- galaxy-commits - lists.galaxyproject.org

[galaxyproject/infrastructure-playbook] 50f4d0: Migrate more web stuff from the private playbook, ...
by GitHub 22 Nov '16

22 Nov '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 50f4d01ef91a41ff21f2c181cdc2aa707d60982a https://github.com/galaxyproject/infrastructure-playbook/commit/50f4d01ef91… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-11-22 (Tue, 22 Nov 2016) Changed paths: M common_env/secret_group_vars/sslwebservers.yml M galaxyenv/files/ssl/wildcard_cert.pem M galaxyenv/host_vars/chouffe.galaxyproject.org.yml M galaxyenv/inventory A galaxyenv/secret_host_vars/chouffe.galaxyproject.org.yml M galaxyenv/secret_host_vars/delirium.galaxyproject.org.yml A galaxyenv/templates/nginx/intron.j2 A galaxyenv/templates/nginx/new.j2 A galaxyenv/templates/nginx/wiki.j2 Log Message: ----------- Migrate more web stuff from the private playbook, add new.galaxyproject.org

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[galaxyproject/usegalaxy-playbook] 56bf24: Fix IEs
by GitHub 22 Nov '16

22 Nov '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 56bf24a6db259bb80f0fddfea082175185be70cc https://github.com/galaxyproject/usegalaxy-playbook/commit/56bf24a6db259bb8… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-11-22 (Tue, 22 Nov 2016) Changed paths: M galaxy.yml M production/secret_vars/galaxyservers.yml M roles/galaxyprojectdotorg.interactive_environments/defaults/main.yml M roles/galaxyprojectdotorg.interactive_environments/meta/.galaxy_install_info R roles/galaxyprojectdotorg.interactive_environments/templates/ipython_apache.conf.j2 R roles/galaxyprojectdotorg.interactive_environments/templates/ipython_nginx.conf.j2 A roles/galaxyprojectdotorg.interactive_environments/templates/jupyter_apache.conf.j2 A roles/galaxyprojectdotorg.interactive_environments/templates/jupyter_nginx.conf.j2 M stage/secret_vars/galaxyservers.yml Log Message: ----------- Fix IEs

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[galaxyproject/usegalaxy-playbook] 7bd0ad: Disable sentry logging on Main so logs are readabl...
by GitHub 22 Nov '16

22 Nov '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 7bd0ad190d148494f9430b23b1f9ab68e9936524 https://github.com/galaxyproject/usegalaxy-playbook/commit/7bd0ad190d148494… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-11-22 (Tue, 22 Nov 2016) Changed paths: M production/group_vars/galaxyservers.yml Log Message: ----------- Disable sentry logging on Main so logs are readable

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[galaxyproject/usegalaxy-playbook] 34b210: Update Main
by GitHub 22 Nov '16

22 Nov '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 34b210bb6ad8ed489b3466cc041f32518c203fe8 https://github.com/galaxyproject/usegalaxy-playbook/commit/34b210bb6ad8ed48… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-11-21 (Mon, 21 Nov 2016) Changed paths: M production/galaxy_version.yml Log Message: ----------- Update Main

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[galaxyproject/galaxy] c122e7: Fixes for core.galaxy_ui.yaml.
by GitHub 21 Nov '16

21 Nov '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c122e74240fb35222d5d2d0f0b08e783dc0d561a https://github.com/galaxyproject/galaxy/commit/c122e74240fb35222d5d2d0f0b08… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-11-21 (Mon, 21 Nov 2016) Changed paths: M config/plugins/tours/core.galaxy_ui.yaml Log Message: ----------- Fixes for core.galaxy_ui.yaml. Neither of these prevent the tour from working but I think they are bugs. The extra click isn't an elemment that is clickable at that point in the tour and the referenced id isn't available so nothing in particular is tagged in the UI at that point. Commit: 097300ea6219e14b66b23a0e05f2808b16f10015 https://github.com/galaxyproject/galaxy/commit/097300ea6219e14b66b23a0e05f2… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-11-21 (Mon, 21 Nov 2016) Changed paths: M config/plugins/tours/core.galaxy_ui.yaml Log Message: ----------- Merge pull request #3206 from jmchilton/tour_fixes Fixes for core.galaxy_ui.yaml. Compare: https://github.com/galaxyproject/galaxy/compare/d2c95b43fa33...097300ea6219

