362029dba6cf636103cf235fd13 https://github.com/galaxyproject/galaxy/commit/aef5f4fa95c56362029dba6cf636… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-26 (Thu, 26 Oct 2017) Changed paths: M lib/galaxy/dependencies/dev-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt Log Message: ----------- [16.10] Fix test fixtures dependency. It should have never been in the pinned requirements and has disappeared from PyPI. Commit: 7bf2bbfa405029898a65f1ea092d8cacd2903483 https://github.com/galaxyproject/galaxy/commit/7bf2bbfa405029898a65f1ea092d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-27 (Fri, 27 Oct 2017) Changed paths: M lib/galaxy/dependencies/dev-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt Log Message: ----------- Merge pull request #4873 from jmchilton/fix_test_fixtures [16.10] Fix test fixtures dependency. Commit: c7b09f870d31b93dab87a2eaaa95ace7f6f503b4 https://github.com/galaxyproject/galaxy/commit/c7b09f870d31b93dab87a2eaaa95… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-10-30 (Mon, 30 Oct 2017) Changed paths: M lib/galaxy/dependencies/dev-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt Log Message: ----------- Merge branch 'release_16.10' into release_17.01 Conflicts: lib/galaxy/dependencies/pinned-requirements.txt Commit: 7688b057e604f4e6e38a21fca3e47ce65c16c413 https://github.com/galaxyproject/galaxy/commit/7688b057e604f4e6e38a21fca3e4… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-10-30 (Mon, 30 Oct 2017) Changed paths: M lib/galaxy/dependencies/dev-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt Log Message: ----------- Merge branch 'release_17.01' into release_17.05 Compare: https://github.com/galaxyproject/galaxy/compare/a537aa4ca4f7...7688b057e604

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[galaxyproject/galaxy] aef5f4: [16.10] Fix test fixtures dependency.
by GitHub 30 Oct '17

30 Oct '17

Branch: refs/heads/release_17.01 Home: https://github.com/galaxyproject/galaxy Commit: aef5f4fa95c56362029dba6cf636103cf235fd13 https://github.com/galaxyproject/galaxy/commit/aef5f4fa95c56362029dba6cf636… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-26 (Thu, 26 Oct 2017) Changed paths: M lib/galaxy/dependencies/dev-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt Log Message: ----------- [16.10] Fix test fixtures dependency. It should have never been in the pinned requirements and has disappeared from PyPI. Commit: 7bf2bbfa405029898a65f1ea092d8cacd2903483 https://github.com/galaxyproject/galaxy/commit/7bf2bbfa405029898a65f1ea092d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-27 (Fri, 27 Oct 2017) Changed paths: M lib/galaxy/dependencies/dev-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt Log Message: ----------- Merge pull request #4873 from jmchilton/fix_test_fixtures [16.10] Fix test fixtures dependency. Commit: c7b09f870d31b93dab87a2eaaa95ace7f6f503b4 https://github.com/galaxyproject/galaxy/commit/c7b09f870d31b93dab87a2eaaa95… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-10-30 (Mon, 30 Oct 2017) Changed paths: M lib/galaxy/dependencies/dev-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt Log Message: ----------- Merge branch 'release_16.10' into release_17.01 Conflicts: lib/galaxy/dependencies/pinned-requirements.txt Compare: https://github.com/galaxyproject/galaxy/compare/a7bf1601a1ad...c7b09f870d31

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[galaxyproject/galaxy] 676f6a: Fix uploadbox text content formatting.
by GitHub 30 Oct '17

30 Oct '17

Branch: refs/heads/release_17.09 Home: https://github.com/galaxyproject/galaxy Commit: 676f6a5960a185c80d7400b9cb8c92d5217bfae4 https://github.com/galaxyproject/galaxy/commit/676f6a5960a185c80d7400b9cb8c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-10-30 (Mon, 30 Oct 2017) Changed paths: M client/galaxy/style/less/upload.less M static/style/blue/base.css Log Message: ----------- Fix uploadbox text content formatting. Commit: 1664a2c7e644ee12a3bd599bfd08c5a618443ef0 https://github.com/galaxyproject/galaxy/commit/1664a2c7e644ee12a3bd599bfd08… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-10-30 (Mon, 30 Oct 2017) Changed paths: M client/galaxy/style/less/upload.less M static/style/blue/base.css Log Message: ----------- Merge pull request #4897 from dannon/uploadbox_wrap_fix [17.09] Fix uploadbox text content formatting. Compare: https://github.com/galaxyproject/galaxy/compare/45d4fefe63d5...1664a2c7e644

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[galaxyproject/galaxy] 59e5b1: Fix path to example conda mapping
by GitHub 30 Oct '17

30 Oct '17

Branch: refs/heads/release_17.05 Home: https://github.com/galaxyproject/galaxy Commit: 59e5b17ac704e1c45cf693187174225d3eefe994 https://github.com/galaxyproject/galaxy/commit/59e5b17ac704e1c45cf693187174… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-10-04 (Wed, 04 Oct 2017) Changed paths: M config/local_conda_mapping.yml.sample Log Message: ----------- Fix path to example conda mapping Commit: a537aa4ca4f7622bafe20da7339d5652e263d78f https://github.com/galaxyproject/galaxy/commit/a537aa4ca4f7622bafe20da7339d… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-10-30 (Mon, 30 Oct 2017) Changed paths: M config/local_conda_mapping.yml.sample Log Message: ----------- Merge pull request #4749 from mvdbeek/conda_mapping_path_fix [17.05] Fix path to example conda mapping Compare: https://github.com/galaxyproject/galaxy/compare/20621b7d0944...a537aa4ca4f7

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[galaxyproject/galaxy] 09fdac: Fix extra index URL call in common startup.
by GitHub 30 Oct '17

30 Oct '17

Branch: refs/heads/release_17.09 Home: https://github.com/galaxyproject/galaxy Commit: 09fdac513d59ca6dad440616a53daa97751ff905 https://github.com/galaxyproject/galaxy/commit/09fdac513d59ca6dad440616a53d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-30 (Mon, 30 Oct 2017) Changed paths: M scripts/common_startup.sh Log Message: ----------- Fix extra index URL call in common startup. - Use it for dev requirements also. - Use more correct API target that supports older versions of dependencies on PyPI. xref https://gist.github.com/jmchilton/ad8f180f5ac1eb5f689f815b04f603fa Commit: 45d4fefe63d59627063cbacaf6cdd797ee81d158 https://github.com/galaxyproject/galaxy/commit/45d4fefe63d59627063cbacaf6cd… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-10-30 (Mon, 30 Oct 2017) Changed paths: M scripts/common_startup.sh Log Message: ----------- Merge pull request #4898 from jmchilton/fix_extra_index [17.09] Fix extra index URL call in common startup. Compare: https://github.com/galaxyproject/galaxy/compare/b9adcc81e866...45d4fefe63d5

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[galaxyproject/galaxy] e57f3c: Fix a typo.
by GitHub 30 Oct '17

30 Oct '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e57f3cfe328e28f8758d9c047a2911b03f5603f9 https://github.com/galaxyproject/galaxy/commit/e57f3cfe328e28f8758d9c047a29… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-10-30 (Mon, 30 Oct 2017) Changed paths: M client/galaxy/scripts/apps/panels/admin-panel.js M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Fix a typo. Commit: 144928fbebabc3cf1938d2b415a8132c2b08f474 https://github.com/galaxyproject/galaxy/commit/144928fbebabc3cf1938d2b415a8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-10-30 (Mon, 30 Oct 2017) Changed paths: M client/galaxy/style/less/ui.less M static/style/blue/base.css Log Message: ----------- Fix admin side panel not being full container height Commit: c2f4b5ac8f8d7743a87fe9175dafa380b6028d18 https://github.com/galaxyproject/galaxy/commit/c2f4b5ac8f8d7743a87fe9175daf… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-10-30 (Mon, 30 Oct 2017) Changed paths: M client/galaxy/scripts/apps/panels/admin-panel.js M client/galaxy/style/less/ui.less M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/style/blue/base.css Log Message: ----------- Merge pull request #4895 from dannon/minor_admin_panel_fixes Minor admin panel fixes Compare: https://github.com/galaxyproject/galaxy/compare/26a9f8916d64...c2f4b5ac8f8d

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[galaxyproject/galaxy] aa66d7: Remove unnecessary tool dependency installation st...
by GitHub 30 Oct '17

