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

[galaxyproject/galaxy] d964d5: [18.01] Do not reload page when deleting collectio...
by GitHub 19 Feb '18

19 Feb '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: d964d594a5314b85def7676f5ae39c949420f4f0 https://github.com/galaxyproject/galaxy/commit/d964d594a5314b85def7676f5ae3… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-02-19 (Mon, 19 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/history/hdca-li-edit.js Log Message: ----------- [18.01] Do not reload page when deleting collections. Fixes #5499 reported by @mvdbeek (thanks for catching that). Commit: e7f7d5e29a0fc746625d5c8634d8976d4c2b667c https://github.com/galaxyproject/galaxy/commit/e7f7d5e29a0fc746625d5c8634d8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-02-19 (Mon, 19 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/history/hdca-li-edit.js Log Message: ----------- Merge pull request #5558 from jmchilton/deletion_cleanup_1 [18.01] Do not reload page when deleting collections. Compare: https://github.com/galaxyproject/galaxy/compare/0d029b39ac9a...e7f7d5e29a0f

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[galaxyproject/galaxy] 19eee5: added fasta.gz
by GitHub 19 Feb '18

19 Feb '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 19eee525a166b6c9abf03e5a91fd69a356447c20 https://github.com/galaxyproject/galaxy/commit/19eee525a166b6c9abf03e5a91fd… Author: nekrut <anton(a)nekrut.org> Date: 2018-02-16 (Fri, 16 Feb 2018) Changed paths: M config/datatypes_conf.xml.sample A lib/galaxy/datatypes/converters/fastagz_to_fasta.xml M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py Log Message: ----------- added fasta.gz Commit: 0c2c9ba49e70f19cd4ec9f4c93bf19af14fa348e https://github.com/galaxyproject/galaxy/commit/0c2c9ba49e70f19cd4ec9f4c93bf… Author: nekrut <anton(a)nekrut.org> Date: 2018-02-16 (Fri, 16 Feb 2018) Changed paths: M lib/galaxy/datatypes/sequence.py Log Message: ----------- fixed flake8 errors Commit: 84e818577a162b507fa4f1a69006fdee20ad8e5f https://github.com/galaxyproject/galaxy/commit/84e818577a162b507fa4f1a69006… Author: nekrut <anton(a)nekrut.org> Date: 2018-02-16 (Fri, 16 Feb 2018) Changed paths: M lib/galaxy/datatypes/sequence.py Log Message: ----------- removing stray whitespace Commit: 4390cd4142605efbf062126fdf0082940d7dfe30 https://github.com/galaxyproject/galaxy/commit/4390cd4142605efbf062126fdf00… Author: nekrut <anton(a)nekrut.org> Date: 2018-02-19 (Mon, 19 Feb 2018) Changed paths: M lib/galaxy/datatypes/converters/fastagz_to_fasta.xml Log Message: ----------- fixed name of fastagz->fasta converter Commit: 6359262b3ce3632bd859278201bcd9e6e893fba9 https://github.com/galaxyproject/galaxy/commit/6359262b3ce3632bd859278201bc… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-02-19 (Mon, 19 Feb 2018) Changed paths: M lib/galaxy/datatypes/converters/fastagz_to_fasta.xml Log Message: ----------- fix copypasta Commit: 55a405f18a1b493c7e0249f8e56b12b254603d3c https://github.com/galaxyproject/galaxy/commit/55a405f18a1b493c7e0249f8e56b… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-02-19 (Mon, 19 Feb 2018) Changed paths: M lib/galaxy/datatypes/sequence.py Log Message: ----------- fix more fasta copypasta Commit: ca7cbaf2bffb4b1a622386e5651acf396db65cfd https://github.com/galaxyproject/galaxy/commit/ca7cbaf2bffb4b1a622386e5651a… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-02-19 (Mon, 19 Feb 2018) Changed paths: M config/datatypes_conf.xml.sample A lib/galaxy/datatypes/converters/fastagz_to_fasta.xml M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py Log Message: ----------- Merge pull request #5553 from nekrut/fasta_gz added fasta.gz Compare: https://github.com/galaxyproject/galaxy/compare/a5bea5f885fb...ca7cbaf2bffb

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[galaxyproject/usegalaxy-playbook] 0af54a: Decrease client request size, increase staging req...
by GitHub 19 Feb '18

19 Feb '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 0af54a769a5be23b38ce64e922504998675f12be https://github.com/galaxyproject/usegalaxy-playbook/commit/0af54a769a5be23b… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-02-19 (Mon, 19 Feb 2018) Changed paths: M env/main/group_vars/galaxystagingservers.yml M env/main/group_vars/galaxywebservers.yml M env/main/group_vars/webservers.yml Log Message: ----------- Decrease client request size, increase staging request size