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[galaxyproject/galaxy] 74d8fa: Change 'History Actions' to 'Current History' in h...
by GitHub 21 Nov '16

21 Nov '16

Branch: refs/heads/release_16.10 Home: https://github.com/galaxyproject/galaxy Commit: 74d8faac9f07407ac9df344a78c9ecb06c178f93 https://github.com/galaxyproject/galaxy/commit/74d8faac9f07407ac9df344a78c9… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-11-21 (Mon, 21 Nov 2016) Changed paths: M client/galaxy/scripts/mvc/history/options-menu.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/history/options-menu.js Log Message: ----------- Change 'History Actions' to 'Current History' in history options menu. as it was before 1cc57b1eb2c295dbd68837c864740b6ff079b83d. Commit: ec08ec60bb4dadaf6f8759f9dce79f764f26c909 https://github.com/galaxyproject/galaxy/commit/ec08ec60bb4dadaf6f8759f9dce7… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-11-21 (Mon, 21 Nov 2016) Changed paths: M client/galaxy/scripts/mvc/history/options-menu.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/history/options-menu.js Log Message: ----------- Merge pull request #3205 from blankenberg/history-current-options-name_16.10 [16.10] Change 'History Actions' to 'Current History' in history options menu. Compare: https://github.com/galaxyproject/galaxy/compare/aadc14d967c3...ec08ec60bb4d

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[galaxyproject/usegalaxy-playbook] 74f97c: First pass at a uWSGI zerg mode setup. Requires th...
by GitHub 21 Nov '16

21 Nov '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 74f97c6ac5b03d254759e2f5582d28348ad7f9e4 https://github.com/galaxyproject/usegalaxy-playbook/commit/74f97c6ac5b03d25… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-11-21 (Mon, 21 Nov 2016) Changed paths: M templates/galaxy/test.galaxyproject.org/config/uwsgi.ini.j2 M templates/galaxy/usegalaxy.org/config/uwsgi.ini.j2 M templates/supervisor/galaxy.j2 Log Message: ----------- First pass at a uWSGI zerg mode setup. Requires the uWSGI author's one-off spinningfifo plugin from an email and has a bad race condition encountered when starting zerglings simultaneously: Both will attempt to write `2p` to the running fifo at the same time and both will attempt to grab the `new` fifo at the same time, and one or both will end up in the running state, unpaused. Staggering starting/restarting can be used to solve this but hopefully I can come up with a better solution. uWSGI/server full restarts will need to be hand-held for now. But `galaxy graceful` and the new `galaxy gracefuluwsgi` work very nice.

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[galaxyproject/usegalaxy-playbook] 70201c: Take down downtime message
by GitHub 21 Nov '16

21 Nov '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 70201ca9de45477f2a7c082fce3d4799580c0ff0 https://github.com/galaxyproject/usegalaxy-playbook/commit/70201ca9de45477f… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-11-21 (Mon, 21 Nov 2016) Changed paths: M production/group_vars/galaxyservers.yml M stage/group_vars/galaxyservers.yml Log Message: ----------- Take down downtime message

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[galaxyproject/galaxy] 6fd58a: Merge pull request #3191 from dannon/version-16.10
by GitHub 21 Nov '16

