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

[galaxyproject/galaxy] 02410b: Register job monitor as postfork function
by GitHub 12 Oct '18

12 Oct '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: 02410b270d025e5fb8cb4e2036fb627051c7850a https://github.com/galaxyproject/galaxy/commit/02410b270d025e5fb8cb4e2036fb… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-10-08 (Mon, 08 Oct 2018) Changed paths: M lib/galaxy/util/monitors.py Log Message: ----------- Register job monitor as postfork function This should fix https://github.com/galaxyproject/galaxy/issues/6831, and might fix https://github.com/galaxyproject/galaxy/issues/6261. Commit: baa992d217032b809d321cb800cd2f41af401c63 https://github.com/galaxyproject/galaxy/commit/baa992d217032b809d321cb800cd… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-10-11 (Thu, 11 Oct 2018) Changed paths: M lib/galaxy/util/monitors.py Log Message: ----------- Merge pull request #6836 from mvdbeek/fix_job_monitor_thread [18.01] Register job monitor thread as postfork function Commit: a8fa5a1d4a6c801fc230c037129671978955916c https://github.com/galaxyproject/galaxy/commit/a8fa5a1d4a6c801fc230c0371296… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-10-12 (Fri, 12 Oct 2018) Changed paths: M lib/galaxy/util/monitors.py Log Message: ----------- Merge branch 'release_18.01' into release_18.05 Compare: https://github.com/galaxyproject/galaxy/compare/fd0b24ecd2bf...a8fa5a1d4a6c **NOTE:** This service has 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.

1 0

[galaxyproject/galaxy] 20f60a: update paramiko dep
by GitHub 11 Oct '18

11 Oct '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: 20f60a5a44842dda8ffe7b97d1b60b6c5ecfdd9d https://github.com/galaxyproject/galaxy/commit/20f60a5a44842dda8ffe7b97d1b6… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-10-11 (Thu, 11 Oct 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt Log Message: ----------- update paramiko dep Commit: 2c14c2afc4d39626096c3d15828b8c3001aab40f https://github.com/galaxyproject/galaxy/commit/2c14c2afc4d39626096c3d15828b… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2018-10-12 (Fri, 12 Oct 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt Log Message: ----------- Merge pull request #6859 from martenson/paramiko-update [18.09] update paramiko dep Compare: https://github.com/galaxyproject/galaxy/compare/9251484e7236...2c14c2afc4d3 **NOTE:** This service has 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.

1 0

[galaxyproject/usegalaxy-playbook] cd00b4: Increase Du Novo: Correct barcodes to 16GB
by GitHub 11 Oct '18

11 Oct '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: cd00b451d2f0e5ce13d3b695e7bbb9ead163a71c https://github.com/galaxyproject/usegalaxy-playbook/commit/cd00b451d2f0e5ce… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-10-11 (Thu, 11 Oct 2018) Changed paths: M env/main/templates/galaxy/config/job_conf.xml.j2 M env/test/templates/galaxy/config/job_conf.xml.j2 Log Message: ----------- Increase Du Novo: Correct barcodes to 16GB **NOTE:** This service has 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.

1 0

[galaxyproject/galaxy] df07b2: Revert selective metadata flushing - seems to brea...
by GitHub 11 Oct '18

11 Oct '18

Branch: refs/heads/usegalaxy Home: https://github.com/galaxyproject/galaxy Commit: df07b28b2ed5f4b89393344435b5aa6102db2316 https://github.com/galaxyproject/galaxy/commit/df07b28b2ed5f4b89393344435b5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-10-11 (Thu, 11 Oct 2018) Changed paths: M lib/galaxy/model/metadata.py Log Message: ----------- Revert selective metadata flushing - seems to break upload changes. **NOTE:** This service has 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.

1 0

[galaxyproject/galaxy] 0eded6: Revert "Optimized dataset copying during histories...
by GitHub 11 Oct '18

11 Oct '18

Branch: refs/heads/usegalaxy Home: https://github.com/galaxyproject/galaxy Commit: 0eded6c2b2a8a03952ac6bc775c08c217ee80279 https://github.com/galaxyproject/galaxy/commit/0eded6c2b2a8a03952ac6bc775c0… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-10-11 (Thu, 11 Oct 2018) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/model/metadata.py Log Message: ----------- Revert "Optimized dataset copying during histories." This reverts commit 9780d069c8646fb4f02de848d62159680d95ae79. **NOTE:** This service has 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.