30 Oct '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: aa66d7fdfd363bd34112d5d15d783f7921e487df https://github.com/galaxyproject/galaxy/commit/aa66d7fdfd363bd34112d5d15d78… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-17 (Tue, 17 Oct 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py R templates/admin/tool_shed_repository/tool_dependencies_grid.mako Log Message: ----------- Remove unnecessary tool dependency installation status grid Commit: d616878f85f2b0bb3cbc8fb2cd5ac7f18a114e5c https://github.com/galaxyproject/galaxy/commit/d616878f85f2b0bb3cbc8fb2cd5a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-17 (Tue, 17 Oct 2017) Changed paths: M client/galaxy/scripts/admin.toolshed.js M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/login.js M client/galaxy/scripts/apps/panels/admin-panel.js M client/galaxy/scripts/apps/panels/history-panel.js M client/galaxy/scripts/apps/panels/tool-panel.js M client/galaxy/scripts/galaxy.interactive_environments.js M client/galaxy/scripts/galaxy.js M client/galaxy/scripts/galaxy.library.js M client/galaxy/scripts/galaxy.pages.js M client/galaxy/scripts/i18n.js M client/galaxy/scripts/layout/generic-nav-view.js M client/galaxy/scripts/layout/masthead.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/modal.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/layout/panel.js M client/galaxy/scripts/layout/router.js M client/galaxy/scripts/layout/scratchbook.js M client/galaxy/scripts/mvc/annotation.js M client/galaxy/scripts/mvc/base-mvc.js M client/galaxy/scripts/mvc/base/controlled-fetch-collection.js M client/galaxy/scripts/mvc/citation/citation-model.js M client/galaxy/scripts/mvc/citation/citation-view.js M client/galaxy/scripts/mvc/collection/base-creator.js M client/galaxy/scripts/mvc/collection/collection-li-edit.js M client/galaxy/scripts/mvc/collection/collection-li.js M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/collection/collection-view-edit.js M client/galaxy/scripts/mvc/collection/collection-view.js M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/collection/pair-collection-creator.js M client/galaxy/scripts/mvc/dataset/data.js M client/galaxy/scripts/mvc/dataset/dataset-choice.js M client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js M client/galaxy/scripts/mvc/dataset/dataset-error.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/dataset/dataset-list.js M client/galaxy/scripts/mvc/dataset/dataset-model.js M client/galaxy/scripts/mvc/dataset/states.js M 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static/maps/mvc/dataset/dataset-list.js.map M static/maps/mvc/dataset/dataset-model.js.map M static/maps/mvc/dataset/states.js.map M static/maps/mvc/form/form-data.js.map M static/maps/mvc/form/form-input.js.map M static/maps/mvc/form/form-parameters.js.map M static/maps/mvc/form/form-repeat.js.map M static/maps/mvc/form/form-section.js.map M static/maps/mvc/form/form-view.js.map M static/maps/mvc/form/form-wrapper.js.map M static/maps/mvc/grid/grid-model.js.map M static/maps/mvc/grid/grid-shared.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/copy-dialog.js.map M static/maps/mvc/history/hda-li-edit.js.map M static/maps/mvc/history/hda-li.js.map M static/maps/mvc/history/hda-model.js.map M static/maps/mvc/history/hdca-li-edit.js.map M static/maps/mvc/history/hdca-li.js.map M static/maps/mvc/history/hdca-model.js.map M static/maps/mvc/history/history-content-model.js.map M 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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 M static/maps/mvc/toolshed/workflows-view.js.map M static/maps/mvc/tours.js.map M static/maps/mvc/ui/error-modal.js.map M static/maps/mvc/ui/icon-button.js.map M static/maps/mvc/ui/popup-menu.js.map M static/maps/mvc/ui/ui-buttons.js.map M static/maps/mvc/ui/ui-color-picker.js.map M static/maps/mvc/ui/ui-drilldown.js.map M static/maps/mvc/ui/ui-frames.js.map M static/maps/mvc/ui/ui-list.js.map M static/maps/mvc/ui/ui-misc.js.map M static/maps/mvc/ui/ui-modal.js.map M static/maps/mvc/ui/ui-options.js.map M static/maps/mvc/ui/ui-popover.js.map M static/maps/mvc/ui/ui-portlet.js.map M static/maps/mvc/ui/ui-select-content.js.map M static/maps/mvc/ui/ui-select-default.js.map M static/maps/mvc/ui/ui-select-ftp.js.map M static/maps/mvc/ui/ui-select-genomespace.js.map M static/maps/mvc/ui/ui-select-library.js.map M static/maps/mvc/ui/ui-select.js.map M static/maps/mvc/ui/ui-slider.js.map M static/maps/mvc/ui/ui-table.js.map M static/maps/mvc/ui/ui-tabs.js.map M static/maps/mvc/ui/ui-thumbnails.js.map M static/maps/mvc/upload/collection/collection-row.js.map M static/maps/mvc/upload/collection/collection-view.js.map M static/maps/mvc/upload/composite/composite-row.js.map M static/maps/mvc/upload/composite/composite-view.js.map M static/maps/mvc/upload/default/default-row.js.map M static/maps/mvc/upload/default/default-view.js.map M static/maps/mvc/upload/upload-button.js.map M static/maps/mvc/upload/upload-extension.js.map M static/maps/mvc/upload/upload-ftp.js.map M static/maps/mvc/upload/upload-model.js.map M static/maps/mvc/upload/upload-settings.js.map M static/maps/mvc/upload/upload-view.js.map M static/maps/mvc/user/user-custom-builds.js.map M static/maps/mvc/user/user-model.js.map M static/maps/mvc/user/user-preferences.js.map M static/maps/mvc/user/user-quotameter.js.map M static/maps/mvc/visualization/visualization-model.js.map M static/maps/mvc/webhooks.js.map M static/maps/mvc/workflow/workflow-canvas.js.map M static/maps/mvc/workflow/workflow-connector.js.map M static/maps/mvc/workflow/workflow-forms.js.map M static/maps/mvc/workflow/workflow-icons.js.map M static/maps/mvc/workflow/workflow-manager.js.map M static/maps/mvc/workflow/workflow-model.js.map M static/maps/mvc/workflow/workflow-node.js.map M static/maps/mvc/workflow/workflow-terminals.js.map M static/maps/mvc/workflow/workflow-view-data.js.map M static/maps/mvc/workflow/workflow-view-node.js.map M static/maps/mvc/workflow/workflow-view-terminals.js.map M static/maps/mvc/workflow/workflow-view.js.map M static/maps/mvc/workflow/workflow.js.map M static/maps/nls/de/locale.js.map M static/maps/nls/es/locale.js.map M static/maps/nls/fr/locale.js.map M static/maps/nls/ja/locale.js.map M static/maps/nls/locale.js.map M static/maps/nls/zh/locale.js.map M static/maps/onload.js.map M static/maps/polyfills.js.map M static/maps/reports_webapp/run_stats.js.map M static/maps/ui/autocom_tagging.js.map M static/maps/ui/editable-text.js.map M static/maps/ui/fa-icon-button.js.map M static/maps/ui/filter-control.js.map M static/maps/ui/hoverhighlight.js.map M static/maps/ui/loading-indicator.js.map M static/maps/ui/mode-button.js.map M static/maps/ui/pagination.js.map M static/maps/ui/peek-column-selector.js.map M static/maps/ui/popupmenu.js.map M static/maps/ui/scroll-panel.js.map M static/maps/ui/search-input.js.map M static/maps/utils/add-logging.js.map M static/maps/utils/ajax-queue.js.map M static/maps/utils/async-save-text.js.map M static/maps/utils/config.js.map M static/maps/utils/deferred.js.map M static/maps/utils/graph.js.map M static/maps/utils/levenshtein.js.map M static/maps/utils/localization.js.map M static/maps/utils/metrics-logger.js.map M static/maps/utils/natural-sort.js.map M static/maps/utils/query-string-parsing.js.map M static/maps/utils/uploadbox.js.map M static/maps/utils/utils.js.map M static/maps/viz/bbi-data-manager.js.map M static/maps/viz/circster.js.map M static/maps/viz/phyloviz.js.map M static/maps/viz/sweepster.js.map M static/maps/viz/trackster.js.map M static/maps/viz/trackster/filters.js.map M static/maps/viz/trackster/painters.js.map M static/maps/viz/trackster/slotting.js.map M static/maps/viz/trackster/tracks.js.map M static/maps/viz/trackster/util.js.map M static/maps/viz/visualization.js.map M static/maps/viz/viz_views.js.map M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map M test/functional/tools/collection_split_on_column.xml Log Message: ----------- Merge branch 'remove_toolshed_grids' into remove_toolshed_dependency_grid Commit: c9d87cc2e524307953e0d200854a1b35abe6fe73 https://github.com/galaxyproject/galaxy/commit/c9d87cc2e524307953e0d200854a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-18 (Wed, 18 Oct 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py M static/maps/layout/page.js.map M static/maps/mvc/dataset/dataset-li-edit.js.map M static/maps/mvc/form/form-parameters.js.map M static/maps/mvc/grid/grid-view.js.map M static/scripts/layout/page.js M static/scripts/mvc/dataset/dataset-li-edit.js M static/scripts/mvc/form/form-parameters.js M static/scripts/mvc/grid/grid-view.js Log Message: ----------- Remove unused variables and imports Commit: f0484351dcb7e1256bcf476b656f38f7eb3460bd https://github.com/galaxyproject/galaxy/commit/f0484351dcb7e1256bcf476b656f… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-18 (Wed, 18 Oct 2017) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/form/form-parameters.js M config/datatypes_conf.xml.sample M config/plugins/webhooks/demo/tour_generator/static/script.js M doc/source/slideshow/architecture/galaxy_architecture.md A lib/galaxy/datatypes/annotation.py M lib/galaxy/datatypes/converters/sam_to_bam.py M lib/galaxy/jobs/handler.py M lib/galaxy_ext/metadata/set_metadata.py M static/maps/layout/page.js.map M static/maps/mvc/dataset/dataset-li-edit.js.map M static/maps/mvc/form/form-parameters.js.map M static/maps/mvc/grid/grid-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.map M static/scripts/layout/page.js M static/scripts/mvc/dataset/dataset-li-edit.js M static/scripts/mvc/form/form-parameters.js M static/scripts/mvc/grid/grid-view.js Log Message: ----------- Merge branch 'dev' into remove_toolshed_dependency_grid Commit: fd098c97043b672bdaeaa2ee3abc352b6d06d343 https://github.com/galaxyproject/galaxy/commit/fd098c97043b672bdaeaa2ee3abc… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-19 (Thu, 19 Oct 2017) Changed paths: M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py Log Message: ----------- Remove installation grid from admin toolshed grids Commit: 3c22c31bd77f239a1887ccf3aa13f257f0f8ac17 https://github.com/galaxyproject/galaxy/commit/3c22c31bd77f239a1887ccf3aa13… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-19 (Thu, 19 Oct 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py Log Message: ----------- Remove installation grid reference from admin toolshed controller Commit: 5b0635b833a9efa4be38bcdfeb8ad22ff5f27786 https://github.com/galaxyproject/galaxy/commit/5b0635b833a9efa4be38bcdfeb8a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-19 (Thu, 19 Oct 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py Log Message: ----------- Remove uninstall handling from manage repositories endpoint Commit: fe1cbca9aaad0079348a73ef9632c51dde93e5ca https://github.com/galaxyproject/galaxy/commit/fe1cbca9aaad0079348a73ef9632… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-19 (Thu, 19 Oct 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py Log Message: ----------- Rename to install repositories, remove operation switch Commit: 0c5c8a95abca26d3c447a3a2b6d9903d2eedbd8d https://github.com/galaxyproject/galaxy/commit/0c5c8a95abca26d3c447a3a2b6d9… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-19 (Thu, 19 Oct 2017) Changed paths: M client/galaxy/scripts/mvc/toolshed/repository-queue-view.js M client/galaxy/scripts/mvc/toolshed/repository-view.js M static/maps/mvc/toolshed/repository-queue-view.js.map M static/maps/mvc/toolshed/repository-view.js.map M static/scripts/mvc/toolshed/repository-queue-view.js M static/scripts/mvc/toolshed/repository-view.js Log Message: ----------- Redirect client request urls Commit: 5207476dce338ba5860d7bdfb0e6a3f1cddea4c9 https://github.com/galaxyproject/galaxy/commit/5207476dce338ba5860d7bdfb0e6… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-19 (Thu, 19 Oct 2017) Changed paths: M templates/admin/tool_shed_repository/initiate_repository_installation.mako Log Message: ----------- Request url in mako file Commit: 41eaf0a7820235bd1fb12e7920597c40e059b0ca https://github.com/galaxyproject/galaxy/commit/41eaf0a7820235bd1fb12e792059… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-19 (Thu, 19 Oct 2017) Changed paths: M templates/admin/tool_shed_repository/initiate_repository_installation.mako Log Message: ----------- Remove unnecessary operation specifier from request Commit: 9052c592758e50cdba427cfd96e4fdd03d3c7ccf https://github.com/galaxyproject/galaxy/commit/9052c592758e50cdba427cfd96e4… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-19 (Thu, 19 Oct 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M templates/admin/tool_shed_repository/initiate_repository_installation.mako Log Message: ----------- Remove unused api flag from repository installation controller Commit: 21f21113eb7667a03870528e5c07a37ce029e9a4 https://github.com/galaxyproject/galaxy/commit/21f21113eb7667a03870528e5c07… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-19 (Thu, 19 Oct 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py R templates/admin/tool_shed_repository/repository_installation_grid.mako Log Message: ----------- Fix Commit: b218aae1de1bf35606e964e6fb6ecd94b9054910 https://github.com/galaxyproject/galaxy/commit/b218aae1de1bf35606e964e6fb6e… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-19 (Thu, 19 Oct 2017) Changed paths: M client/galaxy/scripts/apps/panels/admin-panel.js M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M templates/admin/tool_shed_repository/initiate_repository_installation.mako Log Message: ----------- Use installation monitoring view instead of installation monitoring grid Commit: 77f6b7bacbdf752c993e7a1a02a830c3418fb149 https://github.com/galaxyproject/galaxy/commit/77f6b7bacbdf752c993e7a1a02a8… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-19 (Thu, 19 Oct 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py R templates/admin/tool_shed_repository/initiate_repository_installation.mako A templates/admin/tool_shed_repository/monitor_repository_installation.mako Log Message: ----------- Rename mako to emphasize new role, add message handler Commit: f0b5caff5fed1e125e80e07b7f2b43bc4d98f5e7 https://github.com/galaxyproject/galaxy/commit/f0b5caff5fed1e125e80e07b7f2b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-19 (Thu, 19 Oct 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M templates/admin/tool_shed_repository/monitor_repository_installation.mako Log Message: ----------- Fix variable testing Commit: 50ecbea171f19587516a6d91da97250b9280c3da https://github.com/galaxyproject/galaxy/commit/50ecbea171f19587516a6d91da97… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-19 (Thu, 19 Oct 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py Log Message: ----------- Escape message Commit: b76e0559dd3b3ba464b40acec10088f8d68da568 https://github.com/galaxyproject/galaxy/commit/b76e0559dd3b3ba464b40acec100… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-19 (Thu, 19 Oct 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py Log Message: ----------- Fix lint Commit: f622a4367981e9b4a60343e77984bfc6f3147baf https://github.com/galaxyproject/galaxy/commit/f622a4367981e9b4a60343e77984… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-19 (Thu, 19 Oct 2017) Changed paths: M test/shed_functional/base/twilltestcase.py Log Message: ----------- Revise install repositories route Commit: 435044b48b5b02c66df14637dc36bb3545e642df https://github.com/galaxyproject/galaxy/commit/435044b48b5b02c66df14637dc36… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-19 (Thu, 19 Oct 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py Log Message: ----------- Add message, fix escaping Commit: 401870453059aef380952fa2c816fdcda701ebcf https://github.com/galaxyproject/galaxy/commit/401870453059aef380952fa2c816… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-19 (Thu, 19 Oct 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M templates/admin/tool_shed_repository/monitor_repository_installation.mako Log Message: ----------- Fix update query, add message Commit: 9ba393400100c2ed6b913c75840439b396817c0c 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R templates/admin/external_service/reload_external_service_types.mako R templates/admin/external_service/view_external_service.mako R templates/admin/request_type/common.mako R templates/admin/request_type/create_request_type.mako R templates/admin/request_type/edit_request_type.mako R templates/admin/request_type/grid.mako R templates/admin/request_type/request_type_permissions.mako R templates/admin/request_type/view_request_type.mako R templates/admin/requests/grid.mako R templates/admin/requests/reject.mako R templates/admin/requests/rename_datasets.mako R templates/admin/requests/sample_datasets_grid.mako R templates/admin/requests/view_sample_dataset.mako M templates/webapps/galaxy/admin/center.mako R templates/webapps/galaxy/requests/common/add_samples.mako R templates/webapps/galaxy/requests/common/common.mako R templates/webapps/galaxy/requests/common/create_request.mako R templates/webapps/galaxy/requests/common/edit_basic_request_info.mako R templates/webapps/galaxy/requests/common/edit_samples.mako R templates/webapps/galaxy/requests/common/find_samples.mako R templates/webapps/galaxy/requests/common/index.mako R templates/webapps/galaxy/requests/common/sample_dataset_transfer_status.mako R templates/webapps/galaxy/requests/common/sample_datasets.mako R templates/webapps/galaxy/requests/common/sample_state.mako R templates/webapps/galaxy/requests/common/view_request.mako R templates/webapps/galaxy/requests/common/view_request_history.mako R templates/webapps/galaxy/requests/common/view_sample.mako R templates/webapps/galaxy/requests/common/view_sample_datasets.mako R templates/webapps/galaxy/requests/common/view_sample_history.mako R templates/webapps/galaxy/requests/find_samples_index.mako R templates/webapps/galaxy/requests/grid.mako R templates/webapps/galaxy/requests/index.mako M test/base/testcase.py M test/functional/twilltestcase.py M test/shed_functional/base/twilltestcase.py M test/unit/managers/test_UserManager.py M test/unit/tools/test_tool_deps.py M tools/data_source/data_source.py M tools/data_source/import.py M tools/data_source/microbial_import.py M tools/data_source/microbial_import_code.py M tools/data_source/upload.py M tools/evolution/codingSnps_filter.py M tools/extract/extract_genomic_dna.py M tools/extract/liftOver_wrapper.py M tools/filters/axt_to_lav.py M tools/filters/bed_to_gff_converter.py M tools/filters/catWrapper.py M tools/filters/convert_characters.py M tools/filters/gff/extract_GFF_Features.py M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_feature_count.py M tools/filters/gff_to_bed_converter.py M tools/filters/gtf_to_bedgraph_converter.py M tools/filters/join.py M tools/filters/lav_to_bed_code.py M tools/filters/mergeCols.py M tools/filters/sff_extract.py M tools/filters/ucsc_gene_bed_to_exon_bed.py M tools/filters/ucsc_gene_bed_to_intron_bed.py M tools/filters/ucsc_gene_table_to_intervals.py M tools/genomespace/genomespace_importer.py M tools/maf/maf_by_block_number.py M tools/maf/maf_filter.py M tools/maf/maf_limit_size.py M tools/maf/maf_limit_to_species.py M tools/maf/maf_reverse_complement.py M tools/maf/maf_stats.py M tools/maf/maf_thread_for_species.py M tools/maf/maf_to_bed.py M tools/maf/vcf_to_maf_customtrack.py M tools/metag_tools/blat_wrapper.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/plotting/bar_chart.py M tools/solid_tools/maq_cs_wrapper.py M tools/solid_tools/solid_qual_stats.py M tools/sr_mapping/bfast_wrapper.py M 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 branch 'dev' into remove_toolshed_installation_grid Commit: ec82e2bf2fe4df3f0af6ae78a8eb84123aeafe7b https://github.com/galaxyproject/galaxy/commit/ec82e2bf2fe4df3f0af6ae78a8eb… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-10-30 (Mon, 30 Oct 2017) Changed paths: M client/galaxy/scripts/apps/panels/admin-panel.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Prettier, rebuild for merge. Commit: 26a9f8916d64e535a7abbd39394a765e9392a1ea https://github.com/galaxyproject/galaxy/commit/26a9f8916d64e535a7abbd39394a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-10-30 (Mon, 30 Oct 2017) Changed paths: M client/galaxy/scripts/apps/panels/admin-panel.js M client/galaxy/scripts/mvc/toolshed/repository-queue-view.js M client/galaxy/scripts/mvc/toolshed/repository-view.js M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py M static/maps/mvc/toolshed/repository-queue-view.js.map M static/maps/mvc/toolshed/repository-view.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/toolshed/repository-queue-view.js M static/scripts/mvc/toolshed/repository-view.js R templates/admin/tool_shed_repository/initiate_repository_installation.mako A templates/admin/tool_shed_repository/monitor_repository_installation.mako R templates/admin/tool_shed_repository/repository_installation_grid.mako R templates/admin/tool_shed_repository/tool_dependencies_grid.mako M test/shed_functional/base/twilltestcase.py Log Message: ----------- Merge branch 'remove_toolshed_installation_grid' into dev (post-prettier merge was simple to resolve) Compare: https://github.com/galaxyproject/galaxy/compare/62637405b591...26a9f8916d64

