May 2018 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] c0c8aa: Fix history shared with me 'view' link
by GitHub 31 May '18

31 May '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: c0c8aad528d9164fb7aaf88c3a202c66044c0134 https://github.com/galaxyproject/galaxy/commit/c0c8aad528d9164fb7aaf88c3a20… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-31 (Thu, 31 May 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Fix history shared with me 'view' link Commit: 692465d4ec9a4493ae1326cbc8b118cf49f5cbff https://github.com/galaxyproject/galaxy/commit/692465d4ec9a4493ae1326cbc8b1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-31 (Thu, 31 May 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Standard quotes. Commit: 8a0427a6e8eeffde3022ed1187b114265b73447f https://github.com/galaxyproject/galaxy/commit/8a0427a6e8eeffde3022ed1187b1… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-31 (Thu, 31 May 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Merge pull request #6257 from dannon/sharing_link_fix [18.05] Fix history shared with me 'view' link Compare: https://github.com/galaxyproject/galaxy/compare/44b42e7e7e01...8a0427a6e8ee **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/infrastructure-playbook] 8ecbb5: WIP Jetstream autoscaling
by GitHub 31 May '18

31 May '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 8ecbb55376f5ae76d114fa506a67f58f5a772943 https://github.com/galaxyproject/infrastructure-playbook/commit/8ecbb55376f… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-05-31 (Thu, 31 May 2018) Changed paths: M env/jsiu/group_vars/all.yml R env/jsiu/group_vars/controllers.yml A env/jsiu/group_vars/controllers/vars.yml A env/jsiu/group_vars/controllers/vault.yml A env/jsiu/slurmscale.yml A roles/slurmscale/defaults/main.yml A roles/slurmscale/files/ansible.cfg A roles/slurmscale/files/config.yml A roles/slurmscale/files/group_vars/all/cluster.yml A roles/slurmscale/files/group_vars/all/spawn.yml A roles/slurmscale/files/group_vars/jetstream-large.yml A roles/slurmscale/files/group_vars/jetstream-medium.yml A roles/slurmscale/files/group_vars/jetstream-small.yml A roles/slurmscale/files/inventory/flavors A roles/slurmscale/files/inventory/openstack_inventory.py A roles/slurmscale/files/spawn.yml A roles/slurmscale/files/start.yml A roles/slurmscale/files/stop.yml A roles/slurmscale/files/templates/auto.jetstream.j2 A roles/slurmscale/files/templates/slurm/slurm.conf.j2 A roles/slurmscale/tasks/main.yml A roles/slurmscale/templates/group_vars/all/cloud.yml.j2 A roles/slurmscale/templates/slurm_resume.sh.j2 A roles/slurmscale/templates/slurm_suspend.sh.j2 Log Message: ----------- WIP Jetstream autoscaling **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 94ae2e: permit actual numbers in conf file
by GitHub 31 May '18

31 May '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 94ae2e6a958e611c6cdcfe56dc72d47f2dfb66c3 https://github.com/galaxyproject/galaxy/commit/94ae2e6a958e611c6cdcfe56dc72… Author: Helena Rasche <hxr(a)hx42.org> Date: 2018-05-23 (Wed, 23 May 2018) Changed paths: M scripts/grt/upload.py Log Message: ----------- permit actual numbers in conf file Commit: 53d2664b0b7bafc5d91243ad897e7fcd3ab1c13a https://github.com/galaxyproject/galaxy/commit/53d2664b0b7bafc5d91243ad897e… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-31 (Thu, 31 May 2018) Changed paths: M scripts/grt/upload.py Log Message: ----------- Merge pull request #6200 from erasche/grt-asdf Permit numeric values of GRT instance ID in config Compare: https://github.com/galaxyproject/galaxy/compare/06d0fcc0de1a...53d2664b0b7b **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] ce9b67: Hack paster args to not duplicate pid file stuff f...
by GitHub 31 May '18

