- galaxy-commits - lists.galaxyproject.org

[galaxyproject/usegalaxy-playbook] 0b9825: pylon1 -> pylon5
by GitHub 19 Apr '17

19 Apr '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 0b9825782968350d7b888360a2941fffcadc9793 https://github.com/galaxyproject/usegalaxy-playbook/commit/0b9825782968350d… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-04-18 (Tue, 18 Apr 2017) Changed paths: M production/host_vars/br005.bridges.psc.edu.yml Log Message: ----------- pylon1 -> pylon5

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[galaxyproject/usegalaxy-playbook] bd96bc: Drop the bootstrap script
by GitHub 18 Apr '17

18 Apr '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: bd96bc4406cc67bc067eeffaf5af66f1f52ea11f https://github.com/galaxyproject/usegalaxy-playbook/commit/bd96bc4406cc67bc… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-04-04 (Tue, 04 Apr 2017) Changed paths: R bootstrap-ansible.bash Log Message: ----------- Drop the bootstrap script Commit: 9ae7ebd5030a611879af50da0123089c621c73ad https://github.com/galaxyproject/usegalaxy-playbook/commit/9ae7ebd5030a6118… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-04-18 (Tue, 18 Apr 2017) Changed paths: M production/files/interactive_environments/plugins/bam_iobio/config/bam_iobio.ini.sample M production/files/interactive_environments/plugins/bam_iobio/static/js/bam_iobio.js M production/files/interactive_environments/plugins/bam_iobio/templates/bam_iobio.mako M production/files/interactive_environments/plugins/common/templates/ie.mako R production/files/interactive_environments/plugins/ethercalc/config/allowed_images.yml.sample R production/files/interactive_environments/plugins/ethercalc/config/ethercalc.ini.sample R production/files/interactive_environments/plugins/ethercalc/config/ethercalc.xml R production/files/interactive_environments/plugins/ethercalc/static/js/ethercalc.js R production/files/interactive_environments/plugins/ethercalc/templates/ethercalc.mako M production/files/interactive_environments/plugins/jupyter/config/allowed_images.yml.sample M production/files/interactive_environments/plugins/jupyter/config/jupyter.ini.sample M production/files/interactive_environments/plugins/jupyter/config/jupyter.xml M production/files/interactive_environments/plugins/jupyter/static/js/jupyter.js M production/files/interactive_environments/plugins/jupyter/templates/jupyter.mako M production/files/interactive_environments/plugins/neo/config/neo.ini.sample M production/files/interactive_environments/plugins/neo/static/js/neo.js M production/files/interactive_environments/plugins/neo/templates/neo.mako M production/files/interactive_environments/plugins/phinch/config/phinch.ini.sample M production/files/interactive_environments/plugins/phinch/static/js/phinch.js M production/files/interactive_environments/plugins/phinch/templates/phinch.mako M production/files/interactive_environments/plugins/rstudio/config/rstudio.ini.sample M production/files/interactive_environments/plugins/rstudio/static/js/rstudio.js M production/files/interactive_environments/plugins/rstudio/templates/rstudio.mako M production/files/interactive_environments/proxy/lib/mapper.js M roles/galaxyprojectdotorg.interactive_environments/meta/.galaxy_install_info M roles/galaxyprojectdotorg.interactive_environments/tasks/extract_component.yml M roles/galaxyprojectdotorg.interactive_environments/tasks/synchronize_components.yml M templates/galaxy/usegalaxy.org/config/job_conf.xml.j2 Log Message: ----------- Merge branch 'master' of github.com:/galaxyproject/usegalaxy-playbook Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/ccadc26f89c4...…

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[galaxyproject/usegalaxy-playbook] 1a0914: Upgrade Test
by GitHub 18 Apr '17

18 Apr '17

Branch: refs/heads/reorg Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 1a09141d4a929d05c02cfbf998efc19eee10caea https://github.com/galaxyproject/usegalaxy-playbook/commit/1a09141d4a929d05… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-04-18 (Tue, 18 Apr 2017) Changed paths: M env/test/files/galaxy/galaxy_version.yml M env/test/files/interactive_environments/plugins/.ansible_ie_role_current_version M env/test/files/interactive_environments/proxy/.ansible_ie_role_current_version Log Message: ----------- Upgrade Test Commit: 7b02be926f63742dab881d38cda7492af18d1ba6 https://github.com/galaxyproject/usegalaxy-playbook/commit/7b02be926f63742d… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-04-18 (Tue, 18 Apr 2017) Changed paths: M env/test/host_vars/br005.bridges.psc.edu.yml Log Message: ----------- pylon1 -> pylon5 Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/8dd328d77980...…

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[galaxyproject/usegalaxy-playbook] 8dd328: Fix GIE proxy port
by GitHub 18 Apr '17

18 Apr '17

Branch: refs/heads/reorg Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 8dd328d77980aaff3353f0cc554ebf76fbcb8e7f https://github.com/galaxyproject/usegalaxy-playbook/commit/8dd328d77980aaff… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-04-18 (Tue, 18 Apr 2017) Changed paths: M env/common/templates/supervisor/galaxy_gie_proxy.j2 Log Message: ----------- Fix GIE proxy port

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[galaxyproject/usegalaxy-playbook] 812c4c: Move Test GIEs to Swarm
by GitHub 18 Apr '17