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[galaxyproject/galaxy] 5a276e: start work on new lirbary comparators
by GitHub 30 Oct '17

30 Oct '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 5a276ec3e69de63dc574759db59cd083c1b80b8b https://github.com/galaxyproject/galaxy/commit/5a276ec3e69de63dc574759db59c… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-10-26 (Thu, 26 Oct 2017) Changed paths: M client/galaxy/scripts/apps/panels/admin-panel.js M client/galaxy/scripts/mvc/library/library-folderlist-view.js M client/galaxy/scripts/mvc/library/library-folderrow-view.js M client/galaxy/scripts/mvc/library/library-librarylist-view.js M client/galaxy/scripts/mvc/library/library-model.js A client/galaxy/scripts/mvc/library/library-util.js M static/maps/mvc/library/library-folderlist-view.js.map M static/maps/mvc/library/library-folderrow-view.js.map M static/maps/mvc/library/library-librarylist-view.js.map M static/maps/mvc/library/library-model.js.map A static/maps/mvc/library/library-util.js.map M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/library/library-folderlist-view.js M static/scripts/mvc/library/library-folderrow-view.js M static/scripts/mvc/library/library-librarylist-view.js M static/scripts/mvc/library/library-model.js A static/scripts/mvc/library/library-util.js Log Message: ----------- start work on new lirbary comparators Commit: 987f016246ebb5e7474c3e5f2bedeb38a8786e0e https://github.com/galaxyproject/galaxy/commit/987f016246ebb5e7474c3e5f2bed… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-10-26 (Thu, 26 Oct 2017) Changed paths: M client/galaxy/scripts/mvc/library/library-folderlist-view.js M client/galaxy/scripts/mvc/library/library-util.js M static/maps/mvc/library/library-folderlist-view.js.map M static/maps/mvc/library/library-util.js.map M static/scripts/mvc/library/library-folderlist-view.js M static/scripts/mvc/library/library-util.js Log Message: ----------- rework the comparator to work when key is missing from object Commit: 8bde43214cbca1eb31958b4280e1bda93b43fd3a https://github.com/galaxyproject/galaxy/commit/8bde43214cbca1eb31958b4280e1… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-10-26 (Thu, 26 Oct 2017) Changed paths: M client/galaxy/scripts/mvc/library/library-folderlist-view.js M static/maps/mvc/library/library-folderlist-view.js.map Log Message: ----------- remove forgotten comment Commit: c41225b422662a29aa7a43922beac2ffafd2a81b https://github.com/galaxyproject/galaxy/commit/c41225b422662a29aa7a43922bea… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-10-27 (Fri, 27 Oct 2017) Changed paths: M client/galaxy/scripts/mvc/library/library-folderlist-view.js M client/galaxy/scripts/mvc/library/library-folderrow-view.js M client/galaxy/scripts/mvc/library/library-util.js M static/maps/mvc/library/library-folderlist-view.js.map M static/maps/mvc/library/library-folderrow-view.js.map M static/maps/mvc/library/library-util.js.map M static/scripts/mvc/library/library-folderlist-view.js M static/scripts/mvc/library/library-folderrow-view.js M static/scripts/mvc/library/library-util.js Log Message: ----------- datalibs add func to sort folder by desc/state refactor the comparator a bit to not change the actual obejcts' prperties Commit: be4ddd3cd0acdd1d8049f23fbaff577447aaf78f https://github.com/galaxyproject/galaxy/commit/be4ddd3cd0acdd1d8049f23fbaff… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-10-27 (Fri, 27 Oct 2017) Changed paths: M .travis.yml M Makefile M client/galaxy/scripts/mvc/tours.js M client/galaxy/style/less/base.less M client/gulpfile.js M client/package.json M client/yarn.lock M config/plugins/tours/core.galaxy_ui.yaml M config/plugins/tours/core.history.yaml M config/plugins/tours/core.scratchbook.yaml M doc/schema_template.md M lib/galaxy/managers/workflows.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/tours/__init__.py M lib/galaxy/util/path/ntpath.py M run_tests.sh M static/maps/mvc/tours.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tours.js M static/style/blue/base.css M test/api/test_tools.py A test/functional/tools/data_source.py M test/functional/tools/samples_tool_conf.xml A test/functional/tools/test_data_source.xml M test/qunit/Gruntfile.js M test/qunit/package.json M test/qunit/test-app.js M test/qunit/test-common.js R test/qunit/test-libs/qunit-1.23.1.css R test/qunit/test-libs/qunit-1.23.1.js R test/qunit/test-libs/sinon-1.17.7.js R test/qunit/test-libs/sinon-qunit-1.0.0.js M test/qunit/tests/form_tests.js M test/qunit/tests/galaxy-app-base.js M test/qunit/tests/graph.js M test/qunit/tests/hda-base.js M test/qunit/tests/history_contents_model_tests.js M test/qunit/tests/job-dag.js M test/qunit/tests/list-of-pairs-collection-creator.js M test/qunit/tests/masthead_tests.js M test/qunit/tests/metrics-logger.js M test/qunit/tests/modal_tests.js M test/qunit/tests/page_tests.js M test/qunit/tests/popover_tests.js M test/qunit/tests/ui_tests.js M test/qunit/tests/upload_dialog_tests.js M test/qunit/tests/utils_test.js M test/qunit/tests/workflow_editor_tests.js M tox.ini Log Message: ----------- Merge branch 'dev' into lib-comparators Commit: 81a2163c87c28ae3ba4a3d4114a0c7e1c28441c6 https://github.com/galaxyproject/galaxy/commit/81a2163c87c28ae3ba4a3d4114a0… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-10-27 (Fri, 27 Oct 2017) Changed paths: M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- repack Commit: 62637405b591b8b9dc1d061bd7d19055cb363c8d https://github.com/galaxyproject/galaxy/commit/62637405b591b8b9dc1d061bd7d1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-10-30 (Mon, 30 Oct 2017) Changed paths: M client/galaxy/scripts/mvc/library/library-folderlist-view.js M client/galaxy/scripts/mvc/library/library-folderrow-view.js M client/galaxy/scripts/mvc/library/library-librarylist-view.js M client/galaxy/scripts/mvc/library/library-model.js A client/galaxy/scripts/mvc/library/library-util.js M static/maps/mvc/library/library-folderlist-view.js.map M static/maps/mvc/library/library-folderrow-view.js.map M static/maps/mvc/library/library-librarylist-view.js.map M static/maps/mvc/library/library-model.js.map A static/maps/mvc/library/library-util.js.map M static/scripts/mvc/library/library-folderlist-view.js M static/scripts/mvc/library/library-folderrow-view.js M static/scripts/mvc/library/library-librarylist-view.js M static/scripts/mvc/library/library-model.js A static/scripts/mvc/library/library-util.js Log Message: ----------- Merge pull request #4877 from martenson/lib-comparators add sorting options for data library folders Compare: https://github.com/galaxyproject/galaxy/compare/9257e93faf9b...62637405b591