21 Nov '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 6fd58afa6daf708f373513782ac907c154c266da https://github.com/galaxyproject/galaxy/commit/6fd58afa6daf708f373513782ac9… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-11-17 (Thu, 17 Nov 2016) Changed paths: M lib/galaxy/version.py Log Message: ----------- Merge pull request #3191 from dannon/version-16.10 Update version to 16.10.rc1 Commit: 5c4ac18b44263df72b25826c03d8c2509ca68a1a https://github.com/galaxyproject/galaxy/commit/5c4ac18b44263df72b25826c03d8… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-11-18 (Fri, 18 Nov 2016) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/tool-panel.js M client/galaxy/scripts/mvc/tool/tools.js M lib/galaxy/webapps/galaxy/controllers/root.py M static/maps/mvc/tool/tools.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tools.js Log Message: ----------- remove unused override this caused Help/Search to point at /root/tool_search Commit: 3f27777e76086ac94c95003882bb82003c277b4e https://github.com/galaxyproject/galaxy/commit/3f27777e76086ac94c95003882bb… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-11-18 (Fri, 18 Nov 2016) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/tool-panel.js M client/galaxy/scripts/mvc/tool/tools.js M lib/galaxy/webapps/galaxy/controllers/root.py M static/maps/mvc/tool/tools.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tools.js Log Message: ----------- Merge pull request #3198 from martenson/fix-search-config [16.10] remove unused (and unintended) config override Commit: 548d3e6f05b722301deefada71d5dafda81a1881 https://github.com/galaxyproject/galaxy/commit/548d3e6f05b722301deefada71d5… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-11-21 (Mon, 21 Nov 2016) Changed paths: M client/galaxy/scripts/mvc/history/options-menu.js Log Message: ----------- Fixes for deleting histories broken in 1cc57b1eb2c295dbd68837c864740b6ff079b83d Commit: 5ba820116365ad42dd24e099b747b40d399e6dee https://github.com/galaxyproject/galaxy/commit/5ba820116365ad42dd24e099b747… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-11-21 (Mon, 21 Nov 2016) Changed paths: M static/maps/mvc/history/options-menu.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/history/options-menu.js Log Message: ----------- Pack scripts Commit: aadc14d967c30683a10e68df61b82bb4f805de98 https://github.com/galaxyproject/galaxy/commit/aadc14d967c30683a10e68df61b8… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-11-21 (Mon, 21 Nov 2016) Changed paths: M client/galaxy/scripts/mvc/history/options-menu.js M static/maps/mvc/history/options-menu.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/history/options-menu.js Log Message: ----------- Merge pull request #3203 from blankenberg/fix_history_delete_16.10 [16.10] Fixes for deleting histories Commit: d2c95b43fa33f9f4b14d274ffa60beb03a80fbb6 https://github.com/galaxyproject/galaxy/commit/d2c95b43fa33f9f4b14d274ffa60… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-11-21 (Mon, 21 Nov 2016) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/tool-panel.js M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/mvc/tool/tools.js M lib/galaxy/webapps/galaxy/controllers/root.py M static/maps/mvc/history/options-menu.js.map M static/maps/mvc/tool/tools.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/history/options-menu.js M static/scripts/mvc/tool/tools.js Log Message: ----------- Merge pull request #3204 from galaxyproject/release_16.10 Merge release_16.10 into dev Compare: https://github.com/galaxyproject/galaxy/compare/78b533d1b544...d2c95b43fa33

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[galaxyproject/galaxy] 548d3e: Fixes for deleting histories broken in 1cc57b1eb2c...
by GitHub 21 Nov '16

21 Nov '16

Branch: refs/heads/release_16.10 Home: https://github.com/galaxyproject/galaxy Commit: 548d3e6f05b722301deefada71d5dafda81a1881 https://github.com/galaxyproject/galaxy/commit/548d3e6f05b722301deefada71d5… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-11-21 (Mon, 21 Nov 2016) Changed paths: M client/galaxy/scripts/mvc/history/options-menu.js Log Message: ----------- Fixes for deleting histories broken in 1cc57b1eb2c295dbd68837c864740b6ff079b83d Commit: 5ba820116365ad42dd24e099b747b40d399e6dee https://github.com/galaxyproject/galaxy/commit/5ba820116365ad42dd24e099b747… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-11-21 (Mon, 21 Nov 2016) Changed paths: M static/maps/mvc/history/options-menu.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/history/options-menu.js Log Message: ----------- Pack scripts Commit: aadc14d967c30683a10e68df61b82bb4f805de98 https://github.com/galaxyproject/galaxy/commit/aadc14d967c30683a10e68df61b8… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-11-21 (Mon, 21 Nov 2016) Changed paths: M client/galaxy/scripts/mvc/history/options-menu.js M static/maps/mvc/history/options-menu.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/history/options-menu.js Log Message: ----------- Merge pull request #3203 from blankenberg/fix_history_delete_16.10 [16.10] Fixes for deleting histories Compare: https://github.com/galaxyproject/galaxy/compare/3f27777e7608...aadc14d967c3

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