1 0

[galaxyproject/galaxy] 12746a: Align history and tool panel margins
by GitHub 11 Oct '18

11 Oct '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 12746a92ada7041a47c52566e236d24b2e7d3a14 https://github.com/galaxyproject/galaxy/commit/12746a92ada7041a47c52566e236… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-10-11 (Thu, 11 Oct 2018) Changed paths: M client/galaxy/style/scss/base.scss M client/galaxy/style/scss/history.scss M client/galaxy/style/scss/list-item.scss M static/style/blue/base.css Log Message: ----------- Align history and tool panel margins Commit: 0cafc64c158b174eaf9ab7d0d17e33e73e032cc6 https://github.com/galaxyproject/galaxy/commit/0cafc64c158b174eaf9ab7d0d17e… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-10-11 (Thu, 11 Oct 2018) Changed paths: M client/galaxy/style/scss/base.scss M static/style/blue/base.css Log Message: ----------- Align search bars in both panels Commit: 93ec1e6ad6b24df3fb13bcd5a9caf940d0e029e3 https://github.com/galaxyproject/galaxy/commit/93ec1e6ad6b24df3fb13bcd5a9ca… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-10-11 (Thu, 11 Oct 2018) Changed paths: M client/galaxy/style/scss/history.scss M static/style/blue/base.css Log Message: ----------- Fix empty message Commit: 62b39e9c9829bddfff4ae0af3d72a187082c42a4 https://github.com/galaxyproject/galaxy/commit/62b39e9c9829bddfff4ae0af3d72… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-10-11 (Thu, 11 Oct 2018) Changed paths: M client/galaxy/style/scss/history.scss M static/style/blue/base.css Log Message: ----------- Compensate for editable text plugins margin shift Commit: b2477d1223dfa62dfb17bee0d567f1fd4eba653e https://github.com/galaxyproject/galaxy/commit/b2477d1223dfa62dfb17bee0d567… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-10-11 (Thu, 11 Oct 2018) Changed paths: M client/galaxy/style/scss/base.scss M client/galaxy/style/scss/history.scss M client/galaxy/style/scss/list-item.scss M static/style/blue/base.css Log Message: ----------- Merge pull request #6854 from guerler/styles-refresh-2018-panel-header Fix panel header margins in history and tool panel Compare: https://github.com/galaxyproject/galaxy/compare/85d470666296...b2477d1223df **NOTE:** This service has 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.

1 0

[galaxyproject/galaxy]
by GitHub 11 Oct '18

11 Oct '18

Branch: refs/heads/18.09_release_notes Home: https://github.com/galaxyproject/galaxy **NOTE:** This service has 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.

1 0

[galaxyproject/galaxy] 6233a4: Release notes templated; still needs manual curati...
by GitHub 11 Oct '18