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[galaxyproject/infrastructure-playbook] f04f81: Improved chaining/inheriting variable support
by GitHub 27 Oct '17

27 Oct '17

Branch: refs/heads/galaxyenv Home: https://github.com/galaxyproject/infrastructure-playbook Commit: f04f810c343d1c4ebf15316507301d82c0e68394 https://github.com/galaxyproject/infrastructure-playbook/commit/f04f810c343… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-27 (Fri, 27 Oct 2017) Changed paths: M ansible.cfg M common_roles Log Message: ----------- Improved chaining/inheriting variable support Commit: b4c6fda29ece985296971c729bc06038350ee4e9 https://github.com/galaxyproject/infrastructure-playbook/commit/b4c6fda29ec… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-27 (Fri, 27 Oct 2017) Changed paths: M galaxyenv/secret_group_vars/jenkinsslaves.yml M galaxyenv/secret_host_vars/mjolnir0.galaxyproject.org.yml Log Message: ----------- Fix Jenkins' access to mjolnir0 caused by variable/authorized key clobbering Commit: 34342b8a13b1dc3ec2a5fe86023d492d85b78c9c https://github.com/galaxyproject/infrastructure-playbook/commit/34342b8a13b… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-27 (Fri, 27 Oct 2017) Changed paths: M ansible.cfg M common_roles M env/galaxy/secret_host_vars/mjolnir0.galaxyproject.org.yml Log Message: ----------- Merge branch 'master' into galaxyenv Commit: 0b47750f8f09715ddcaea949280c692d62506492 https://github.com/galaxyproject/infrastructure-playbook/commit/0b47750f8f0… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-27 (Fri, 27 Oct 2017) Changed paths: M env/galaxy/playbook.yml Log Message: ----------- Remove manual inclusion of secret variables in galaxy env playbook Commit: 1647adbf58e9494de222d1ae83e47138390dc09b https://github.com/galaxyproject/infrastructure-playbook/commit/1647adbf58e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-27 (Fri, 27 Oct 2017) Changed paths: M env/galaxy/group_vars/all.yml Log Message: ----------- Drop unncessary deploy_env Commit: 6c73e832fbe10ee23d770ca3fcacd7e04820dc5b https://github.com/galaxyproject/infrastructure-playbook/commit/6c73e832fbe… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-27 (Fri, 27 Oct 2017) Changed paths: M env/common/group_vars/sslservers/vars.yml M env/common/group_vars/sslservers/vault.yml R env/common/secret_group_vars/sslwebservers.yml M env/galaxy/inventory R env/galaxy/secret_group_vars/sslwebservers.yml M taccenv/inventory R taccenv/secret_group_vars/sslwebservers.yml Log Message: ----------- Convert sslkeys to automatic vault files Commit: 46d754c2b74c11c09d274bb3f09de07d668418bf https://github.com/galaxyproject/infrastructure-playbook/commit/46d754c2b74… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-27 (Fri, 27 Oct 2017) Changed paths: R env/galaxy/group_vars/baseenv.yml A env/galaxy/group_vars/baseenv/vars.yml A env/galaxy/group_vars/baseenv/vault.yml A env/galaxy/group_vars/cvmfsservers/vars.yml A env/galaxy/group_vars/cvmfsservers/vault.yml R env/galaxy/group_vars/jenkinsservers.yml A env/galaxy/group_vars/jenkinsservers/vars.yml A env/galaxy/group_vars/jenkinsservers/vault.yml A env/galaxy/group_vars/jetstreamhosts/vars.yml A env/galaxy/group_vars/jetstreamhosts/vault.yml R env/galaxy/host_vars/athena.galaxyproject.org.yml A env/galaxy/host_vars/athena.galaxyproject.org/vars.yml A env/galaxy/host_vars/athena.galaxyproject.org/vault.yml A env/galaxy/host_vars/biostar.usegalaxy.org/vars.yml A env/galaxy/host_vars/biostar.usegalaxy.org/vault.yml R env/galaxy/host_vars/chouffe.galaxyproject.org.yml A env/galaxy/host_vars/chouffe.galaxyproject.org/vars.yml A env/galaxy/host_vars/chouffe.galaxyproject.org/vault.yml R env/galaxy/host_vars/cvmfs0-psu0.galaxyproject.org.yml A env/galaxy/host_vars/cvmfs0-psu0.galaxyproject.org/vars.yml A env/galaxy/host_vars/cvmfs0-psu0.galaxyproject.org/vault.yml R env/galaxy/host_vars/cvmfs0-tacc0.galaxyproject.org.yml A env/galaxy/host_vars/cvmfs0-tacc0.galaxyproject.org/vars.yml A env/galaxy/host_vars/cvmfs0-tacc0.galaxyproject.org/vault.yml R env/galaxy/host_vars/cvmfs1-psu0.galaxyproject.org.yml A env/galaxy/host_vars/cvmfs1-psu0.galaxyproject.org/vars.yml A env/galaxy/host_vars/cvmfs1-psu0.galaxyproject.org/vault.yml R env/galaxy/host_vars/delirium.galaxyproject.org.yml A env/galaxy/host_vars/delirium.galaxyproject.org/vars.yml A env/galaxy/host_vars/delirium.galaxyproject.org/vault.yml M env/galaxy/host_vars/leeroy.galaxyproject.org.yml A env/galaxy/host_vars/mjolnir0.galaxyproject.org/vars.yml A env/galaxy/host_vars/mjolnir0.galaxyproject.org/vault.yml R env/galaxy/host_vars/orval.galaxyproject.org.yml A env/galaxy/host_vars/orval.galaxyproject.org/vars.yml A env/galaxy/host_vars/orval.galaxyproject.org/vault.yml A env/galaxy/host_vars/radegast.galaxyproject.org/vars.yml A env/galaxy/host_vars/radegast.galaxyproject.org/vault.yml R env/galaxy/host_vars/westvleteren.galaxyproject.org.yml A env/galaxy/host_vars/westvleteren.galaxyproject.org/vars.yml A env/galaxy/host_vars/westvleteren.galaxyproject.org/vault.yml M env/galaxy/playbook.yml R env/galaxy/secret_host_vars/athena.galaxyproject.org.yml R env/galaxy/secret_host_vars/biostar.usegalaxy.org.yml R env/galaxy/secret_host_vars/chouffe.galaxyproject.org.yml R env/galaxy/secret_host_vars/cvmfs0-psu0.galaxyproject.org.yml R env/galaxy/secret_host_vars/cvmfs0-tacc0.galaxyproject.org.yml R env/galaxy/secret_host_vars/cvmfs1-iu0.galaxyproject.org.yml R env/galaxy/secret_host_vars/cvmfs1-psu0.galaxyproject.org.yml R env/galaxy/secret_host_vars/cvmfs1-tacc0.galaxyproject.org.yml R env/galaxy/secret_host_vars/default.yml R env/galaxy/secret_host_vars/delirium.galaxyproject.org.yml R env/galaxy/secret_host_vars/leeroy.galaxyproject.org.yml R env/galaxy/secret_host_vars/mjolnir0.galaxyproject.org.yml R env/galaxy/secret_host_vars/orval.galaxyproject.org.yml R env/galaxy/secret_host_vars/radegast.galaxyproject.org.yml R env/galaxy/secret_host_vars/westvleteren.galaxyproject.org.yml Log Message: ----------- Remove secret_host_vars from galaxy env Compare: https://github.com/galaxyproject/infrastructure-playbook/compare/7dcb2ac120…

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[galaxyproject/usegalaxy-playbook] dd7360: Upgrades to DuNovo.
by GitHub 27 Oct '17

27 Oct '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: dd7360f4342c56bcb08dd4a545094ddc95117e2d https://github.com/galaxyproject/usegalaxy-playbook/commit/dd7360f4342c56bc… Author: Dave B <dave(a)bx.psu.edu> Date: 2017-10-27 (Fri, 27 Oct 2017) Changed paths: M env/main/files/galaxy/var/integrated_tool_panel.xml M env/main/files/galaxy/var/shed_tool_conf.xml Log Message: ----------- Upgrades to DuNovo. Commit: a5f40a8694edcf729b44a1fe2aeddeab4f7f7034 https://github.com/galaxyproject/usegalaxy-playbook/commit/a5f40a8694edcf72… Author: Dave B <dave(a)bx.psu.edu> Date: 2017-10-27 (Fri, 27 Oct 2017) Changed paths: M env/test/templates/galaxy/config/job_conf.xml.j2 Log Message: ----------- Allocate 32G for IDEAS. Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/51582db4caee...…

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[galaxyproject/galaxy] c97990: Updates and enhancements for the Docker testing Do...
by GitHub 27 Oct '17

27 Oct '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c9799013ee910d74a8d1953275822305ab128749 https://github.com/galaxyproject/galaxy/commit/c9799013ee910d74a8d195327582… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-27 (Fri, 27 Oct 2017) Changed paths: M test/docker/base/Dockerfile M test/docker/base/ansible_vars.yml M test/docker/base/run_test_wrapper.sh Log Message: ----------- Updates and enhancements for the Docker testing Dockerfile. - Target dev on Github instead of stable on bitbucket for base dependencies and migrations. - Update to Ubuntu 16.04 ahead of trying to merge in Selenium support (should be a bit slimmer without the TS requirements layer also). - Use fancy new Node compatible with yarn. Commit: 9257e93faf9bc5cc8c96d1e07afce9614897d5ec https://github.com/galaxyproject/galaxy/commit/9257e93faf9bc5cc8c96d1e07afc… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-10-27 (Fri, 27 Oct 2017) Changed paths: M test/docker/base/Dockerfile M test/docker/base/ansible_vars.yml M test/docker/base/run_test_wrapper.sh Log Message: ----------- Merge pull request #4885 from jmchilton/testing_dockerfile_0 Updates and enhancements for the testing Dockerfile. Compare: https://github.com/galaxyproject/galaxy/compare/235a590b69e4...9257e93faf9b

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[galaxyproject/infrastructure-playbook] f04f81: Improved chaining/inheriting variable support
by GitHub 27 Oct '17

27 Oct '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: f04f810c343d1c4ebf15316507301d82c0e68394 https://github.com/galaxyproject/infrastructure-playbook/commit/f04f810c343… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-27 (Fri, 27 Oct 2017) Changed paths: M ansible.cfg M common_roles Log Message: ----------- Improved chaining/inheriting variable support Commit: b4c6fda29ece985296971c729bc06038350ee4e9 https://github.com/galaxyproject/infrastructure-playbook/commit/b4c6fda29ec… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-27 (Fri, 27 Oct 2017) Changed paths: M galaxyenv/secret_group_vars/jenkinsslaves.yml M galaxyenv/secret_host_vars/mjolnir0.galaxyproject.org.yml Log Message: ----------- Fix Jenkins' access to mjolnir0 caused by variable/authorized key clobbering Compare: https://github.com/galaxyproject/infrastructure-playbook/compare/fd646f57d3…

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[galaxyproject/galaxy] 5e584b: Update various Galaxy requirements.
by GitHub 27 Oct '17

27 Oct '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 5e584bbe5557b265f1c4f1bfe8386239678032e5 https://github.com/galaxyproject/galaxy/commit/5e584bbe5557b265f1c4f1bfe838… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-27 (Fri, 27 Oct 2017) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt Log Message: ----------- Update various Galaxy requirements. At least requests and Babel are required to get the latest "locked" version of the dev requirements compatible with our current locked versions in requirements.txt. Removed repoze.lru from an earlier variant of this since the wheel didn't work - good catch @nsoranzo. Commit: 235a590b69e431cf6f060da004834ae482e607de https://github.com/galaxyproject/galaxy/commit/235a590b69e431cf6f060da00483… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-10-27 (Fri, 27 Oct 2017) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt Log Message: ----------- Merge pull request #4884 from jmchilton/update_babel Update various Galaxy requirements. Compare: https://github.com/galaxyproject/galaxy/compare/64cf2946f2c0...235a590b69e4

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[galaxyproject/galaxy] aef5f4: [16.10] Fix test fixtures dependency.
by GitHub 27 Oct '17

