- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] fdfe79: Fix library to list of pairs collection builder.
by GitHub 30 Apr '18

30 Apr '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: fdfe79f67edd3af8967f916badffcd13aadb78d6 https://github.com/galaxyproject/galaxy/commit/fdfe79f67edd3af8967f916badff… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-04-30 (Mon, 30 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M lib/galaxy/webapps/galaxy/api/history_contents.py Log Message: ----------- Fix library to list of pairs collection builder. Commit: f50fe5d455594996ba4eb900e0adbf1face67de3 https://github.com/galaxyproject/galaxy/commit/f50fe5d455594996ba4eb900e0ad… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-04-30 (Mon, 30 Apr 2018) Changed paths: M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/extended.bundled.js M static/scripts/bundled/extended.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/collection/list-of-pairs-collection-creator.js Log Message: ----------- Rebuild client. Commit: b477329842e7209b2fa2b9389e48b0606b7d8824 https://github.com/galaxyproject/galaxy/commit/b477329842e7209b2fa2b9389e48… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-04-30 (Mon, 30 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M lib/galaxy/webapps/galaxy/api/history_contents.py M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/extended.bundled.js M static/scripts/bundled/extended.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/collection/list-of-pairs-collection-creator.js Log Message: ----------- Merge pull request #6015 from jmchilton/fix_library_paired [18.01] Fix library to list of pairs collection builder. Compare: https://github.com/galaxyproject/galaxy/compare/abf23cdc0bb2...b477329842e7

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[galaxyproject/usegalaxy-playbook] bc5263: Bring ansible.cfg options from infrastructure-play...
by GitHub 30 Apr '18

30 Apr '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: bc5263adbfddbd642f705f61afb76b0034c0db72 https://github.com/galaxyproject/usegalaxy-playbook/commit/bc5263adbfddbd64… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-30 (Mon, 30 Apr 2018) Changed paths: A .pass M ansible.cfg Log Message: ----------- Bring ansible.cfg options from infrastructure-playbook to fix missing inheritance_chain lookup plugin error

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[galaxyproject/usegalaxy-playbook] 98e633: Move Test and Main to Stampede2
by GitHub 30 Apr '18

30 Apr '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 98e633c616037f137d616f70227fd7b4e3736635 https://github.com/galaxyproject/usegalaxy-playbook/commit/98e633c616037f13… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-30 (Mon, 30 Apr 2018) Changed paths: A env/main/host_vars/login2.stampede2.tacc.utexas.edu.yml R env/main/host_vars/login5.stampede.tacc.utexas.edu.yml M env/main/inventory M env/test/inventory Log Message: ----------- Move Test and Main to Stampede2

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[galaxyproject/usegalaxy-playbook] 89bbee: Move Test to Stampede2
by GitHub 30 Apr '18

30 Apr '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 89bbee2e9ea7de43739322f9298fb59ab722e1c7 https://github.com/galaxyproject/usegalaxy-playbook/commit/89bbee2e9ea7de43… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-30 (Mon, 30 Apr 2018) Changed paths: A .ssh-keyboard-interactive A env/test/host_vars/login2.stampede2.tacc.utexas.edu R env/test/host_vars/login5.stampede.tacc.utexas.edu.yml M env/test/inventory Log Message: ----------- Move Test to Stampede2

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[galaxyproject/galaxy] 1f3a8d: Fix typos
by GitHub 30 Apr '18

30 Apr '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1f3a8d4954abfc8222976dd2a2bee987936b91c5 https://github.com/galaxyproject/galaxy/commit/1f3a8d4954abfc8222976dd2a2be… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-04-30 (Mon, 30 Apr 2018) Changed paths: M config/tool_destinations.yml.sample M lib/galaxy/managers/collections_util.py Log Message: ----------- Fix typos Commit: 0bcb69df456ea903461e712aa8e83b624f779d0e https://github.com/galaxyproject/galaxy/commit/0bcb69df456ea903461e712aa8e8… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-04-30 (Mon, 30 Apr 2018) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Fix link formatting We cannot use backquote characters in the link text, because pandoc generates a broken RST, see https://github.com/jgm/pandoc/issues/3973 Commit: f2ce39323364c9cf578235c00800816b5208956e https://github.com/galaxyproject/galaxy/commit/f2ce39323364c9cf578235c00800… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-04-30 (Mon, 30 Apr 2018) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Small tool XML doc fixes Commit: 479e76ff13c9a2e232efda5b3d3db7b25a2701c3 https://github.com/galaxyproject/galaxy/commit/479e76ff13c9a2e232efda5b3d3d… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-04-30 (Mon, 30 Apr 2018) Changed paths: M scripts/bootstrap_history.py Log Message: ----------- Add closing old milestone to release issue Commit: 9f5a1fa9a613bfe6d6b49e3460be1a2e15ca6bce https://github.com/galaxyproject/galaxy/commit/9f5a1fa9a613bfe6d6b49e3460be… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-04-30 (Mon, 30 Apr 2018) Changed paths: M config/tool_destinations.yml.sample M lib/galaxy/managers/collections_util.py M lib/galaxy/tools/xsd/galaxy.xsd M scripts/bootstrap_history.py Log Message: ----------- Merge pull request #6013 from nsoranzo/misc Documentation and typo fixes Compare: https://github.com/galaxyproject/galaxy/compare/8c152bda45cb...9f5a1fa9a613

