galaxy-commits July 2017

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[galaxyproject/usegalaxy-playbook] 692663: Fix integrated_tool_panel (from old version).
by GitHub 20 Jul '17

20 Jul '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 692663d7eab7dad49fe73f602f0b49f609ac3437 https://github.com/galaxyproject/usegalaxy-playbook/commit/692663d7eab7dad4… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-07-20 (Thu, 20 Jul 2017) Changed paths: M env/main/files/galaxy/var/integrated_tool_panel.xml Log Message: ----------- Fix integrated_tool_panel (from old version).

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[galaxyproject/infrastructure-playbook] 91921f: Set up everyone's favorite midday email
by GitHub 19 Jul '17

19 Jul '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 91921fe7701a9f7b42936da7f648123cf842f31a https://github.com/galaxyproject/infrastructure-playbook/commit/91921fe7701… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-07-19 (Wed, 19 Jul 2017) Changed paths: A taccenv/files/galaxy/cancelled.sh M taccenv/host_vars/galaxy-db-02.tacc.utexas.edu/vars.yml Log Message: ----------- Set up everyone's favorite midday email

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[galaxyproject/usegalaxy-playbook] deaf45: Updated integrated tool panel (hope this is correc...
by GitHub 19 Jul '17

19 Jul '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: deaf45fb36877cf49a2b65baf95f3d8a271c8a55 https://github.com/galaxyproject/usegalaxy-playbook/commit/deaf45fb36877cf4… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-07-19 (Wed, 19 Jul 2017) Changed paths: M env/main/files/galaxy/var/integrated_tool_panel.xml Log Message: ----------- Updated integrated tool panel (hope this is correct?) Commit: 7c21a8e8e511076c9d71d46f9a518815de1874ff https://github.com/galaxyproject/usegalaxy-playbook/commit/7c21a8e8e511076c… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-07-19 (Wed, 19 Jul 2017) Changed paths: M env/common/files/galaxy/dynamic_rules/multi_dynamic_walltime.py Log Message: ----------- Increased logging for rnastar rule Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/6f7c495ed478...…

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[galaxyproject/usegalaxy-playbook] 6f7c49: Additional Main -> CentOS 7 fixes and configs
by GitHub 19 Jul '17

19 Jul '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 6f7c495ed478bee9e5a54956f520ba543594ffe1 https://github.com/galaxyproject/usegalaxy-playbook/commit/6f7c495ed478bee9… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-07-19 (Wed, 19 Jul 2017) Changed paths: A env/common/_inc_gie.yml A env/common/gie.yml M env/common/stack.yml M env/common/update.yml A env/main/_inc_gie.yml M env/main/files/galaxy/var/shed_tool_conf.xml A env/main/gie.yml M env/main/group_vars/galaxyjobservers.yml M env/main/group_vars/galaxyservers/vars.yml M env/main/group_vars/galaxyservers/vault.yml M env/main/group_vars/galaxystagingservers.yml M env/main/group_vars/galaxywebservers.yml M env/main/group_vars/pulsarservers/vault.yml M env/main/group_vars/webservers.yml M env/main/templates/nginx/usegalaxy.j2 A env/test/_inc_gie.yml A env/test/gie.yml M env/test/group_vars/galaxyservers/vars.yml M env/test/group_vars/galaxyservers/vault.yml M env/test/group_vars/pulsarservers/vault.yml M roles/usegalaxy/defaults M roles/usegalaxy/templates/galaxyctl.j2 Log Message: ----------- Additional Main -> CentOS 7 fixes and configs

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[galaxyproject/infrastructure-playbook] a2f70b: Distribute docker SSL certs
by GitHub 19 Jul '17

19 Jul '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: a2f70be85d41484064a66aad78a17f69eb415aa8 https://github.com/galaxyproject/infrastructure-playbook/commit/a2f70be85d4… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-07-19 (Wed, 19 Jul 2017) Changed paths: M taccenv/group_vars/maingalaxyservers/vars.yml Log Message: ----------- Distribute docker SSL certs

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[galaxyproject/infrastructure-playbook] efce45: Added GIE dirs
by GitHub 19 Jul '17

19 Jul '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: efce455add8edc98be60473bb812676ce7ff2d8c https://github.com/galaxyproject/infrastructure-playbook/commit/efce455add8… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-07-19 (Wed, 19 Jul 2017) Changed paths: M taccenv/group_vars/galaxyservers.yml Log Message: ----------- Added GIE dirs

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[galaxyproject/galaxy] d07913: Use dict format for saved visualizations grid
by GitHub 19 Jul '17

