galaxy-commits April 2016

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[galaxyproject/galaxy] 03c857: Multi-history: open rerun button in new tab
by GitHub 15 Apr '16

15 Apr '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 03c85737319dbce1a3c9aa258c7c22d2d97d5c35 https://github.com/galaxyproject/galaxy/commit/03c85737319dbce1a3c9aa258c7c… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-04-14 (Thu, 14 Apr 2016) Changed paths: M client/galaxy/scripts/mvc/history/multi-panel.js M static/maps/mvc/history/multi-panel.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/history/multi-panel.js Log Message: ----------- Multi-history: open rerun button in new tab Commit: e193e46e30d84d7f844a2941f72ed65af11f69b3 https://github.com/galaxyproject/galaxy/commit/e193e46e30d84d7f844a2941f72e… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-04-15 (Fri, 15 Apr 2016) Changed paths: M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh Log Message: ----------- Place $headers before integrity_check PBS needs the resource selection (which will be filled in using $headers) to appear before anything else (except the shebang), so this changes the order. Commit: 434321915a61f53cd668170da076251a8c15889f https://github.com/galaxyproject/galaxy/commit/434321915a61f53cd668170da076… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-04-15 (Fri, 15 Apr 2016) Changed paths: M lib/galaxy/jobs/runners/util/job_script/CLUSTER_SLOTS_STATEMENT.sh Log Message: ----------- Use "$NCPUS" if defined to set GALAXY_SLOTS On our PBS cluster we do not have $PBS_NCPUS, and $PBS_NODEFILE contains the hostname of the nodes the task runs on. But we do have "$NCPUS" with the correct number of CPUS. Commit: 8e72b3095bacdac90a6fa7dea6125f489826bcfd https://github.com/galaxyproject/galaxy/commit/8e72b3095bacdac90a6fa7dea612… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-04-15 (Fri, 15 Apr 2016) Changed paths: M lib/galaxy/jobs/runners/util/job_script/CLUSTER_SLOTS_STATEMENT.sh M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh Log Message: ----------- Merge pull request #2174 from mvdbeek/reorder_job_template [16.01] Backport #2146 #2145 Commit: 3e79a574bea53731c734b568e1c6eeab4199cbdd https://github.com/galaxyproject/galaxy/commit/3e79a574bea53731c734b568e1c6… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-15 (Fri, 15 Apr 2016) Changed paths: M client/galaxy/scripts/mvc/history/multi-panel.js M static/maps/mvc/history/multi-panel.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/history/multi-panel.js Log Message: ----------- Merge #2167 manually to resolve conflicts. Commit: 9e278de3959200a1432cca6ba33bc6e7ddd89b60 https://github.com/galaxyproject/galaxy/commit/9e278de3959200a1432cca6ba33b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-15 (Fri, 15 Apr 2016) Changed paths: M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Rebuild client. Commit: 1c38b9723cc2ed8c42b55095484814e89e99b436 https://github.com/galaxyproject/galaxy/commit/1c38b9723cc2ed8c42b550954848… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-15 (Fri, 15 Apr 2016) Changed paths: M client/galaxy/scripts/mvc/history/multi-panel.js M lib/galaxy/jobs/runners/util/job_script/CLUSTER_SLOTS_STATEMENT.sh M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh M static/maps/mvc/history/multi-panel.js.map M static/scripts/mvc/history/multi-panel.js Log Message: ----------- Merge 16.01->16.04 Commit: d8e4f571aebc356ff0b943526c9795096420d35a https://github.com/galaxyproject/galaxy/commit/d8e4f571aebc356ff0b943526c97… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-15 (Fri, 15 Apr 2016) Changed paths: M client/galaxy/scripts/mvc/history/multi-panel.js M static/maps/mvc/history/multi-panel.js.map M static/scripts/mvc/history/multi-panel.js Log Message: ----------- Merge branch 'release_16.04' into dev Compare: https://github.com/galaxyproject/galaxy/compare/cdadaa436ccf...d8e4f571aebc

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[galaxyproject/galaxy] 03c857: Multi-history: open rerun button in new tab
by GitHub 15 Apr '16