27 Oct '17

Branch: refs/heads/release_16.10 Home: https://github.com/galaxyproject/galaxy Commit: aef5f4fa95c56362029dba6cf636103cf235fd13 https://github.com/galaxyproject/galaxy/commit/aef5f4fa95c56362029dba6cf636… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-26 (Thu, 26 Oct 2017) Changed paths: M lib/galaxy/dependencies/dev-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt Log Message: ----------- [16.10] Fix test fixtures dependency. It should have never been in the pinned requirements and has disappeared from PyPI. Commit: 7bf2bbfa405029898a65f1ea092d8cacd2903483 https://github.com/galaxyproject/galaxy/commit/7bf2bbfa405029898a65f1ea092d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-27 (Fri, 27 Oct 2017) Changed paths: M lib/galaxy/dependencies/dev-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt Log Message: ----------- Merge pull request #4873 from jmchilton/fix_test_fixtures [16.10] Fix test fixtures dependency. Compare: https://github.com/galaxyproject/galaxy/compare/90289b6116c6...7bf2bbfa4050

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[galaxyproject/galaxy] 3cab51: Rev to a newer version of the testing image.
by GitHub 27 Oct '17

27 Oct '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 3cab512b423eedf908a3bc3ac1fe70abb051622d https://github.com/galaxyproject/galaxy/commit/3cab512b423eedf908a3bc3ac1fe… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-27 (Fri, 27 Oct 2017) Changed paths: M run_tests.sh Log Message: ----------- Rev to a newer version of the testing image. Commit: 64cf2946f2c07177003942cebc8c863d641eeda3 https://github.com/galaxyproject/galaxy/commit/64cf2946f2c07177003942cebc8c… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-10-27 (Fri, 27 Oct 2017) Changed paths: M run_tests.sh Log Message: ----------- Merge pull request #4879 from jmchilton/testing_image_update_3 Rev to a newer version of the testing image. Compare: https://github.com/galaxyproject/galaxy/compare/de9f8a6094f0...64cf2946f2c0

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[galaxyproject/galaxy] 7b9cd4: Added tour groups for more clarity if there are a ...
by GitHub 26 Oct '17