19 Jul '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d0791360997d23a4550317dbbcf689740cf0c51a https://github.com/galaxyproject/galaxy/commit/d0791360997d23a4550317dbbcf6… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-07-13 (Thu, 13 Jul 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/layout/menu.js M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M static/maps/layout/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/layout/menu.js R templates/webapps/galaxy/visualization/list.mako Log Message: ----------- Use dict format for saved visualizations grid Commit: ab56aad7311346d3386aefa87b739c40443bfc90 https://github.com/galaxyproject/galaxy/commit/ab56aad7311346d3386aefa87b73… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-07-13 (Thu, 13 Jul 2017) Changed paths: A client/galaxy/scripts/mvc/visualization/visualization-list.js A static/maps/mvc/visualization/visualization-list.js.map A static/scripts/mvc/visualization/visualization-list.js Log Message: ----------- Add packed files Commit: c2727661073e985fa55b5ec73a32df599b0e9e32 https://github.com/galaxyproject/galaxy/commit/c2727661073e985fa55b5ec73a32… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-07-13 (Thu, 13 Jul 2017) Changed paths: M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/viz/circster.js M client/galaxy/scripts/viz/trackster.js M static/maps/layout/menu.js.map M static/maps/viz/circster.js.map M static/maps/viz/trackster.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/menu.js M static/scripts/viz/circster.js M static/scripts/viz/trackster.js Log Message: ----------- Adjust existing urls to new client side route Commit: 03369c3ec481c998605fe8bc1f5192769c671cca https://github.com/galaxyproject/galaxy/commit/03369c3ec481c998605fe8bc1f51… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-07-13 (Thu, 13 Jul 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js A client/galaxy/scripts/mvc/grid/grid-shared.js R client/galaxy/scripts/mvc/page/page-list.js R client/galaxy/scripts/mvc/visualization/visualization-list.js M lib/galaxy/webapps/galaxy/controllers/page.py M lib/galaxy/webapps/galaxy/controllers/visualization.py A static/maps/mvc/grid/grid-shared.js.map R static/maps/mvc/page/page-list.js.map R static/maps/mvc/visualization/visualization-list.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 A static/scripts/mvc/grid/grid-shared.js R static/scripts/mvc/page/page-list.js R static/scripts/mvc/visualization/visualization-list.js Log Message: ----------- Unify shared grid views for visualizations and pages, always display directly shared visualizations Commit: 533b1e4faded54afe29cbf59892a785a19feccef https://github.com/galaxyproject/galaxy/commit/533b1e4faded54afe29cbf59892a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-07-13 (Thu, 13 Jul 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/visualization.py Log Message: ----------- Fix controller side routing Commit: f4f063b2f7ed3912c2223daa898cc66a261ba4a3 https://github.com/galaxyproject/galaxy/commit/f4f063b2f7ed3912c2223daa898c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-07-13 (Thu, 13 Jul 2017) Changed paths: M templates/webapps/galaxy/requests/common/common.mako Log Message: ----------- Adjust list route for histories in request template Commit: 3bf019b03ed5901dd147ab319b11c03ad66740f6 https://github.com/galaxyproject/galaxy/commit/3bf019b03ed5901dd147ab319b11… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-07-17 (Mon, 17 Jul 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js A client/package-lock.json M lib/galaxy/jobs/actions/post.py M lib/galaxy/managers/collections.py M lib/galaxy/managers/tags.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/data/__init__.py M lib/galaxy/tools/toolbox/base.py M scripts/runtime_stats.py M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Merge branch 'dev' into grid_saved_viz Commit: fe038dcb4e977766593cea48d293c589a094d001 https://github.com/galaxyproject/galaxy/commit/fe038dcb4e977766593cea48d293… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-07-19 (Wed, 19 Jul 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/layout/menu.js A client/galaxy/scripts/mvc/grid/grid-shared.js R client/galaxy/scripts/mvc/page/page-list.js M client/galaxy/scripts/viz/circster.js M client/galaxy/scripts/viz/trackster.js M client/package-lock.json M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/page.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M static/maps/layout/menu.js.map A static/maps/mvc/grid/grid-shared.js.map R static/maps/mvc/page/page-list.js.map M static/maps/viz/circster.js.map M static/maps/viz/trackster.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/menu.js A static/scripts/mvc/grid/grid-shared.js R static/scripts/mvc/page/page-list.js M static/scripts/viz/circster.js M static/scripts/viz/trackster.js M templates/webapps/galaxy/requests/common/common.mako R templates/webapps/galaxy/visualization/list.mako Log Message: ----------- Merge remote-tracking branch 'guerler/grid_saved_viz' into dev Rebuild and package-lock update. Compare: https://github.com/galaxyproject/galaxy/compare/7351252b21c9...fe038dcb4e97

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[galaxyproject/infrastructure-playbook] d40f43: Dead JS instances
by GitHub 19 Jul '17

19 Jul '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: d40f437dc360604c41305959de9b1195ddb55e0d https://github.com/galaxyproject/infrastructure-playbook/commit/d40f437dc36… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-07-19 (Wed, 19 Jul 2017) Changed paths: M jetstreamiuenv/inventory M jetstreamtaccenv/inventory Log Message: ----------- Dead JS instances

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[galaxyproject/infrastructure-playbook] bd7908: Update SlurmDBD port
by GitHub 19 Jul '17

19 Jul '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: bd79089db069295b7e653405239fe3a4d67be4d5 https://github.com/galaxyproject/infrastructure-playbook/commit/bd79089db06… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-07-19 (Wed, 19 Jul 2017) Changed paths: M jetstream_common/templates/slurm/slurm.conf.j2 M taccenv/group_vars/slurmclients.yml M taccenv/templates/slurm/slurm.conf.j2 Log Message: ----------- Update SlurmDBD port

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[galaxyproject/infrastructure-playbook] a2e6b9: Slurm upgrades
by GitHub 19 Jul '17

19 Jul '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: a2e6b9c3537903a681075613ebfa388837fd7b67 https://github.com/galaxyproject/infrastructure-playbook/commit/a2e6b9c3537… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-07-19 (Wed, 19 Jul 2017) Changed paths: M jetstream_common/templates/slurm/slurm.conf.j2 M roles/slurm/tasks/main.yml M roles/slurm/tasks/slurmctld.yml M roles/slurm/tasks/slurmd.yml M roles/slurm/tasks/slurmdbd.yml M taccenv/group_vars/slurmclients.yml M taccenv/inventory Log Message: ----------- Slurm upgrades

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galaxy-commits July 2017