18 Apr '17

Branch: refs/heads/reorg Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 812c4c3451e2174aa07dd1566b0365210c408eee https://github.com/galaxyproject/usegalaxy-playbook/commit/812c4c3451e2174a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-04-18 (Tue, 18 Apr 2017) Changed paths: M env/common/config.yml M env/test/group_vars/galaxyservers/vars.yml Log Message: ----------- Move Test GIEs to Swarm

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[galaxyproject/usegalaxy-playbook] 6cca38: IE fixes
by GitHub 18 Apr '17

18 Apr '17

Branch: refs/heads/reorg Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 6cca389e2fa650cb6479eead5b6866b6f3f0622d https://github.com/galaxyproject/usegalaxy-playbook/commit/6cca389e2fa650cb… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-04-17 (Mon, 17 Apr 2017) Changed paths: M env/common/config.yml M env/common/templates/supervisor/galaxy.j2 M env/common/update.yml M env/test/files/galaxy/var/integrated_tool_panel.xml M env/test/files/interactive_environments/plugins/.ansible_ie_role_current_version A env/test/files/interactive_environments/plugins/ethercalc/config/allowed_images.yml.sample M env/test/files/interactive_environments/plugins/ethercalc/config/ethercalc.ini.sample M env/test/files/interactive_environments/proxy/.ansible_ie_role_current_version M env/test/group_vars/galaxyservers/vars.yml M roles/galaxyprojectdotorg.galaxy/README.md M roles/galaxyprojectdotorg.galaxy/defaults/main.yml M roles/galaxyprojectdotorg.galaxy/meta/.galaxy_install_info M roles/galaxyprojectdotorg.galaxy/tasks/main.yml Log Message: ----------- IE fixes Commit: 86cafa4afe3c594cb25340990388f589cac0d3f6 https://github.com/galaxyproject/usegalaxy-playbook/commit/86cafa4afe3c594c… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-04-18 (Tue, 18 Apr 2017) Changed paths: M env/test/templates/galaxy/config/job_conf.xml.j2 Log Message: ----------- Merge branch 'reorg' of github.com:/galaxyproject/usegalaxy-playbook into reorg Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/b56a94393f25...…

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[galaxyproject/usegalaxy-playbook] ccadc2: pylon1 -> pylon5
by GitHub 18 Apr '17

18 Apr '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: ccadc26f89c4d2cdeaacb9a1dd940cc067bdac7c https://github.com/galaxyproject/usegalaxy-playbook/commit/ccadc26f89c4d2cd… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-04-18 (Tue, 18 Apr 2017) Changed paths: M templates/galaxy/usegalaxy.org/config/job_conf.xml.j2 Log Message: ----------- pylon1 -> pylon5

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[galaxyproject/usegalaxy-playbook] b56a94: pylon1 -> pylon5
by GitHub 18 Apr '17

18 Apr '17

Branch: refs/heads/reorg Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: b56a94393f25cfc03515801c4d83256562da8e68 https://github.com/galaxyproject/usegalaxy-playbook/commit/b56a94393f25cfc0… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-04-18 (Tue, 18 Apr 2017) Changed paths: M env/test/templates/galaxy/config/job_conf.xml.j2 Log Message: ----------- pylon1 -> pylon5

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[galaxyproject/infrastructure-playbook] 4a72e3: Additional Test fixes
by GitHub 17 Apr '17

17 Apr '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 4a72e362611797e43916a0751dd629ad5f53a2d2 https://github.com/galaxyproject/infrastructure-playbook/commit/4a72e362611… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-04-17 (Mon, 17 Apr 2017) Changed paths: A taccenv/group_vars/all.yml M taccenv/group_vars/galaxyservers.yml M taccenv/group_vars/maingalaxyservers.yml M taccenv/group_vars/testgalaxyservers.yml Log Message: ----------- Additional Test fixes Commit: 6d1e7866bbc8a8765b7e4c2946302923b215e432 https://github.com/galaxyproject/infrastructure-playbook/commit/6d1e7866bbc… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-04-17 (Mon, 17 Apr 2017) Changed paths: M jetstreamdockerenv/group_vars/imageinstances.yml M jetstreamdockerenv/inventory M jetstreamdockerenv/snapshot_docker_image.yml Log Message: ----------- Use a single volume for swarm workers Compare: https://github.com/galaxyproject/infrastructure-playbook/compare/33e4f2e997…

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[galaxyproject/galaxy] 77caed: Update text.py Add interaction annotations to Snp...
by GitHub 17 Apr '17

17 Apr '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 77caed9861d3666150c49442df9374b63660c2e5 https://github.com/galaxyproject/galaxy/commit/77caed9861d3666150c49442df93… Author: Jim Johnson <jj(a)umn.edu> Date: 2017-04-17 (Mon, 17 Apr 2017) Changed paths: M lib/galaxy/datatypes/text.py Log Message: ----------- Update text.py Add interaction annotations to SnpEffDb metadata Interaction annotations are now included in SnpEff v4.3 Commit: e9011488f2f5bfe91f542d173a9f7b3132e414ad https://github.com/galaxyproject/galaxy/commit/e9011488f2f5bfe91f542d173a9f… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-04-17 (Mon, 17 Apr 2017) Changed paths: M lib/galaxy/datatypes/text.py Log Message: ----------- Merge pull request #3938 from jj-umn/patch-6 Update text.py Add interaction annotations to SnpEffDb metadata Compare: https://github.com/galaxyproject/galaxy/compare/695293f01563...e9011488f2f5

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