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[galaxyproject/galaxy] 84af64: Cgroup metric plugin: attempt to deal with multili...
by GitHub 30 Apr '18

30 Apr '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: 84af648f017dad95871bb43b65e8d860391066c8 https://github.com/galaxyproject/galaxy/commit/84af648f017dad95871bb43b65e8… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-26 (Thu, 26 Apr 2018) Changed paths: M lib/galaxy/jobs/metrics/instrumenters/cgroup.py M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py M lib/galaxy/util/__init__.py Log Message: ----------- Cgroup metric plugin: attempt to deal with multiline params, and store numeric values in the numeric table. Also fix a display bug. Commit: 3ee40bfe53088b57da6b3a44efd5ac835ec6f1e7 https://github.com/galaxyproject/galaxy/commit/3ee40bfe53088b57da6b3a44efd5… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-04-30 (Mon, 30 Apr 2018) Changed paths: M lib/galaxy/jobs/metrics/instrumenters/cgroup.py M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py M lib/galaxy/util/__init__.py Log Message: ----------- Merge pull request #5989 from natefoo/cgroup-metric-fixes [18.05] Fixes for the Cgroup metric plugin Compare: https://github.com/galaxyproject/galaxy/compare/916078beb0b5...3ee40bfe5308

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[galaxyproject/galaxy] f50715: Remove __global__
by GitHub 30 Apr '18

30 Apr '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f50715df8377af74afce2231aa857a98684f6868 https://github.com/galaxyproject/galaxy/commit/f50715df8377af74afce2231aa85… Author: E Rasche <hxr(a)hx42.org> Date: 2018-04-30 (Mon, 30 Apr 2018) Changed paths: M lib/galaxy/web/framework/middleware/graphite.py M lib/galaxy/web/framework/middleware/statsd.py Log Message: ----------- Remove __global__ Commit: 8c152bda45cbf3b49610a9933bd6c38f1724942a https://github.com/galaxyproject/galaxy/commit/8c152bda45cbf3b49610a9933bd6… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-04-30 (Mon, 30 Apr 2018) Changed paths: M lib/galaxy/web/framework/middleware/graphite.py M lib/galaxy/web/framework/middleware/statsd.py Log Message: ----------- Merge pull request #6011 from erasche/remove_global Remove duplicate metric sending Compare: https://github.com/galaxyproject/galaxy/compare/c2ee91508bcc...8c152bda45cb

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[galaxyproject/galaxy] 717e11: enable testing for more BAM types
by GitHub 30 Apr '18

30 Apr '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: 717e1104c1e32f79b84de6ffbc481b105087f17f https://github.com/galaxyproject/galaxy/commit/717e1104c1e32f79b84de6ffbc48… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2018-04-28 (Sat, 28 Apr 2018) Changed paths: M lib/galaxy/tools/verify/__init__.py Log Message: ----------- enable testing for more BAM types Commit: abf23cdc0bb22542577e5ddefac38242c9ddf8ee https://github.com/galaxyproject/galaxy/commit/abf23cdc0bb22542577e5ddefac3… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-04-30 (Mon, 30 Apr 2018) Changed paths: M lib/galaxy/tools/verify/__init__.py Log Message: ----------- Merge pull request #6010 from bgruening/test_bam_subtypes [18.01] enable testing for more BAM types Compare: https://github.com/galaxyproject/galaxy/compare/103cb51ec368...abf23cdc0bb2

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[galaxyproject/infrastructure-playbook] f4186c: Install Data::Dumper perl module on nodes for olde...
by GitHub 28 Apr '18

28 Apr '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: f4186c1ab8ea0414a875247bfe59d9aa84bd6f9e https://github.com/galaxyproject/infrastructure-playbook/commit/f4186c1ab8e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-28 (Sat, 28 Apr 2018) Changed paths: M env/tacc/group_vars/galaxynodes.yml Log Message: ----------- Install Data::Dumper perl module on nodes for older tools

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[galaxyproject/galaxy] 0875b8: fix bowtie2 link
by GitHub 28 Apr '18

28 Apr '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 0875b8e65d6d5d7130c829ec8e5b7f9bffcced3a https://github.com/galaxyproject/galaxy/commit/0875b8e65d6d5d7130c829ec8e5b… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2018-04-28 (Sat, 28 Apr 2018) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- fix bowtie2 link Commit: c2ee91508bcc96cadfd7b23fba8a8d60e6f5547a https://github.com/galaxyproject/galaxy/commit/c2ee91508bcc96cadfd7b23fba8a… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-04-28 (Sat, 28 Apr 2018) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Merge pull request #6009 from galaxyproject/bowtie2_link fix bowtie2 link Compare: https://github.com/galaxyproject/galaxy/compare/acc988981546...c2ee91508bcc

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