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

[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 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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

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[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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