31 May '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ce9b671bd4747cd29af9dc25074b0831bb3068e1 https://github.com/galaxyproject/galaxy/commit/ce9b671bd4747cd29af9dc25074b… Author: Lance Parsons <lparsons(a)princeton.edu> Date: 2018-05-29 (Tue, 29 May 2018) Changed paths: M scripts/common_startup_functions.sh Log Message: ----------- Hack paster args to not duplicate pid file stuff for RUN_ALL. Commit: 88c94fc49b3f5869b6746bb0fe8f3248e33f440e https://github.com/galaxyproject/galaxy/commit/88c94fc49b3f5869b6746bb0fe8f… Author: Lance Parsons <lparsons(a)princeton.edu> Date: 2018-05-31 (Thu, 31 May 2018) Changed paths: M scripts/common_startup_functions.sh Log Message: ----------- Set pid and log file for paster in server_args This avoids setting log and pid file in paster_args so that with GALAXY_RUN_ALL they can be set individually, but ensures they are set when running paster otherwise. Commit: b137d5cf3461d4d7edb10b8510e36aa02fce6797 https://github.com/galaxyproject/galaxy/commit/b137d5cf3461d4d7edb10b8510e3… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-05-31 (Thu, 31 May 2018) Changed paths: M scripts/common_startup_functions.sh Log Message: ----------- Merge pull request #6239 from lparsons/fix_paster_args [18.01] Hack paster args to not duplicate pid file stuff for RUN_ALL. Commit: 44b42e7e7e01c8471777cf87251499f3bbfbf3f9 https://github.com/galaxyproject/galaxy/commit/44b42e7e7e01c8471777cf872514… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-31 (Thu, 31 May 2018) Changed paths: M scripts/common_startup_functions.sh Log Message: ----------- Merge remote-tracking branch 'upstream/release_18.01' into release_18.05 Commit: 06d0fcc0de1a7634df5cb71f4225e11af2ebb345 https://github.com/galaxyproject/galaxy/commit/06d0fcc0de1a7634df5cb71f4225… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-31 (Thu, 31 May 2018) Changed paths: M scripts/common_startup_functions.sh Log Message: ----------- Merge remote-tracking branch 'upstream/release_18.05' into dev Compare: https://github.com/galaxyproject/galaxy/compare/fb78fabcd757...06d0fcc0de1a **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] ce9b67: Hack paster args to not duplicate pid file stuff f...
by GitHub 31 May '18

31 May '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/galaxy Commit: ce9b671bd4747cd29af9dc25074b0831bb3068e1 https://github.com/galaxyproject/galaxy/commit/ce9b671bd4747cd29af9dc25074b… Author: Lance Parsons <lparsons(a)princeton.edu> Date: 2018-05-29 (Tue, 29 May 2018) Changed paths: M scripts/common_startup_functions.sh Log Message: ----------- Hack paster args to not duplicate pid file stuff for RUN_ALL. Commit: 88c94fc49b3f5869b6746bb0fe8f3248e33f440e https://github.com/galaxyproject/galaxy/commit/88c94fc49b3f5869b6746bb0fe8f… Author: Lance Parsons <lparsons(a)princeton.edu> Date: 2018-05-31 (Thu, 31 May 2018) Changed paths: M scripts/common_startup_functions.sh Log Message: ----------- Set pid and log file for paster in server_args This avoids setting log and pid file in paster_args so that with GALAXY_RUN_ALL they can be set individually, but ensures they are set when running paster otherwise. Commit: b137d5cf3461d4d7edb10b8510e36aa02fce6797 https://github.com/galaxyproject/galaxy/commit/b137d5cf3461d4d7edb10b8510e3… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-05-31 (Thu, 31 May 2018) Changed paths: M scripts/common_startup_functions.sh Log Message: ----------- Merge pull request #6239 from lparsons/fix_paster_args [18.01] Hack paster args to not duplicate pid file stuff for RUN_ALL. Commit: 44b42e7e7e01c8471777cf87251499f3bbfbf3f9 https://github.com/galaxyproject/galaxy/commit/44b42e7e7e01c8471777cf872514… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-31 (Thu, 31 May 2018) Changed paths: M scripts/common_startup_functions.sh Log Message: ----------- Merge remote-tracking branch 'upstream/release_18.01' into release_18.05 Compare: https://github.com/galaxyproject/galaxy/compare/c9641e1f1384...44b42e7e7e01 **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] ce9b67: Hack paster args to not duplicate pid file stuff f...
by GitHub 31 May '18