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[galaxyproject/infrastructure-playbook] 6ae3b1: update grafana
by GitHub 19 Feb '18

19 Feb '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 6ae3b1a0c18f6ad7b428c5041b65b2b977d6a037 https://github.com/galaxyproject/infrastructure-playbook/commit/6ae3b1a0c18… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-02-19 (Mon, 19 Feb 2018) Changed paths: M roles/stats/tasks/main.yml Log Message: ----------- update grafana Commit: f9205a79e9cf8791c9ab1b5d929e9bfaba208ebc https://github.com/galaxyproject/infrastructure-playbook/commit/f9205a79e9c… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-02-19 (Mon, 19 Feb 2018) Changed paths: M roles/stats/tasks/main.yml Log Message: ----------- Merge pull request #20 from galaxyproject/grafana-update update grafana Compare: https://github.com/galaxyproject/infrastructure-playbook/compare/669ca93ed1…

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[galaxyproject/infrastructure-playbook] 6ae3b1: update grafana
by GitHub 19 Feb '18

19 Feb '18

Branch: refs/heads/grafana-update Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 6ae3b1a0c18f6ad7b428c5041b65b2b977d6a037 https://github.com/galaxyproject/infrastructure-playbook/commit/6ae3b1a0c18… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-02-19 (Mon, 19 Feb 2018) Changed paths: M roles/stats/tasks/main.yml Log Message: ----------- update grafana

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[galaxyproject/galaxy] 9023dd: Ensure jobStateSummariesCollection exists; events ...
by GitHub 18 Feb '18

18 Feb '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 9023dd4e2edc940be9fb718dd85a157cbb6f663f https://github.com/galaxyproject/galaxy/commit/9023dd4e2edc940be9fb718dd85a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-02-02 (Fri, 02 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/history/history-contents.js Log Message: ----------- Ensure jobStateSummariesCollection exists; events can fire during deletion actions causing this event to fail Commit: 6211f8bd18eaf47703c92d27cf2b0025c94731b9 https://github.com/galaxyproject/galaxy/commit/6211f8bd18eaf47703c92d27cf2b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-02-02 (Fri, 02 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/history/history-contents.js Log Message: ----------- Import cleanup; remove unnecessary try...catch statement, use const. Commit: eb03d877a83e74c3d2c0124ec5bf7b36bf680564 https://github.com/galaxyproject/galaxy/commit/eb03d877a83e74c3d2c0124ec5bf… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-02-02 (Fri, 02 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/history/history-contents.js Log Message: ----------- More refactoring, removal of 'self' references in history-contents Commit: a5bea5f885fb5a5205bac518c895710e4b7f9965 https://github.com/galaxyproject/galaxy/commit/a5bea5f885fb5a5205bac518c895… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-02-18 (Sun, 18 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/history/history-contents.js Log Message: ----------- Merge pull request #5448 from dannon/multidelete_fix_and_refactor History contents refactoring Compare: https://github.com/galaxyproject/galaxy/compare/788934c3aa0c...a5bea5f885fb

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[galaxyproject/galaxy] 25952e: Map static content by default for Reports and Tool...
by GitHub 16 Feb '18