26 Oct '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 7b9cd447004daedca6e18b4e97a67fce8c0667e0 https://github.com/galaxyproject/galaxy/commit/7b9cd447004daedca6e18b4e97a6… Author: Peter Selten <peter.selten98(a)gmail.com> Date: 2017-10-18 (Wed, 18 Oct 2017) Changed paths: M client/galaxy/scripts/mvc/tours.js M config/plugins/tours/core.galaxy_ui.yaml M config/plugins/tours/core.history.yaml M config/plugins/tours/core.scratchbook.yaml A config/plugins/tours/test.yaml M lib/galaxy/tours/__init__.py Log Message: ----------- Added tour groups for more clarity if there are a lot of tours. Commit: d9045deea69e74590d079b05a1bec02e29a6aa18 https://github.com/galaxyproject/galaxy/commit/d9045deea69e74590d079b05a1be… Author: selten <selten(a)users.noreply.github.com> Date: 2017-10-18 (Wed, 18 Oct 2017) Changed paths: R config/plugins/tours/test.yaml Log Message: ----------- Delete test.yaml Accidentally added file to GIT for design checking. Commit: dea036f66a790444a3aae473617bf48d4a1b4827 https://github.com/galaxyproject/galaxy/commit/dea036f66a790444a3aae473617b… Author: Peter Selten <peter.selten98(a)gmail.com> Date: 2017-10-19 (Thu, 19 Oct 2017) Changed paths: M client/galaxy/scripts/mvc/tours.js M config/plugins/tours/core.galaxy_ui.yaml M config/plugins/tours/core.history.yaml M config/plugins/tours/core.scratchbook.yaml M lib/galaxy/tours/__init__.py Log Message: ----------- Use tags instead of groups Commit: 49b9543b77a1419e1bfd13d502239d9c35fe2a1e https://github.com/galaxyproject/galaxy/commit/49b9543b77a1419e1bfd13d50223… Author: Peter Selten <peter.selten98(a)gmail.com> Date: 2017-10-19 (Thu, 19 Oct 2017) Changed paths: R config/plugins/tours/test.yaml Log Message: ----------- Merge remote-tracking branch 'origin/dev' into dev Commit: 19445547298d9b9405965cf83a928cc8afaeccf4 https://github.com/galaxyproject/galaxy/commit/19445547298d9b9405965cf83a92… Author: Peter Selten <peter.selten98(a)gmail.com> Date: 2017-10-19 (Thu, 19 Oct 2017) Changed paths: M client/galaxy/scripts/mvc/tours.js Log Message: ----------- Added hiding of tags. Commit: 75117e407e0b03ee2537cd029b8fbbc345c1e7a6 https://github.com/galaxyproject/galaxy/commit/75117e407e0b03ee2537cd029b8f… Author: Peter Selten <peter.selten98(a)gmail.com> Date: 2017-10-19 (Thu, 19 Oct 2017) Changed paths: M client/galaxy/scripts/mvc/tours.js Log Message: ----------- Make sure description is still shown Commit: a3c00c122c02d3b183c90da83818005fadafda86 https://github.com/galaxyproject/galaxy/commit/a3c00c122c02d3b183c90da83818… Author: Peter Selten <peter.selten98(a)gmail.com> Date: 2017-10-19 (Thu, 19 Oct 2017) Changed paths: M client/galaxy/scripts/mvc/form/form-parameters.js M config/datatypes_conf.xml.sample M config/plugins/webhooks/demo/tour_generator/static/script.js A lib/galaxy/datatypes/annotation.py M lib/galaxy/datatypes/converters/sam_to_bam.py M lib/galaxy/datatypes/dataproviders/external.py M lib/galaxy/jobs/handler.py M lib/galaxy/util/__init__.py M lib/galaxy_ext/metadata/set_metadata.py M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py M static/maps/mvc/form/form-parameters.js.map M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into dev Commit: 4dc97ceb5950ee1bda5c2de2a9e569a7fab2735b https://github.com/galaxyproject/galaxy/commit/4dc97ceb5950ee1bda5c2de2a9e5… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-10-24 (Tue, 24 Oct 2017) Changed paths: M client/galaxy/scripts/mvc/tours.js M static/maps/mvc/tours.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tours.js Log Message: ----------- Build client/formatting. Commit: b777762524ea856962ec3c1c13baa140e9fab766 https://github.com/galaxyproject/galaxy/commit/b777762524ea856962ec3c1c13ba… Author: selten <selten(a)users.noreply.github.com> Date: 2017-10-24 (Tue, 24 Oct 2017) Changed paths: M client/galaxy/scripts/mvc/tours.js M static/maps/mvc/tours.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tours.js Log Message: ----------- Merge pull request #1 from dannon/selten_dev Build client/formatting. Commit: 4fcf2a329f66e29c16898d0c4897f49f20e0fd9a https://github.com/galaxyproject/galaxy/commit/4fcf2a329f66e29c16898d0c4897… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-10-24 (Tue, 24 Oct 2017) Changed paths: M client/galaxy/scripts/mvc/tours.js M static/maps/mvc/tours.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tours.js Log Message: ----------- Untagged tour support/rendering. Commit: df1b7fbf548ad5ffd85b127eb12a3fbead82b7d2 https://github.com/galaxyproject/galaxy/commit/df1b7fbf548ad5ffd85b127eb12a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-10-24 (Tue, 24 Oct 2017) Changed paths: M client/galaxy/scripts/mvc/tours.js M static/maps/mvc/tours.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tours.js Log Message: ----------- Capitalize tag rendering Commit: 7d1a8d8553765ef72da7c8e500a6ca31647d2ab9 https://github.com/galaxyproject/galaxy/commit/7d1a8d8553765ef72da7c8e500a6… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-10-24 (Tue, 24 Oct 2017) Changed paths: M config/plugins/tours/core.scratchbook.yaml Log Message: ----------- Minor typo, consistent use of form for 'visualization/visualisation' Commit: 3138e025366dd088a184d952e76cf5e748077711 https://github.com/galaxyproject/galaxy/commit/3138e025366dd088a184d952e76c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-10-24 (Tue, 24 Oct 2017) Changed paths: M client/galaxy/scripts/mvc/tours.js M client/galaxy/style/less/base.less M static/maps/mvc/tours.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tours.js M static/style/blue/base.css Log Message: ----------- Add a little bit of padding between labels. Commit: f5ae8d26fee5c74fff827cba10fda2b516577353 https://github.com/galaxyproject/galaxy/commit/f5ae8d26fee5c74fff827cba10fd… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-10-24 (Tue, 24 Oct 2017) Changed paths: M config/plugins/tours/core.galaxy_ui.yaml M config/plugins/tours/core.history.yaml M config/plugins/tours/core.scratchbook.yaml Log Message: ----------- Swap from default to 'core' to be consistent with the namespace of the file. Commit: 32ffcaf990037db4ca58c0071f6aed48bd3abb13 https://github.com/galaxyproject/galaxy/commit/32ffcaf990037db4ca58c0071f6a… Author: selten <selten(a)users.noreply.github.com> Date: 2017-10-24 (Tue, 24 Oct 2017) Changed paths: M client/galaxy/scripts/mvc/tours.js M client/galaxy/style/less/base.less M config/plugins/tours/core.galaxy_ui.yaml M config/plugins/tours/core.history.yaml M config/plugins/tours/core.scratchbook.yaml M static/maps/mvc/tours.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tours.js M static/style/blue/base.css Log Message: ----------- Merge pull request #2 from dannon/selten_dev A few more tweaks to tours Commit: b3866bae1623cd8c67cee8fd787fc823e1da31c9 https://github.com/galaxyproject/galaxy/commit/b3866bae1623cd8c67cee8fd787f… Author: Peter Selten <peter.selten98(a)gmail.com> Date: 2017-10-25 (Wed, 25 Oct 2017) Changed paths: M .ci/flake8_lint_include_list.txt M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/panels/admin-panel.js M client/galaxy/scripts/galaxy.interactive_environments.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/mvc/grid/grid-view.js M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-folderlist-view.js M client/galaxy/scripts/mvc/library/library-folderrow-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-libraryrow-view.js M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js M client/galaxy/scripts/utils/utils.js M client/galaxy/style/less/library.less M config/datatypes_conf.xml.sample M config/galaxy.ini.sample M config/plugins/interactive_environments/jupyter/static/js/jupyter.js M config/plugins/webhooks/demo/tour_generator/helper/__init__.py M cron/add_manual_builds.py M cron/build_chrom_db.py M cron/parse_builds.py M cron/parse_builds_3_sites.py M lib/galaxy/auth/providers/ldap_ad.py M lib/galaxy/config.py M lib/galaxy/containers/docker_model.py M lib/galaxy/datatypes/annotation.py M lib/galaxy/datatypes/assembly.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/constructive_solid_geometry.py M lib/galaxy/datatypes/converters/bed_to_gff_converter.py M lib/galaxy/datatypes/converters/fastqsolexa_to_qual_converter.py M lib/galaxy/datatypes/converters/gff_to_bed_converter.py M lib/galaxy/datatypes/converters/interval_to_bed_converter.py M lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.py M lib/galaxy/datatypes/converters/interval_to_coverage.py M lib/galaxy/datatypes/converters/interval_to_fli.py M lib/galaxy/datatypes/converters/lped_to_fped_converter.py M lib/galaxy/datatypes/converters/lped_to_pbed_converter.py M lib/galaxy/datatypes/converters/pbed_ldreduced_converter.py M lib/galaxy/datatypes/converters/pbed_to_lped_converter.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/display_applications/application.py M lib/galaxy/datatypes/genetics.py M lib/galaxy/datatypes/images.py M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/molecules.py M lib/galaxy/datatypes/msa.py M lib/galaxy/datatypes/ngsindex.py M lib/galaxy/datatypes/plant_tribes.py M lib/galaxy/datatypes/proteomics.py M lib/galaxy/datatypes/qualityscore.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/text.py M lib/galaxy/datatypes/tracks.py M lib/galaxy/datatypes/util/generic_util.py M lib/galaxy/dependencies/__init__.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/deferred/__init__.py M lib/galaxy/jobs/handler.py M lib/galaxy/jobs/output_checker.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/cli.py M lib/galaxy/jobs/runners/condor.py M lib/galaxy/jobs/runners/drmaa.py M lib/galaxy/jobs/runners/godocker.py M 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lib/galaxy/model/migrate/versions/0041_workflow_invocation.py M lib/galaxy/model/migrate/versions/0042_workflow_invocation_fix.py M lib/galaxy/model/migrate/versions/0056_workflow_outputs.py M lib/galaxy/model/migrate/versions/0061_tasks.py M lib/galaxy/model/migrate/versions/0076_fix_form_values_data_corruption.py M lib/galaxy/model/migrate/versions/0115_longer_user_password_field.py M lib/galaxy/model/tool_shed_install/migrate/check.py M lib/galaxy/sample_tracking/external_service_types.py M lib/galaxy/sample_tracking/request_types.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/actions/metadata.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/tools/deps/resolvers/unlinked_tool_shed_packages.py M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/dynamic_options.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/tools/parameters/validation.py M lib/galaxy/tools/parser/output_actions.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/util/maf_utilities.py M lib/galaxy/tools/wrappers.py M lib/galaxy/util/__init__.py M lib/galaxy/util/checkers.py M lib/galaxy/util/dictifiable.py M lib/galaxy/util/hash_util.py M lib/galaxy/util/heartbeat.py M lib/galaxy/util/image_util.py M lib/galaxy/util/object_wrapper.py A lib/galaxy/util/path/__init__.py A lib/galaxy/util/path/ntpath.py A lib/galaxy/util/path/posixpath.py M lib/galaxy/util/sanitize_html.py M lib/galaxy/visualization/data_providers/basic.py M lib/galaxy/visualization/data_providers/genome.py M lib/galaxy/visualization/genomes.py M lib/galaxy/visualization/plugins/interactive_environments.py M lib/galaxy/visualization/plugins/plugin.py M lib/galaxy/web/base/controller.py M lib/galaxy/web/framework/decorators.py M lib/galaxy/web/framework/helpers/grids.py M 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lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/dataset.py R lib/galaxy/webapps/galaxy/controllers/external_service.py R lib/galaxy/webapps/galaxy/controllers/external_services.py M lib/galaxy/webapps/galaxy/controllers/library.py M lib/galaxy/webapps/galaxy/controllers/library_common.py R lib/galaxy/webapps/galaxy/controllers/request_type.py R lib/galaxy/webapps/galaxy/controllers/requests.py R lib/galaxy/webapps/galaxy/controllers/requests_admin.py R lib/galaxy/webapps/galaxy/controllers/requests_common.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/galaxy/controllers/tool_runner.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/galaxy/webapps/reports/buildapp.py M lib/galaxy/webapps/reports/controllers/system.py M lib/galaxy/webapps/tool_shed/buildapp.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/webapps/tool_shed/model/migrate/check.py M 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scripts/drmaa_external_runner.py M scripts/helper.py M scripts/loc_files/create_all_fasta_loc.py M scripts/microbes/BeautifulSoup.py M scripts/microbes/create_bacteria_loc_file.py M scripts/microbes/create_bacteria_table.py M scripts/microbes/create_nib_seq_loc_file.py M scripts/microbes/get_builds_lengths.py M scripts/microbes/harvest_bacteria.py M scripts/microbes/ncbi_to_ucsc.py M scripts/microbes/util.py M scripts/others/incorrect_gops_jobs.py M scripts/others/incorrect_gops_join_jobs.py M scripts/paster.py M scripts/rst2html.py M scripts/runtime_stats.py M scripts/tool_shed/migrate_tools_to_repositories.py M setup.cfg M static/maps/galaxy.interactive_environments.js.map M static/maps/layout/menu.js.map M static/maps/layout/page.js.map M static/maps/libs/backbone.js.map M static/maps/libs/bibtex.js.map M static/maps/libs/d3.js.map A static/maps/libs/jquery/jquery.complexify.js.map M static/maps/libs/jquery/jquery.cookie.js.map M static/maps/libs/jquery/jquery.js.map M static/maps/libs/jquery/jquery.migrate.js.map M static/maps/libs/jquery/jquery.mousewheel.js.map M static/maps/libs/raven.js.map M static/maps/libs/require.js.map M static/maps/libs/underscore.js.map M static/maps/mvc/grid/grid-view.js.map M static/maps/mvc/library/library-dataset-view.js.map M static/maps/mvc/library/library-folderlist-view.js.map M static/maps/mvc/library/library-folderrow-view.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/mvc/library/library-libraryrow-view.js.map M static/maps/mvc/library/library-librarytoolbar-view.js.map M static/maps/utils/utils.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/galaxy.interactive_environments.js M static/scripts/layout/menu.js M static/scripts/layout/page.js M static/scripts/mvc/grid/grid-view.js M static/scripts/mvc/library/library-dataset-view.js M static/scripts/mvc/library/library-folderlist-view.js M static/scripts/mvc/library/library-folderrow-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/library/library-libraryrow-view.js M static/scripts/mvc/library/library-librarytoolbar-view.js M static/scripts/utils/utils.js M static/style/blue/base.css M static/style/blue/library.css R templates/admin/external_service/common.mako R templates/admin/external_service/create_external_service.mako R templates/admin/external_service/edit_external_service.mako R templates/admin/external_service/grid.mako R templates/admin/external_service/reload_external_service_types.mako R templates/admin/external_service/view_external_service.mako R templates/admin/request_type/common.mako R templates/admin/request_type/create_request_type.mako R templates/admin/request_type/edit_request_type.mako R templates/admin/request_type/grid.mako R templates/admin/request_type/request_type_permissions.mako R templates/admin/request_type/view_request_type.mako R templates/admin/requests/grid.mako R templates/admin/requests/reject.mako R templates/admin/requests/rename_datasets.mako R templates/admin/requests/sample_datasets_grid.mako R templates/admin/requests/view_sample_dataset.mako R templates/admin/tool_shed_repository/repair_repository.mako M templates/admin/tool_shed_repository/repository_actions_menu.mako M templates/webapps/galaxy/admin/center.mako R templates/webapps/galaxy/requests/common/add_samples.mako R templates/webapps/galaxy/requests/common/common.mako R templates/webapps/galaxy/requests/common/create_request.mako R templates/webapps/galaxy/requests/common/edit_basic_request_info.mako R templates/webapps/galaxy/requests/common/edit_samples.mako R templates/webapps/galaxy/requests/common/find_samples.mako R templates/webapps/galaxy/requests/common/index.mako R templates/webapps/galaxy/requests/common/sample_dataset_transfer_status.mako R templates/webapps/galaxy/requests/common/sample_datasets.mako R templates/webapps/galaxy/requests/common/sample_state.mako R templates/webapps/galaxy/requests/common/view_request.mako R templates/webapps/galaxy/requests/common/view_request_history.mako R templates/webapps/galaxy/requests/common/view_sample.mako R templates/webapps/galaxy/requests/common/view_sample_datasets.mako R templates/webapps/galaxy/requests/common/view_sample_history.mako R templates/webapps/galaxy/requests/find_samples_index.mako R templates/webapps/galaxy/requests/grid.mako R templates/webapps/galaxy/requests/index.mako M test/base/testcase.py M test/functional/twilltestcase.py M test/shed_functional/base/twilltestcase.py M test/shed_functional/functional/test_1100_install_updated_repository_dependencies.py M test/shed_functional/functional/test_1430_repair_installed_repository.py M test/unit/managers/test_UserManager.py M test/unit/tools/test_tool_deps.py M tools/data_source/data_source.py M tools/data_source/import.py M tools/data_source/microbial_import.py M tools/data_source/microbial_import_code.py M tools/data_source/upload.py M tools/evolution/codingSnps_filter.py M tools/extract/extract_genomic_dna.py M tools/extract/liftOver_wrapper.py M tools/filters/axt_to_lav.py M tools/filters/bed_to_gff_converter.py M tools/filters/catWrapper.py M tools/filters/convert_characters.py M tools/filters/gff/extract_GFF_Features.py M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_feature_count.py M tools/filters/gff_to_bed_converter.py M tools/filters/gtf_to_bedgraph_converter.py M tools/filters/join.py M tools/filters/lav_to_bed_code.py M tools/filters/mergeCols.py M tools/filters/sff_extract.py M tools/filters/ucsc_gene_bed_to_exon_bed.py M tools/filters/ucsc_gene_bed_to_intron_bed.py M tools/filters/ucsc_gene_table_to_intervals.py M tools/genomespace/genomespace_importer.py M tools/maf/maf_by_block_number.py M tools/maf/maf_filter.py M tools/maf/maf_limit_size.py M tools/maf/maf_limit_to_species.py M tools/maf/maf_reverse_complement.py M tools/maf/maf_stats.py M tools/maf/maf_thread_for_species.py M tools/maf/maf_to_bed.py M tools/maf/vcf_to_maf_customtrack.py M tools/metag_tools/blat_wrapper.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/plotting/bar_chart.py M tools/solid_tools/maq_cs_wrapper.py M tools/solid_tools/solid_qual_stats.py M tools/sr_mapping/bfast_wrapper.py M tools/stats/aggregate_scores_in_intervals.py M tools/stats/filtering.py M tools/stats/grouping.py M tools/stats/gsummary.py Log Message: ----------- Ensure Galaxy doesn't crash when a tour is malformed. Commit: 89e843730e23ee46a6152a4683f37d99d1251cc0 https://github.com/galaxyproject/galaxy/commit/89e843730e23ee46a6152a4683f3… Author: Peter Selten <peter.selten98(a)gmail.com> Date: 2017-10-25 (Wed, 25 Oct 2017) Changed paths: M lib/galaxy/tours/__init__.py Log Message: ----------- Ensure galaxy can boot even with a malformed tour. Commit: 7b3235a71cc229988a3641c27a8d05712aa8171f https://github.com/galaxyproject/galaxy/commit/7b3235a71cc229988a3641c27a8d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-10-26 (Thu, 26 Oct 2017) Changed paths: M client/galaxy/scripts/apps/panels/admin-panel.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Rebuild client. Commit: de9f8a6094f0bc4eac9b038c0ba9efdfbd0c61bc https://github.com/galaxyproject/galaxy/commit/de9f8a6094f0bc4eac9b038c0ba9… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-10-26 (Thu, 26 Oct 2017) Changed paths: M client/galaxy/scripts/apps/panels/admin-panel.js M client/galaxy/scripts/mvc/tours.js M client/galaxy/style/less/base.less M config/plugins/tours/core.galaxy_ui.yaml M config/plugins/tours/core.history.yaml M config/plugins/tours/core.scratchbook.yaml M lib/galaxy/tours/__init__.py M static/maps/mvc/tours.js.map M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tours.js M static/style/blue/base.css Log Message: ----------- Merge branch 'selten/dev' into dev Compare: https://github.com/galaxyproject/galaxy/compare/862212ad40f4...de9f8a6094f0

1 0

[galaxyproject/infrastructure-playbook] fe919a: Relocate galaxyenv to env/galaxy
by GitHub 26 Oct '17