31 May '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: ce9b671bd4747cd29af9dc25074b0831bb3068e1 https://github.com/galaxyproject/galaxy/commit/ce9b671bd4747cd29af9dc25074b… Author: Lance Parsons <lparsons(a)princeton.edu> Date: 2018-05-29 (Tue, 29 May 2018) Changed paths: M scripts/common_startup_functions.sh Log Message: ----------- Hack paster args to not duplicate pid file stuff for RUN_ALL. Commit: 88c94fc49b3f5869b6746bb0fe8f3248e33f440e https://github.com/galaxyproject/galaxy/commit/88c94fc49b3f5869b6746bb0fe8f… Author: Lance Parsons <lparsons(a)princeton.edu> Date: 2018-05-31 (Thu, 31 May 2018) Changed paths: M scripts/common_startup_functions.sh Log Message: ----------- Set pid and log file for paster in server_args This avoids setting log and pid file in paster_args so that with GALAXY_RUN_ALL they can be set individually, but ensures they are set when running paster otherwise. Commit: b137d5cf3461d4d7edb10b8510e36aa02fce6797 https://github.com/galaxyproject/galaxy/commit/b137d5cf3461d4d7edb10b8510e3… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-05-31 (Thu, 31 May 2018) Changed paths: M scripts/common_startup_functions.sh Log Message: ----------- Merge pull request #6239 from lparsons/fix_paster_args [18.01] Hack paster args to not duplicate pid file stuff for RUN_ALL. Commit: 44b42e7e7e01c8471777cf87251499f3bbfbf3f9 https://github.com/galaxyproject/galaxy/commit/44b42e7e7e01c8471777cf872514… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-31 (Thu, 31 May 2018) Changed paths: M scripts/common_startup_functions.sh Log Message: ----------- Merge remote-tracking branch 'upstream/release_18.01' into release_18.05 Compare: https://github.com/galaxyproject/galaxy/compare/c9641e1f1384...44b42e7e7e01 **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 89bf97: Link downlaod attributes are well supported and sh...
by GitHub 31 May '18

31 May '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 89bf971aa8cee76bc624536e0896de38556d806c https://github.com/galaxyproject/galaxy/commit/89bf971aa8cee76bc624536e0896… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-24 (Thu, 24 May 2018) Changed paths: M client/galaxy/scripts/mvc/visualization/chart/components/screenshot.js Log Message: ----------- Link downlaod attributes are well supported and should work here, allowing us to actually name the downloads. Commit: a5840a89bb71c0c17373c7fdac5498f886483b2c https://github.com/galaxyproject/galaxy/commit/a5840a89bb71c0c17373c7fdac54… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-24 (Thu, 24 May 2018) Changed paths: M client/galaxy/scripts/mvc/visualization/chart/components/screenshot.js Log Message: ----------- Refactoring, cleanup, a few bugfixes. Commit: 1656b48323a3110134d0ba3fcc86c54923a75fdc https://github.com/galaxyproject/galaxy/commit/1656b48323a3110134d0ba3fcc86… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-24 (Thu, 24 May 2018) Changed paths: M client/galaxy/scripts/mvc/visualization/chart/components/screenshot.js Log Message: ----------- Minor filename handling tweak, more explicitly better support empty default Commit: 60b5cc5341f2bedd97f6a1da8e187edb1584e2b6 https://github.com/galaxyproject/galaxy/commit/60b5cc5341f2bedd97f6a1da8e18… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-24 (Thu, 24 May 2018) Changed paths: M client/galaxy/scripts/mvc/visualization/chart/components/screenshot.js Log Message: ----------- SVG download titles, more minor refactoring/reuse Commit: ddb6b8692d0eecdaba27a00921875223cef387ef https://github.com/galaxyproject/galaxy/commit/ddb6b8692d0eecdaba27a0092187… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-24 (Thu, 24 May 2018) Changed paths: M client/galaxy/scripts/mvc/visualization/chart/components/screenshot.js Log Message: ----------- Formatting fixes. Commit: fb78fabcd757b80cbe063cddab104f17e2b3a4e2 https://github.com/galaxyproject/galaxy/commit/fb78fabcd757b80cbe063cddab10… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-31 (Thu, 31 May 2018) Changed paths: M client/galaxy/scripts/mvc/visualization/chart/components/screenshot.js Log Message: ----------- Merge pull request #6216 from dannon/chart_download_fix Charts filename download fix Compare: https://github.com/galaxyproject/galaxy/compare/fd25d51b8e47...fb78fabcd757 **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] ce9b67: Hack paster args to not duplicate pid file stuff f...
by GitHub 31 May '18

