September 2015 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] b2e9c8: Fixed broken RData sniffer
by GitHub 18 Sep '15

18 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b2e9c8a36f9b1ba394b0d27bdc8287880abe27cd https://github.com/galaxyproject/galaxy/commit/b2e9c8a36f9b1ba394b0d27bdc82… Author: nitesh1989 <nitesh.turaga(a)gmail.com> Date: 2015-09-18 (Fri, 18 Sep 2015) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Fixed broken RData sniffer

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[galaxyproject/galaxy] 989191: Fix output_format framework test.
by GitHub 18 Sep '15

18 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 989191d3cef70999661668ca9031e6cf39aaca61 https://github.com/galaxyproject/galaxy/commit/989191d3cef70999661668ca9031… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-09-18 (Fri, 18 Sep 2015) Changed paths: M test/functional/tools/output_format.xml Log Message: ----------- Fix output_format framework test. Commit: 92a152d89c507168a6085cc34acfa13566b6eda9 https://github.com/galaxyproject/galaxy/commit/92a152d89c507168a6085cc34acf… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-09-18 (Fri, 18 Sep 2015) Changed paths: M test/api/helpers.py Log Message: ----------- Uniform and slight increase the default timeout of API tests. Commit: d585a4a03d6956404830d63fc6b8872fba241d83 https://github.com/galaxyproject/galaxy/commit/d585a4a03d6956404830d63fc6b8… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-09-18 (Fri, 18 Sep 2015) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Clearer error message when setting metadata for BCF and SAM/BAM files. When the shutil.move() fails. Commit: ca733d33f9c52a630a30132d24974ed1143e6945 https://github.com/galaxyproject/galaxy/commit/ca733d33f9c52a630a30132d2497… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-09-18 (Fri, 18 Sep 2015) Changed paths: M lib/galaxy/datatypes/binary.py M test/api/helpers.py M test/functional/tools/output_format.xml Log Message: ----------- Merge pull request #752 from nsoranzo/dev Fixes for #744. Compare: https://github.com/galaxyproject/galaxy/compare/3de7bb66993c...ca733d33f9c5

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[galaxyproject/infrastructure-playbook] 6e9b69: correct the linuxbrew tasks
by GitHub 18 Sep '15

18 Sep '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 6e9b69584e16bd8fd132368896314759b920a52e https://github.com/galaxyproject/infrastructure-playbook/commit/6e9b69584e1… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-09-18 (Fri, 18 Sep 2015) Changed paths: M roles/linuxbrew/tasks/main.yml Log Message: ----------- correct the linuxbrew tasks

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[galaxyproject/infrastructure-playbook] 0ba7f9: adjust n2 for brew
by GitHub 18 Sep '15

18 Sep '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 0ba7f9c94201c66e7ccfe5e83db5acd24d09869c https://github.com/galaxyproject/infrastructure-playbook/commit/0ba7f9c9420… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-09-18 (Fri, 18 Sep 2015) Changed paths: M galaxyenv/host_vars/n2.galaxyproject.org.yml M playbook.yml M roles/linuxbrew/tasks/main.yml Log Message: ----------- adjust n2 for brew Commit: e10494f3b65859cf71b2b333938773ad6dcbb0b5 https://github.com/galaxyproject/infrastructure-playbook/commit/e10494f3b65… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-09-18 (Fri, 18 Sep 2015) Changed paths: M roles/linuxbrew/tasks/main.yml Log Message: ----------- Merge branch 'master' of https://github.com/galaxyproject/infrastructure-playbook Compare: https://github.com/galaxyproject/infrastructure-playbook/compare/3769c7f3f6…

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[galaxyproject/infrastructure-playbook] 3769c7: Install linuxbrew required packages.
by GitHub 18 Sep '15

18 Sep '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 3769c7f3f62c5c7b8432bc16c0216642509fbfde https://github.com/galaxyproject/infrastructure-playbook/commit/3769c7f3f62… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-09-18 (Fri, 18 Sep 2015) Changed paths: M roles/linuxbrew/tasks/main.yml Log Message: ----------- Install linuxbrew required packages. Using apt.

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[galaxyproject/infrastructure-playbook] 77bb06: WIP: linuxbrew role for jenkins.
by GitHub 18 Sep '15

18 Sep '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 77bb0686461dac5342143a1c6abfd2011ac8e586 https://github.com/galaxyproject/infrastructure-playbook/commit/77bb0686461… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-09-18 (Fri, 18 Sep 2015) Changed paths: A galaxyenv/group_vars/jenkinsservers.yml M playbook.yml A roles/linuxbrew/defaults/main.yml A roles/linuxbrew/tasks/main.yml Log Message: ----------- WIP: linuxbrew role for jenkins. Install planemo and bcftools. Commit: 410c6c010c8f0301c7e1f1713933b0270a01c248 https://github.com/galaxyproject/infrastructure-playbook/commit/410c6c010c8… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-09-18 (Fri, 18 Sep 2015) Changed paths: A galaxyenv/group_vars/jenkinsservers.yml M playbook.yml A roles/linuxbrew/defaults/main.yml A roles/linuxbrew/tasks/main.yml Log Message: ----------- Merge pull request #5 from jmchilton/linuxbrew linuxbrew role for jenkins. Compare: https://github.com/galaxyproject/infrastructure-playbook/compare/a1912b492b…