26 Oct '17

Branch: refs/heads/galaxyenv Home: https://github.com/galaxyproject/infrastructure-playbook Commit: fe919ae973e1c6a2b9c777624ff4b44a2ddef969 https://github.com/galaxyproject/infrastructure-playbook/commit/fe919ae973e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-26 (Thu, 26 Oct 2017) Changed paths: A env/galaxy/files/apache/galaxy-installers.conf A env/galaxy/files/jenkins/jenkins_server_user_ssh_config A env/galaxy/files/jenkins/jenkins_slave_user_ssh_config A env/galaxy/files/orval/rsyncd.xml A env/galaxy/files/ssl/athena.galaxyproject.org_cert.pem A env/galaxy/files/ssl/wildcard_cert.pem A env/galaxy/group_vars/all.yml A env/galaxy/group_vars/baseenv.yml A env/galaxy/group_vars/cvmfsstratum0servers.yml A env/galaxy/group_vars/cvmfsstratum1servers.yml A env/galaxy/group_vars/ec2hosts.yml A env/galaxy/group_vars/jenkinsservers.yml A env/galaxy/group_vars/jenkinsslaves.yml A env/galaxy/group_vars/listservers.yml A env/galaxy/group_vars/liteenv.yml A env/galaxy/group_vars/mailservers.yml A env/galaxy/group_vars/starforgebuilders.yml A env/galaxy/host_vars/athena.galaxyproject.org.yml A env/galaxy/host_vars/chouffe.galaxyproject.org.yml A env/galaxy/host_vars/cvmfs0-psu0.galaxyproject.org.yml A env/galaxy/host_vars/cvmfs0-tacc0.galaxyproject.org.yml A env/galaxy/host_vars/cvmfs1-iu0.galaxyproject.org.yml A env/galaxy/host_vars/cvmfs1-psu0.galaxyproject.org.yml A env/galaxy/host_vars/cvmfs1-tacc0.galaxyproject.org.yml A env/galaxy/host_vars/delirium.galaxyproject.org.yml A env/galaxy/host_vars/duvel.galaxyproject.org.yml A env/galaxy/host_vars/jetstream-iu0.galaxyproject.org.yml A env/galaxy/host_vars/jetstream-tacc0.galaxyproject.org.yml A env/galaxy/host_vars/leeroy.galaxyproject.org.yml A env/galaxy/host_vars/n4.galaxyproject.org.yml A env/galaxy/host_vars/n6.galaxyproject.org.yml A env/galaxy/host_vars/orval.galaxyproject.org.yml A env/galaxy/host_vars/westvleteren.galaxyproject.org.yml A env/galaxy/inventory A env/galaxy/library/README A env/galaxy/library/cron.py A env/galaxy/playbook.yml A env/galaxy/secret_group_vars/all.yml A env/galaxy/secret_group_vars/dockersslservers.yml A env/galaxy/secret_group_vars/dockerswarmmanagers.yml A env/galaxy/secret_group_vars/jenkinsslaves.yml A env/galaxy/secret_group_vars/sslwebservers.yml A env/galaxy/secret_host_vars/athena.galaxyproject.org.yml A env/galaxy/secret_host_vars/biostar.usegalaxy.org.yml A env/galaxy/secret_host_vars/chouffe.galaxyproject.org.yml A env/galaxy/secret_host_vars/cvmfs0-psu0.galaxyproject.org.yml A env/galaxy/secret_host_vars/cvmfs0-tacc0.galaxyproject.org.yml A env/galaxy/secret_host_vars/cvmfs1-iu0.galaxyproject.org.yml A env/galaxy/secret_host_vars/cvmfs1-psu0.galaxyproject.org.yml A env/galaxy/secret_host_vars/cvmfs1-tacc0.galaxyproject.org.yml A env/galaxy/secret_host_vars/default.yml A env/galaxy/secret_host_vars/delirium.galaxyproject.org.yml A env/galaxy/secret_host_vars/leeroy.galaxyproject.org.yml A env/galaxy/secret_host_vars/mjolnir0.galaxyproject.org.yml A env/galaxy/secret_host_vars/orval.galaxyproject.org.yml A env/galaxy/secret_host_vars/radegast.galaxyproject.org.yml A env/galaxy/secret_host_vars/westvleteren.galaxyproject.org.yml A env/galaxy/templates/nginx/bioarchive.j2 A env/galaxy/templates/nginx/cloudlaunch.j2 A env/galaxy/templates/nginx/depot.j2 A env/galaxy/templates/nginx/docs.j2 A env/galaxy/templates/nginx/duvel.j2 A env/galaxy/templates/nginx/eggs.j2 A env/galaxy/templates/nginx/galaxy.tools.j2 A env/galaxy/templates/nginx/galaxydomains.j2 A env/galaxy/templates/nginx/galaxyproject.j2 A env/galaxy/templates/nginx/images-proxy.j2 A env/galaxy/templates/nginx/images.j2 A env/galaxy/templates/nginx/intron.j2 A env/galaxy/templates/nginx/jenkins.j2 A env/galaxy/templates/nginx/lists.j2 A env/galaxy/templates/nginx/moin.j2 A env/galaxy/templates/nginx/new.j2 A env/galaxy/templates/nginx/orval.j2 A env/galaxy/templates/nginx/sample-data.j2 A env/galaxy/templates/nginx/screencast.j2 A env/galaxy/templates/nginx/snpeff-data.j2 A env/galaxy/templates/nginx/toolshed.tools.j2 A env/galaxy/templates/nginx/training.j2 A env/galaxy/templates/nginx/wheels.j2 A env/galaxy/templates/nginx/wiki.j2 A env/galaxy/templates/nginx/wiki_hub_rewrites.conf.j2 A env/galaxy/templates/supervisor/pypiserver.j2 R galaxyenv/files/apache/galaxy-installers.conf R galaxyenv/files/jenkins/jenkins_server_user_ssh_config R galaxyenv/files/jenkins/jenkins_slave_user_ssh_config R galaxyenv/files/orval/rsyncd.xml R galaxyenv/files/ssl/athena.galaxyproject.org_cert.pem R galaxyenv/files/ssl/wildcard_cert.pem R galaxyenv/group_vars/all.yml R galaxyenv/group_vars/baseenv.yml R galaxyenv/group_vars/cvmfsstratum0servers.yml R galaxyenv/group_vars/cvmfsstratum1servers.yml R galaxyenv/group_vars/ec2hosts.yml R galaxyenv/group_vars/jenkinsservers.yml R galaxyenv/group_vars/jenkinsslaves.yml R galaxyenv/group_vars/listservers.yml R galaxyenv/group_vars/liteenv.yml R galaxyenv/group_vars/mailservers.yml R galaxyenv/group_vars/starforgebuilders.yml R galaxyenv/host_vars/athena.galaxyproject.org.yml R galaxyenv/host_vars/chouffe.galaxyproject.org.yml R galaxyenv/host_vars/cvmfs0-psu0.galaxyproject.org.yml R galaxyenv/host_vars/cvmfs0-tacc0.galaxyproject.org.yml R galaxyenv/host_vars/cvmfs1-iu0.galaxyproject.org.yml R galaxyenv/host_vars/cvmfs1-psu0.galaxyproject.org.yml R galaxyenv/host_vars/cvmfs1-tacc0.galaxyproject.org.yml R galaxyenv/host_vars/delirium.galaxyproject.org.yml R galaxyenv/host_vars/duvel.galaxyproject.org.yml R galaxyenv/host_vars/jetstream-iu0.galaxyproject.org.yml R galaxyenv/host_vars/jetstream-tacc0.galaxyproject.org.yml R galaxyenv/host_vars/leeroy.galaxyproject.org.yml R galaxyenv/host_vars/n4.galaxyproject.org.yml R galaxyenv/host_vars/n6.galaxyproject.org.yml R galaxyenv/host_vars/orval.galaxyproject.org.yml R galaxyenv/host_vars/westvleteren.galaxyproject.org.yml R galaxyenv/inventory R galaxyenv/library/README R galaxyenv/library/cron.py R galaxyenv/playbook.yml R galaxyenv/secret_group_vars/all.yml R galaxyenv/secret_group_vars/dockersslservers.yml R galaxyenv/secret_group_vars/dockerswarmmanagers.yml R galaxyenv/secret_group_vars/jenkinsslaves.yml R galaxyenv/secret_group_vars/sslwebservers.yml R galaxyenv/secret_host_vars/athena.galaxyproject.org.yml R galaxyenv/secret_host_vars/biostar.usegalaxy.org.yml R galaxyenv/secret_host_vars/chouffe.galaxyproject.org.yml R galaxyenv/secret_host_vars/cvmfs0-psu0.galaxyproject.org.yml R galaxyenv/secret_host_vars/cvmfs0-tacc0.galaxyproject.org.yml R galaxyenv/secret_host_vars/cvmfs1-iu0.galaxyproject.org.yml R galaxyenv/secret_host_vars/cvmfs1-psu0.galaxyproject.org.yml R galaxyenv/secret_host_vars/cvmfs1-tacc0.galaxyproject.org.yml R galaxyenv/secret_host_vars/default.yml R galaxyenv/secret_host_vars/delirium.galaxyproject.org.yml R galaxyenv/secret_host_vars/leeroy.galaxyproject.org.yml R galaxyenv/secret_host_vars/mjolnir0.galaxyproject.org.yml R galaxyenv/secret_host_vars/orval.galaxyproject.org.yml R galaxyenv/secret_host_vars/radegast.galaxyproject.org.yml R galaxyenv/secret_host_vars/westvleteren.galaxyproject.org.yml R galaxyenv/templates/nginx/bioarchive.j2 R galaxyenv/templates/nginx/cloudlaunch.j2 R galaxyenv/templates/nginx/depot.j2 R galaxyenv/templates/nginx/docs.j2 R galaxyenv/templates/nginx/duvel.j2 R galaxyenv/templates/nginx/eggs.j2 R galaxyenv/templates/nginx/galaxy.tools.j2 R galaxyenv/templates/nginx/galaxydomains.j2 R galaxyenv/templates/nginx/galaxyproject.j2 R galaxyenv/templates/nginx/images-proxy.j2 R galaxyenv/templates/nginx/images.j2 R galaxyenv/templates/nginx/intron.j2 R galaxyenv/templates/nginx/jenkins.j2 R galaxyenv/templates/nginx/lists.j2 R galaxyenv/templates/nginx/moin.j2 R galaxyenv/templates/nginx/new.j2 R galaxyenv/templates/nginx/orval.j2 R galaxyenv/templates/nginx/sample-data.j2 R galaxyenv/templates/nginx/screencast.j2 R galaxyenv/templates/nginx/snpeff-data.j2 R galaxyenv/templates/nginx/toolshed.tools.j2 R galaxyenv/templates/nginx/training.j2 R galaxyenv/templates/nginx/wheels.j2 R galaxyenv/templates/nginx/wiki.j2 R galaxyenv/templates/nginx/wiki_hub_rewrites.conf.j2 R galaxyenv/templates/supervisor/pypiserver.j2 Log Message: ----------- Relocate galaxyenv to env/galaxy Commit: a42ef24ee9383f66633bcdbe21af20fea637b873 https://github.com/galaxyproject/infrastructure-playbook/commit/a42ef24ee93… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-26 (Thu, 26 Oct 2017) Changed paths: A common_env R common_env/files/ssl/docker/ca-key.pem R common_env/files/ssl/docker/ca.pem R common_env/files/ssl/docker/ca.srl R common_env/files/ssl/docker/client.pem R common_env/files/ssl/docker/client_privatekey.yml R common_env/files/ssl/docker/cvmfs1-psu0.galaxyproject.org/server.pem R common_env/files/ssl/docker/cvmfs1-psu0.galaxyproject.org/server_privatekey… R common_env/files/ssl/docker/jetstream-iu0.galaxyproject.org/server.pem R common_env/files/ssl/docker/jetstream-iu0.galaxyproject.org/server_privatek… R common_env/files/ssl/docker/jetstream-tacc0.galaxyproject.org/server-cert.p… R common_env/files/ssl/docker/jetstream-tacc0.galaxyproject.org/server_privat… R common_env/files/ssl/docker_test/ca-key.pem R common_env/files/ssl/docker_test/ca.pem R common_env/files/ssl/docker_test/ca.srl R common_env/files/ssl/docker_test/client.pem R common_env/files/ssl/docker_test/client_privatekey.yml R common_env/files/ssl/docker_test/iu-gie-test/server.pem R common_env/files/ssl/docker_test/iu-gie-test/server_privatekey.yml R common_env/files/ssl/rabbitmq/ca-key.pem R common_env/files/ssl/rabbitmq/ca.pem R common_env/files/ssl/rabbitmq/ca.srl R common_env/files/ssl/rabbitmq/galaxy08.tacc.utexas.edu/server.pem R common_env/files/ssl/rabbitmq/galaxy08.tacc.utexas.edu/server_privatekey.yml R common_env/files/ssl/wildcard_cert.pem R common_env/group_vars/baseenv/vars.yml R common_env/group_vars/baseenv/vault.yml R common_env/group_vars/sslservers/vars.yml R common_env/group_vars/sslservers/vault.yml R common_env/secret_group_vars/sslwebservers.yml R env/common A env/common/files/ssl/docker/ca-key.pem A env/common/files/ssl/docker/ca.pem A env/common/files/ssl/docker/ca.srl A env/common/files/ssl/docker/client.pem A env/common/files/ssl/docker/client_privatekey.yml A env/common/files/ssl/docker/cvmfs1-psu0.galaxyproject.org/server.pem A env/common/files/ssl/docker/cvmfs1-psu0.galaxyproject.org/server_privatekey… A env/common/files/ssl/docker/jetstream-iu0.galaxyproject.org/server.pem A env/common/files/ssl/docker/jetstream-iu0.galaxyproject.org/server_privatek… A env/common/files/ssl/docker/jetstream-tacc0.galaxyproject.org/server-cert.p… A env/common/files/ssl/docker/jetstream-tacc0.galaxyproject.org/server_privat… A env/common/files/ssl/docker_test/ca-key.pem A env/common/files/ssl/docker_test/ca.pem A env/common/files/ssl/docker_test/ca.srl A env/common/files/ssl/docker_test/client.pem A env/common/files/ssl/docker_test/client_privatekey.yml A env/common/files/ssl/docker_test/iu-gie-test/server.pem A env/common/files/ssl/docker_test/iu-gie-test/server_privatekey.yml A env/common/files/ssl/rabbitmq/ca-key.pem A env/common/files/ssl/rabbitmq/ca.pem A env/common/files/ssl/rabbitmq/ca.srl A env/common/files/ssl/rabbitmq/galaxy08.tacc.utexas.edu/server.pem A env/common/files/ssl/rabbitmq/galaxy08.tacc.utexas.edu/server_privatekey.yml A env/common/files/ssl/wildcard_cert.pem A env/common/group_vars/sshservers/vars.yml A env/common/group_vars/sshservers/vault.yml A env/common/group_vars/sslservers/vars.yml A env/common/group_vars/sslservers/vault.yml A env/common/secret_group_vars/sslwebservers.yml Log Message: ----------- Reverse common_env <-> env/common symlink Commit: a0ba5b2bd9a792c608339b4323daedecf921c0e1 https://github.com/galaxyproject/infrastructure-playbook/commit/a0ba5b2bd9a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-26 (Thu, 26 Oct 2017) Changed paths: M env/common/group_vars/sshservers/vars.yml M env/common/group_vars/sshservers/vault.yml A env/galaxy/group_vars/sshclients/vars.yml A env/galaxy/group_vars/sshclients/vault.yml A env/galaxy/group_vars/sshservers/common_vars.yml A env/galaxy/group_vars/sshservers/common_vault.yml A env/galaxy/group_vars/sshservers/vars.yml A env/galaxy/group_vars/sshservers/vault.yml M env/galaxy/inventory R env/galaxy/secret_group_vars/all.yml R jetstreamiuenv/group_vars/baseenv A jetstreamiuenv/group_vars/sshservers/common_vars.yml A jetstreamiuenv/group_vars/sshservers/common_vault.yml A jetstreamiuenv/group_vars/sshservers/vars.yml M jetstreamiuenv/inventory R jetstreamtaccenv/group_vars/baseenv A jetstreamtaccenv/group_vars/sshservers/common_vars.yml A jetstreamtaccenv/group_vars/sshservers/common_vault.yml A jetstreamtaccenv/group_vars/sshservers/vars.yml M jetstreamtaccenv/inventory R taccenv/group_vars/baseenv A taccenv/group_vars/sshservers/common_vars.yml A taccenv/group_vars/sshservers/common_vault.yml A taccenv/group_vars/sshservers/vars.yml M taccenv/inventory Log Message: ----------- Convert ssh keys out of the baseenv group to a separate sshkeys group, allow hash merging by renaming to common_sshkeys Commit: 99fe08fd5b10ce15eed7d70cec11263b11cf6c06 https://github.com/galaxyproject/infrastructure-playbook/commit/99fe08fd5b1… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-26 (Thu, 26 Oct 2017) Changed paths: M common_roles Log Message: ----------- Update common_roles for users role improvements Commit: 7dcb2ac12002fec9ea230fbec1c40b836e822e2a https://github.com/galaxyproject/infrastructure-playbook/commit/7dcb2ac1200… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-26 (Thu, 26 Oct 2017) Changed paths: A env/galaxy/group_vars/dockersslservers/vars.yml A env/galaxy/group_vars/dockersslservers/vault.yml A env/galaxy/group_vars/dockerswarmmanagers/vars.yml A env/galaxy/group_vars/dockerswarmmanagers/vault.yml R env/galaxy/group_vars/jenkinsslaves.yml A env/galaxy/group_vars/jenkinsslaves/vars.yml A env/galaxy/group_vars/jenkinsslaves/vault.yml R env/galaxy/secret_group_vars/dockersslservers.yml R env/galaxy/secret_group_vars/dockerswarmmanagers.yml R env/galaxy/secret_group_vars/jenkinsslaves.yml Log Message: ----------- Mostly convert the galaxy env to standard vars/vault group_vars Compare: https://github.com/galaxyproject/infrastructure-playbook/compare/fe919ae973…