31 May '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: ce9b671bd4747cd29af9dc25074b0831bb3068e1 https://github.com/galaxyproject/galaxy/commit/ce9b671bd4747cd29af9dc25074b… Author: Lance Parsons <lparsons(a)princeton.edu> Date: 2018-05-29 (Tue, 29 May 2018) Changed paths: M scripts/common_startup_functions.sh Log Message: ----------- Hack paster args to not duplicate pid file stuff for RUN_ALL. Commit: 88c94fc49b3f5869b6746bb0fe8f3248e33f440e https://github.com/galaxyproject/galaxy/commit/88c94fc49b3f5869b6746bb0fe8f… Author: Lance Parsons <lparsons(a)princeton.edu> Date: 2018-05-31 (Thu, 31 May 2018) Changed paths: M scripts/common_startup_functions.sh Log Message: ----------- Set pid and log file for paster in server_args This avoids setting log and pid file in paster_args so that with GALAXY_RUN_ALL they can be set individually, but ensures they are set when running paster otherwise. Commit: b137d5cf3461d4d7edb10b8510e36aa02fce6797 https://github.com/galaxyproject/galaxy/commit/b137d5cf3461d4d7edb10b8510e3… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-05-31 (Thu, 31 May 2018) Changed paths: M scripts/common_startup_functions.sh Log Message: ----------- Merge pull request #6239 from lparsons/fix_paster_args [18.01] Hack paster args to not duplicate pid file stuff for RUN_ALL. Compare: https://github.com/galaxyproject/galaxy/compare/0718a083badc...b137d5cf3461 **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/usegalaxy-playbook] 340a1a: Test Jetstream autoscaling
by GitHub 31 May '18

31 May '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 340a1a2402fe9aec74c43f83af5dddf487da1f50 https://github.com/galaxyproject/usegalaxy-playbook/commit/340a1a2402fe9aec… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-05-31 (Thu, 31 May 2018) Changed paths: M env/test/templates/galaxy/config/job_conf.xml.j2 Log Message: ----------- Test Jetstream autoscaling **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] ac7c6e: Refactor to match domain name (follow-up to #6244)
by GitHub 31 May '18

31 May '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ac7c6e5d947f42054105b25fe33e490152dd7d2f https://github.com/galaxyproject/galaxy/commit/ac7c6e5d947f42054105b25fe33e… Author: Katrin Leinweber <9948149+katrinleinweber(a)users.noreply.github.com> Date: 2018-05-31 (Thu, 31 May 2018) Changed paths: M lib/galaxy/managers/citations.py Log Message: ----------- Refactor to match domain name (follow-up to #6244) Commit: fd25d51b8e47bda031aa6a490c6e73741ab15fe9 https://github.com/galaxyproject/galaxy/commit/fd25d51b8e47bda031aa6a490c6e… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-05-31 (Thu, 31 May 2018) Changed paths: M lib/galaxy/managers/citations.py Log Message: ----------- Merge pull request #6252 from katrinleinweber/patch-1 Refactor dx_url to doi_url to match domain name Compare: https://github.com/galaxyproject/galaxy/compare/27106c59e5d6...fd25d51b8e47 **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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