16 Feb '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 25952e81e7cc7c2985379f039915d40bc8142d98 https://github.com/galaxyproject/galaxy/commit/25952e81e7cc7c2985379f039915… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-02-14 (Wed, 14 Feb 2018) Changed paths: M config/reports.yml.sample M config/tool_shed.yml.sample Log Message: ----------- Map static content by default for Reports and Tool Shed webapps. Commit: fa93d4e04bccd31ba347bbb916b9c7b23b6c5c9d https://github.com/galaxyproject/galaxy/commit/fa93d4e04bccd31ba347bbb916b9… Author: Dave B <dave(a)bx.psu.edu> Date: 2018-02-16 (Fri, 16 Feb 2018) Changed paths: M lib/galaxy/tools/repositories.py Log Message: ----------- Close tempfile handles. Commit: 5488cf29eabc835e8e7ee994035557392471c586 https://github.com/galaxyproject/galaxy/commit/5488cf29eabc835e8e7ee9940355… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-02-16 (Fri, 16 Feb 2018) Changed paths: M lib/galaxy/tools/repositories.py Log Message: ----------- Merge pull request #5552 from davebx/18.01 [18.01] Close tempfile handles. Commit: 13e72e84c523bda22bda792bbebf4720d28542d5 https://github.com/galaxyproject/galaxy/commit/13e72e84c523bda22bda792bbebf… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2018-02-16 (Fri, 16 Feb 2018) Changed paths: M config/reports.yml.sample M config/tool_shed.yml.sample Log Message: ----------- Merge pull request #5534 from natefoo/17.09-static-map-fix [17.09] Map static content by default for Reports and Tool Shed webapps Commit: 0d029b39ac9ae6bc21a6c1834fe6e05280d8e0d0 https://github.com/galaxyproject/galaxy/commit/0d029b39ac9ae6bc21a6c1834fe6… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-02-16 (Fri, 16 Feb 2018) Changed paths: M config/reports.yml.sample M config/tool_shed.yml.sample Log Message: ----------- Merge branch 'release_17.09' into release_18.01 Commit: 788934c3aa0c4395dc479d1840a9869a2ee8b42a https://github.com/galaxyproject/galaxy/commit/788934c3aa0c4395dc479d1840a9… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-02-16 (Fri, 16 Feb 2018) Log Message: ----------- Merge branch 'release_18.01' into dev Conflicts: config/reports.yml.sample config/tool_shed.yml.sample Compare: https://github.com/galaxyproject/galaxy/compare/c9c2e968daba...788934c3aa0c

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[galaxyproject/galaxy] 25952e: Map static content by default for Reports and Tool...
by GitHub 16 Feb '18

16 Feb '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: 25952e81e7cc7c2985379f039915d40bc8142d98 https://github.com/galaxyproject/galaxy/commit/25952e81e7cc7c2985379f039915… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-02-14 (Wed, 14 Feb 2018) Changed paths: M config/reports.yml.sample M config/tool_shed.yml.sample Log Message: ----------- Map static content by default for Reports and Tool Shed webapps. Commit: 13e72e84c523bda22bda792bbebf4720d28542d5 https://github.com/galaxyproject/galaxy/commit/13e72e84c523bda22bda792bbebf… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2018-02-16 (Fri, 16 Feb 2018) Changed paths: M config/reports.yml.sample M config/tool_shed.yml.sample Log Message: ----------- Merge pull request #5534 from natefoo/17.09-static-map-fix [17.09] Map static content by default for Reports and Tool Shed webapps Commit: 0d029b39ac9ae6bc21a6c1834fe6e05280d8e0d0 https://github.com/galaxyproject/galaxy/commit/0d029b39ac9ae6bc21a6c1834fe6… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-02-16 (Fri, 16 Feb 2018) Changed paths: M config/reports.yml.sample M config/tool_shed.yml.sample Log Message: ----------- Merge branch 'release_17.09' into release_18.01 Compare: https://github.com/galaxyproject/galaxy/compare/5488cf29eabc...0d029b39ac9a

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[galaxyproject/galaxy] 25952e: Map static content by default for Reports and Tool...
by GitHub 16 Feb '18

16 Feb '18

Branch: refs/heads/release_17.09 Home: https://github.com/galaxyproject/galaxy Commit: 25952e81e7cc7c2985379f039915d40bc8142d98 https://github.com/galaxyproject/galaxy/commit/25952e81e7cc7c2985379f039915… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-02-14 (Wed, 14 Feb 2018) Changed paths: M config/reports.yml.sample M config/tool_shed.yml.sample Log Message: ----------- Map static content by default for Reports and Tool Shed webapps. Commit: 13e72e84c523bda22bda792bbebf4720d28542d5 https://github.com/galaxyproject/galaxy/commit/13e72e84c523bda22bda792bbebf… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2018-02-16 (Fri, 16 Feb 2018) Changed paths: M config/reports.yml.sample M config/tool_shed.yml.sample Log Message: ----------- Merge pull request #5534 from natefoo/17.09-static-map-fix [17.09] Map static content by default for Reports and Tool Shed webapps Compare: https://github.com/galaxyproject/galaxy/compare/c0c95548a3c7...13e72e84c523

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[galaxyproject/usegalaxy-playbook] 8dee0e: Enable client builds on Main during pre-release.
by GitHub 16 Feb '18

16 Feb '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 8dee0eafb9779793bc1362236a53ea0d63532da0 https://github.com/galaxyproject/usegalaxy-playbook/commit/8dee0eafb9779793… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-02-16 (Fri, 16 Feb 2018) Changed paths: A env/main/client.yml M env/main/group_vars/all.yml A env/main/group_vars/cvmfsstratum0servers.yml Log Message: ----------- Enable client builds on Main during pre-release.

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