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[galaxyproject/galaxy] fa1781: Include check for updates to dependencies in tox a...
by GitHub 26 Oct '17

26 Oct '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: fa178108d6bbd1defd2bfcc177f23d98f9d8c9ab https://github.com/galaxyproject/galaxy/commit/fa178108d6bbd1defd2bfcc177f2… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-10 (Tue, 10 Oct 2017) Changed paths: M .travis.yml M Makefile M tox.ini Log Message: ----------- Include check for updates to dependencies in tox and Makefile. Commit: 862212ad40f408978a29dcc2c2e386ba087cb39c https://github.com/galaxyproject/galaxy/commit/862212ad40f408978a29dcc2c2e3… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-10-26 (Thu, 26 Oct 2017) Changed paths: M .travis.yml M Makefile M tox.ini Log Message: ----------- Merge pull request #4788 from jmchilton/check_dependencies Include check for updates to dependencies in tox, Makefile, Travis. Compare: https://github.com/galaxyproject/galaxy/compare/82df013b66f9...862212ad40f4

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[galaxyproject/galaxy] ada0be: Updated QUnit testing.
by GitHub 26 Oct '17

26 Oct '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ada0be18f2e975ecdee8b24a4ba1c3ec06327a5d https://github.com/galaxyproject/galaxy/commit/ada0be18f2e975ecdee8b24a4ba1… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-25 (Wed, 25 Oct 2017) Changed paths: M test/qunit/Gruntfile.js M test/qunit/package.json M test/qunit/test-app.js M test/qunit/test-common.js R test/qunit/test-libs/qunit-1.23.1.css R test/qunit/test-libs/qunit-1.23.1.js R test/qunit/test-libs/sinon-1.17.7.js R test/qunit/test-libs/sinon-qunit-1.0.0.js M test/qunit/tests/form_tests.js M test/qunit/tests/galaxy-app-base.js M test/qunit/tests/graph.js M test/qunit/tests/hda-base.js M test/qunit/tests/history_contents_model_tests.js M test/qunit/tests/job-dag.js M test/qunit/tests/list-of-pairs-collection-creator.js M test/qunit/tests/masthead_tests.js M test/qunit/tests/metrics-logger.js M test/qunit/tests/modal_tests.js M test/qunit/tests/page_tests.js M test/qunit/tests/popover_tests.js M test/qunit/tests/ui_tests.js M test/qunit/tests/upload_dialog_tests.js M test/qunit/tests/utils_test.js M test/qunit/tests/workflow_editor_tests.js Log Message: ----------- Updated QUnit testing. - Update to QUnit from 1.23 to 2.0. - Update Sinon from 1.17 to 4.0.1. - Replace sinon-qunit with just basic calls to sinon itself (sinon-qunit not compatible with QUnit 2.0). - Replace all QUnit globals with dependency injected values (a lot of this had to be done for QUnit 2.0 anyway). - Improved error reporting in test-common.js if things don't go well loading modules. - Improved verbose logging in test Gruntfile. - Replace in-repo sinon and QUnit asserts (JS/CSS) with npm packges. Commit: 82df013b66f94c3acbf5e77202d9d9dec54c7767 https://github.com/galaxyproject/galaxy/commit/82df013b66f94c3acbf5e77202d9… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-10-26 (Thu, 26 Oct 2017) Changed paths: M test/qunit/Gruntfile.js M test/qunit/package.json M test/qunit/test-app.js M test/qunit/test-common.js R test/qunit/test-libs/qunit-1.23.1.css R test/qunit/test-libs/qunit-1.23.1.js R test/qunit/test-libs/sinon-1.17.7.js R test/qunit/test-libs/sinon-qunit-1.0.0.js M test/qunit/tests/form_tests.js M test/qunit/tests/galaxy-app-base.js M test/qunit/tests/graph.js M test/qunit/tests/hda-base.js M test/qunit/tests/history_contents_model_tests.js M test/qunit/tests/job-dag.js M test/qunit/tests/list-of-pairs-collection-creator.js M test/qunit/tests/masthead_tests.js M test/qunit/tests/metrics-logger.js M test/qunit/tests/modal_tests.js M test/qunit/tests/page_tests.js M test/qunit/tests/popover_tests.js M test/qunit/tests/ui_tests.js M test/qunit/tests/upload_dialog_tests.js M test/qunit/tests/utils_test.js M test/qunit/tests/workflow_editor_tests.js Log Message: ----------- Merge pull request #4855 from jmchilton/qunit_2.0 Updated QUnit testing. Compare: https://github.com/galaxyproject/galaxy/compare/efc9dbfb6cee...82df013b66f9

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[galaxyproject/infrastructure-playbook] fd646f: Set the pypiserver fallback URL to https://pypi in...
by GitHub 26 Oct '17

26 Oct '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: fd646f57d366dc1df48b86cf557c89105c07df91 https://github.com/galaxyproject/infrastructure-playbook/commit/fd646f57d36… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-26 (Thu, 26 Oct 2017) Changed paths: M galaxyenv/templates/supervisor/pypiserver.j2 Log Message: ----------- Set the pypiserver fallback URL to https://pypi instead of http:// due to PyPI discontinuing redirection of API endpoints. The default should be fixed with the release of a fix for pypiserver/pypiserver#179.

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[galaxyproject/galaxy] 08cb27: Add various elements to the Tool XML doc page
by GitHub 26 Oct '17

26 Oct '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 08cb278cc9612a70dcb9dd77ff3bfbdfd333ce2b https://github.com/galaxyproject/galaxy/commit/08cb278cc9612a70dcb9dd77ff3b… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-10-26 (Thu, 26 Oct 2017) Changed paths: M doc/schema_template.md M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Add various elements to the Tool XML doc page In particular: - macros - edam_topics - edam_operations - environment_variables and subelement - request_param_translation and subelements Also: - reorder elements to follow IUC coding style - in examples: - use lowercase ``true`` and ``false`` for boolean attributes - add/use single quotes - minor doc fixes Commit: efc9dbfb6ceeaa3b9e2441a14417ba4f3913b8ef https://github.com/galaxyproject/galaxy/commit/efc9dbfb6ceeaa3b9e2441a14417… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-26 (Thu, 26 Oct 2017) Changed paths: M doc/schema_template.md M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Merge pull request #4871 from nsoranzo/tool_schema_improv Add various elements to the Tool XML doc page Compare: https://github.com/galaxyproject/galaxy/compare/7cfbb56a550c...efc9dbfb6cee

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[galaxyproject/usegalaxy-playbook] 9d36d8: Increase memory for cummeRbund and run DEXseq in t...
by GitHub 26 Oct '17

26 Oct '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 9d36d82b142abcca81d79010a78ffa07c6cbd846 https://github.com/galaxyproject/usegalaxy-playbook/commit/9d36d82b142abcca… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-25 (Wed, 25 Oct 2017) Changed paths: M env/main/templates/galaxy/config/job_conf.xml.j2 Log Message: ----------- Increase memory for cummeRbund and run DEXseq in the multi partition. Commit: 51582db4caee56d1769b8a1908a7be962a7b64c0 https://github.com/galaxyproject/usegalaxy-playbook/commit/51582db4caee56d1… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-26 (Thu, 26 Oct 2017) Changed paths: M env/common/files/galaxy/dynamic_rules/multi_dynamic_walltime.py M env/main/files/galaxy/galaxy_version.yml M env/test/files/galaxy/galaxy_version.yml Log Message: ----------- Merge branch 'master' of github.com:/galaxyproject/usegalaxy-playbook Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/6c09553c4706...…

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