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[galaxyproject/galaxy] 4fb487: Jobs API docstring {job_id} to {id} convention fix...
by GitHub 18 Sep '15

18 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4fb4873934ea8857a2e4a694194a97137ba7ae35 https://github.com/galaxyproject/galaxy/commit/4fb4873934ea8857a2e4a694194a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-18 (Fri, 18 Sep 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/jobs.py Log Message: ----------- Jobs API docstring {job_id} to {id} convention fix. Elsewhere we refer to a member's id as simply 'id' in docs, and this is the parameter name. Commit: 3de7bb66993c0094f8ff138fcb768a75fd5f3a0a https://github.com/galaxyproject/galaxy/commit/3de7bb66993c0094f8ff138fcb76… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2015-09-18 (Fri, 18 Sep 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/jobs.py Log Message: ----------- Merge pull request #751 from dannon/api_docstrings Jobs API docstring {job_id} to {id} convention fix. Elsewhere we ref… Compare: https://github.com/galaxyproject/galaxy/compare/35621ca118d2...3de7bb66993c

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[galaxyproject/galaxy] 0ea4ad: Remove deprecated objectstore options from sample; ...
by GitHub 18 Sep '15

18 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 0ea4ad69a013a51b1327a275864a0471ec55c070 https://github.com/galaxyproject/galaxy/commit/0ea4ad69a013a51b1327a275864a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-18 (Fri, 18 Sep 2015) Changed paths: M config/galaxy.ini.sample Log Message: ----------- Remove deprecated objectstore options from sample; the new way is to set object_store_conf and use it. Commit: 35621ca118d278559dee31ff0ac53f77184be7c1 https://github.com/galaxyproject/galaxy/commit/35621ca118d278559dee31ff0ac5… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2015-09-18 (Fri, 18 Sep 2015) Changed paths: M config/galaxy.ini.sample Log Message: ----------- Merge pull request #748 from dannon/sample_cleanup Remove deprecated objectstore options from sample; the new way is to … Compare: https://github.com/galaxyproject/galaxy/compare/fec26b39c26d...35621ca118d2

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[galaxyproject/infrastructure-playbook] a1912b: add samtools to n2
by GitHub 17 Sep '15

17 Sep '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: a1912b492bb16b94f5f2bc285fc7fdd98b094fa0 https://github.com/galaxyproject/infrastructure-playbook/commit/a1912b492bb… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-09-17 (Thu, 17 Sep 2015) Changed paths: M galaxyenv/host_vars/n2.galaxyproject.org.yml Log Message: ----------- add samtools to n2

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[galaxyproject/galaxy] e71826: API, histories: correct copy to copy both non-dele...
by GitHub 17 Sep '15

17 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e71826889f1c4f8f4cab68ac7adab40bf53d3094 https://github.com/galaxyproject/galaxy/commit/e71826889f1c4f8f4cab68ac7ada… Author: Carl Eberhard <carlfeberhard(a)gmail.com> Date: 2015-09-17 (Thu, 17 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/multi-panel.js M lib/galaxy/webapps/galaxy/api/histories.py M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/multi-panel.js.map M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/multi-panel.js Log Message: ----------- API, histories: correct copy to copy both non-deleted and deleted contents by default, add all_datasets flag to support copying only non-deleted; UI, histories: separate out history copy dialog for use in multi-panel (and later: the options menu), include deleted filter in choices Commit: de8bdaf44f0d304ce715e7ff43cf43b1b920f28a https://github.com/galaxyproject/galaxy/commit/de8bdaf44f0d304ce715e7ff43cf… Author: Carl Eberhard <carlfeberhard(a)gmail.com> Date: 2015-09-17 (Thu, 17 Sep 2015) Changed paths: A client/galaxy/scripts/mvc/history/copy-dialog.js A static/maps/mvc/history/copy-dialog.js.map A static/scripts/mvc/history/copy-dialog.js Log Message: ----------- Fix to e718268: add copy-dialog files Commit: 3f71220bcfd6d17593e1f8d7aa7e09e6e5bd9997 https://github.com/galaxyproject/galaxy/commit/3f71220bcfd6d17593e1f8d7aa7e… Author: Carl Eberhard <carlfeberhard(a)gmail.com> Date: 2015-09-17 (Thu, 17 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/history/copy-dialog.js M static/maps/mvc/history/copy-dialog.js.map M static/scripts/mvc/history/copy-dialog.js Log Message: ----------- UI, history: clean up copy dialog Commit: fec26b39c26d1687622dbfc999d244f34afcf264 https://github.com/galaxyproject/galaxy/commit/fec26b39c26d1687622dbfc999d2… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-09-17 (Thu, 17 Sep 2015) Changed paths: A client/galaxy/scripts/mvc/history/copy-dialog.js M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/multi-panel.js M lib/galaxy/webapps/galaxy/api/histories.py A static/maps/mvc/history/copy-dialog.js.map M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/multi-panel.js.map A static/scripts/mvc/history/copy-dialog.js M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/multi-panel.js Log Message: ----------- Merge pull request #742 from carlfeberhard/history.copy-dialog History copy dialog & API fix Compare: https://github.com/galaxyproject/galaxy/compare/63e35965401a...fec26b39c26d

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