11 Oct '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: 6233a408cc93152a379651db3cc143d368f78dda https://github.com/galaxyproject/galaxy/commit/6233a408cc93152a379651db3cc1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-18 (Tue, 18 Sep 2018) Changed paths: A doc/source/releases/18.09.rst A doc/source/releases/18.09_announce.rst A doc/source/releases/19.01_announce.rst Log Message: ----------- Release notes templated; still needs manual curation Commit: 25fc1617030d392f85abb65ccd95f913561919e2 https://github.com/galaxyproject/galaxy/commit/25fc1617030d392f85abb65ccd95… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-24 (Mon, 24 Sep 2018) Changed paths: M doc/source/releases/18.09.rst Log Message: ----------- Update RN with new merges. Commit: 8c05e2f5f1677950a3279ffa30ccbf8949aa35e4 https://github.com/galaxyproject/galaxy/commit/8c05e2f5f1677950a3279ffa30cc… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-24 (Mon, 24 Sep 2018) Changed paths: M doc/source/releases/18.09.rst Log Message: ----------- Add grapdot datatype. Commit: 6ac5966c5e1a95e93c5923a4eddf5fa971518bd6 https://github.com/galaxyproject/galaxy/commit/6ac5966c5e1a95e93c5923a4eddf… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-24 (Mon, 24 Sep 2018) Changed paths: M doc/source/releases/18.09.rst Log Message: ----------- Add removal of upgrade logic specific to datatypes from 17.05 Commit: 0698a71861afadb7f16be765223819178d294c30 https://github.com/galaxyproject/galaxy/commit/0698a71861afadb7f16be7652238… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-25 (Tue, 25 Sep 2018) Changed paths: M doc/source/releases/18.09.rst Log Message: ----------- Another few stragglers. Commit: d3db21fa82a834d0d9fa90106b3fa2b4911708dc https://github.com/galaxyproject/galaxy/commit/d3db21fa82a834d0d9fa90106b3f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-25 (Tue, 25 Sep 2018) Changed paths: M doc/source/releases/18.09.rst Log Message: ----------- Add 6755 Commit: 6cb4c32eb4e613b4d90680450d11804779e5b4a5 https://github.com/galaxyproject/galaxy/commit/6cb4c32eb4e613b4d90680450d11… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-26 (Wed, 26 Sep 2018) Changed paths: M doc/source/releases/18.09.rst Log Message: ----------- Add 6768 Commit: ee47fdb50cef70dd2b940c42594611863e51bde7 https://github.com/galaxyproject/galaxy/commit/ee47fdb50cef70dd2b940c425946… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-26 (Wed, 26 Sep 2018) Changed paths: M doc/source/releases/18.09.rst Log Message: ----------- Add 6753, 6771 Commit: c51178578dcf67c8dbe16d3d8320f660e0c80027 https://github.com/galaxyproject/galaxy/commit/c51178578dcf67c8dbe16d3d8320… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M doc/source/releases/18.09.rst Log Message: ----------- Four more PRs Commit: ff65263ab2ee1351bbed11709d8536de694a5776 https://github.com/galaxyproject/galaxy/commit/ff65263ab2ee1351bbed11709d85… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M doc/source/releases/18.09.rst Log Message: ----------- Add 6789 Commit: 96d77b0791592b35fb6e4201d011f5c223060cfe https://github.com/galaxyproject/galaxy/commit/96d77b0791592b35fb6e4201d011… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-30 (Sun, 30 Sep 2018) Changed paths: M doc/source/releases/18.09.rst M doc/source/releases/18.09_announce.rst Log Message: ----------- More PRs, stub out proposed features. Commit: 3d772dc03bf0ffa1c6d010596488c5cd3a26901d https://github.com/galaxyproject/galaxy/commit/3d772dc03bf0ffa1c6d010596488… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-01 (Mon, 01 Oct 2018) Changed paths: M doc/source/releases/18.09.rst Log Message: ----------- Add 6791 Commit: ce3d43221a8d4e843a25c49c679a4ab75fd3756c https://github.com/galaxyproject/galaxy/commit/ce3d43221a8d4e843a25c49c679a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-01 (Mon, 01 Oct 2018) Changed paths: M doc/source/releases/18.09.rst Log Message: ----------- More Prs for the release notes. Commit: b5f7955c5addba2664b6375aa87c9873b2949fad https://github.com/galaxyproject/galaxy/commit/b5f7955c5addba2664b6375aa87c… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-10-04 (Thu, 04 Oct 2018) Changed paths: M doc/source/releases/18.09_announce.rst Log Message: ----------- Announce Python 3 Beta Support Commit: 90718843096f115324be8a086d7a6089e0086703 https://github.com/galaxyproject/galaxy/commit/90718843096f115324be8a086d7a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-04 (Thu, 04 Oct 2018) Changed paths: M doc/source/releases/18.09_announce.rst Log Message: ----------- Add deprecation notice for username being null Commit: afffd9bdaa66b4fcadbd790a25387654c23e4aa6 https://github.com/galaxyproject/galaxy/commit/afffd9bdaa66b4fcadbd790a2538… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-04 (Thu, 04 Oct 2018) Changed paths: M doc/source/releases/18.09.rst Log Message: ----------- Add final PR. Commit: eacec03d10c00503fdbb4da107254c06082507bb https://github.com/galaxyproject/galaxy/commit/eacec03d10c00503fdbb4da10725… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-10-04 (Thu, 04 Oct 2018) Changed paths: M doc/source/releases/18.09.rst M doc/source/releases/18.09_announce.rst Log Message: ----------- Update.... Commit: 4d165a567139abc3b4ad3baac422c9c0ebbaf554 https://github.com/galaxyproject/galaxy/commit/4d165a567139abc3b4ad3baac422… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-10-04 (Thu, 04 Oct 2018) Changed paths: M doc/source/releases/18.09.rst M doc/source/releases/18.09_announce.rst Log Message: ----------- Merge branch '18.09_release_notes' of github.com:jmchilton/galaxy into 18.09_release_notes Commit: 386229d1ce58522be4bece11b8f9473f5dce56b9 https://github.com/galaxyproject/galaxy/commit/386229d1ce58522be4bece11b8f9… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-04 (Thu, 04 Oct 2018) Changed paths: M doc/source/releases/18.09.rst Log Message: ----------- Re-add removed PRs (bad merge I think) Commit: fdaf9ac8641cfa5fa0aad706310aec2b31692ac1 https://github.com/galaxyproject/galaxy/commit/fdaf9ac8641cfa5fa0aad706310a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-04 (Thu, 04 Oct 2018) Changed paths: M doc/source/releases/18.09_announce.rst Log Message: ----------- Link up workflow PRs Commit: 381d6ad83183a822baebca44622e506d088f10b1 https://github.com/galaxyproject/galaxy/commit/381d6ad83183a822baebca44622e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-08 (Mon, 08 Oct 2018) Changed paths: M doc/source/releases/18.09.rst Log Message: ----------- Add two recently merged PRs. Commit: c1383bc2d55cb6565fbd63eb4088c734a805700e https://github.com/galaxyproject/galaxy/commit/c1383bc2d55cb6565fbd63eb4088… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2018-10-11 (Thu, 11 Oct 2018) Changed paths: M doc/source/releases/18.09_announce.rst Log Message: ----------- Small fixes Commit: c6193ca4406450cdaa01b9c27bcfb871c916544c https://github.com/galaxyproject/galaxy/commit/c6193ca4406450cdaa01b9c27bcf… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-11 (Thu, 11 Oct 2018) Changed paths: M doc/source/releases/18.09.rst M scripts/bootstrap_history.py Log Message: ----------- Update DEVTEAM, rebuild, include a few new PRs. Commit: 7cb2eb57aca559c86b3d938912d8f7bde5da9f74 https://github.com/galaxyproject/galaxy/commit/7cb2eb57aca559c86b3d938912d8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-11 (Thu, 11 Oct 2018) Changed paths: M doc/source/releases/18.09_announce.rst Log Message: ----------- Merge branch '18.09_release_notes' of github.com:galaxyproject/galaxy into 18.09_release_notes Commit: d33006cf33f71f4992eebefb7c3065606088aea1 https://github.com/galaxyproject/galaxy/commit/d33006cf33f71f4992eebefb7c30… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-11 (Thu, 11 Oct 2018) Changed paths: M doc/source/releases/18.09.rst Log Message: ----------- Final docs update Commit: d42b899b7805f722a77153c4e33fffcfad846ce0 https://github.com/galaxyproject/galaxy/commit/d42b899b7805f722a77153c4e33f… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-10-11 (Thu, 11 Oct 2018) Changed paths: M doc/source/releases/18.09.rst M scripts/bootstrap_history.py Log Message: ----------- Embellish 18.09 release notes Commit: 9251484e7236cd881cb4df64265a3cee2e654d83 https://github.com/galaxyproject/galaxy/commit/9251484e7236cd881cb4df64265a… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2018-10-11 (Thu, 11 Oct 2018) Changed paths: A doc/source/releases/18.09.rst A doc/source/releases/18.09_announce.rst A doc/source/releases/19.01_announce.rst M scripts/bootstrap_history.py Log Message: ----------- Merge pull request #6731 from galaxyproject/18.09_release_notes [18.09] 18.09 release notes Compare: https://github.com/galaxyproject/galaxy/compare/cd62461e8486...9251484e7236 **NOTE:** This service has 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.

1 0

[galaxyproject/galaxy] d42b89: Embellish 18.09 release notes
by GitHub 11 Oct '18

11 Oct '18

Branch: refs/heads/18.09_release_notes Home: https://github.com/galaxyproject/galaxy Commit: d42b899b7805f722a77153c4e33fffcfad846ce0 https://github.com/galaxyproject/galaxy/commit/d42b899b7805f722a77153c4e33f… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-10-11 (Thu, 11 Oct 2018) Changed paths: M doc/source/releases/18.09.rst M scripts/bootstrap_history.py Log Message: ----------- Embellish 18.09 release notes **NOTE:** This service has 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.

1 0

[galaxyproject/galaxy] d33006: Final docs update
by GitHub 11 Oct '18

11 Oct '18

Branch: refs/heads/18.09_release_notes Home: https://github.com/galaxyproject/galaxy Commit: d33006cf33f71f4992eebefb7c3065606088aea1 https://github.com/galaxyproject/galaxy/commit/d33006cf33f71f4992eebefb7c30… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-11 (Thu, 11 Oct 2018) Changed paths: M doc/source/releases/18.09.rst Log Message: ----------- Final docs update **NOTE:** This service has 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.

1 0