15 Apr '16

Branch: refs/heads/release_16.04 Home: https://github.com/galaxyproject/galaxy Commit: 03c85737319dbce1a3c9aa258c7c22d2d97d5c35 https://github.com/galaxyproject/galaxy/commit/03c85737319dbce1a3c9aa258c7c… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-04-14 (Thu, 14 Apr 2016) Changed paths: M client/galaxy/scripts/mvc/history/multi-panel.js M static/maps/mvc/history/multi-panel.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/history/multi-panel.js Log Message: ----------- Multi-history: open rerun button in new tab Commit: e193e46e30d84d7f844a2941f72ed65af11f69b3 https://github.com/galaxyproject/galaxy/commit/e193e46e30d84d7f844a2941f72e… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-04-15 (Fri, 15 Apr 2016) Changed paths: M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh Log Message: ----------- Place $headers before integrity_check PBS needs the resource selection (which will be filled in using $headers) to appear before anything else (except the shebang), so this changes the order. Commit: 434321915a61f53cd668170da076251a8c15889f https://github.com/galaxyproject/galaxy/commit/434321915a61f53cd668170da076… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-04-15 (Fri, 15 Apr 2016) Changed paths: M lib/galaxy/jobs/runners/util/job_script/CLUSTER_SLOTS_STATEMENT.sh Log Message: ----------- Use "$NCPUS" if defined to set GALAXY_SLOTS On our PBS cluster we do not have $PBS_NCPUS, and $PBS_NODEFILE contains the hostname of the nodes the task runs on. But we do have "$NCPUS" with the correct number of CPUS. Commit: 8e72b3095bacdac90a6fa7dea6125f489826bcfd https://github.com/galaxyproject/galaxy/commit/8e72b3095bacdac90a6fa7dea612… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-04-15 (Fri, 15 Apr 2016) Changed paths: M lib/galaxy/jobs/runners/util/job_script/CLUSTER_SLOTS_STATEMENT.sh M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh Log Message: ----------- Merge pull request #2174 from mvdbeek/reorder_job_template [16.01] Backport #2146 #2145 Commit: 3e79a574bea53731c734b568e1c6eeab4199cbdd https://github.com/galaxyproject/galaxy/commit/3e79a574bea53731c734b568e1c6… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-15 (Fri, 15 Apr 2016) Changed paths: M client/galaxy/scripts/mvc/history/multi-panel.js M static/maps/mvc/history/multi-panel.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/history/multi-panel.js Log Message: ----------- Merge #2167 manually to resolve conflicts. Commit: 9e278de3959200a1432cca6ba33bc6e7ddd89b60 https://github.com/galaxyproject/galaxy/commit/9e278de3959200a1432cca6ba33b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-15 (Fri, 15 Apr 2016) Changed paths: M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Rebuild client. Commit: 1c38b9723cc2ed8c42b55095484814e89e99b436 https://github.com/galaxyproject/galaxy/commit/1c38b9723cc2ed8c42b550954848… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-15 (Fri, 15 Apr 2016) Changed paths: M client/galaxy/scripts/mvc/history/multi-panel.js M lib/galaxy/jobs/runners/util/job_script/CLUSTER_SLOTS_STATEMENT.sh M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh M static/maps/mvc/history/multi-panel.js.map M static/scripts/mvc/history/multi-panel.js Log Message: ----------- Merge 16.01->16.04 Compare: https://github.com/galaxyproject/galaxy/compare/7488e3b7be05...1c38b9723cc2

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[galaxyproject/galaxy] 03c857: Multi-history: open rerun button in new tab
by GitHub 15 Apr '16

15 Apr '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: 03c85737319dbce1a3c9aa258c7c22d2d97d5c35 https://github.com/galaxyproject/galaxy/commit/03c85737319dbce1a3c9aa258c7c… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-04-14 (Thu, 14 Apr 2016) Changed paths: M client/galaxy/scripts/mvc/history/multi-panel.js M static/maps/mvc/history/multi-panel.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/history/multi-panel.js Log Message: ----------- Multi-history: open rerun button in new tab Commit: 3e79a574bea53731c734b568e1c6eeab4199cbdd https://github.com/galaxyproject/galaxy/commit/3e79a574bea53731c734b568e1c6… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-15 (Fri, 15 Apr 2016) Changed paths: M client/galaxy/scripts/mvc/history/multi-panel.js M static/maps/mvc/history/multi-panel.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/history/multi-panel.js Log Message: ----------- Merge #2167 manually to resolve conflicts. Commit: 9e278de3959200a1432cca6ba33bc6e7ddd89b60 https://github.com/galaxyproject/galaxy/commit/9e278de3959200a1432cca6ba33b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-15 (Fri, 15 Apr 2016) Changed paths: M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Rebuild client. Compare: https://github.com/galaxyproject/galaxy/compare/8e72b3095bac...9e278de39592

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[galaxyproject/infrastructure-playbook] 4b0a10: Added new IU instances
by GitHub 15 Apr '16

15 Apr '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 4b0a104c4decd57882eecf5a77715c625c2b9145 https://github.com/galaxyproject/infrastructure-playbook/commit/4b0a104c4de… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-04-15 (Fri, 15 Apr 2016) Changed paths: M jetstreamiuenv/group_vars/slurmclients.yml M jetstreamiuenv/inventory Log Message: ----------- Added new IU instances

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[galaxyproject/galaxy] 5ff7f9: Fix running tool tests if remote user middleware i...
by GitHub 15 Apr '16

15 Apr '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 5ff7f9a19fd989ae3b4a011c2c5f3ababfb5b508 https://github.com/galaxyproject/galaxy/commit/5ff7f9a19fd989ae3b4a011c2c5f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-04-14 (Thu, 14 Apr 2016) Changed paths: M test/base/interactor.py Log Message: ----------- Fix running tool tests if remote user middleware is enabled. Commit: cdadaa436ccf89ff24c9c7b0935c0d41789fbd8a https://github.com/galaxyproject/galaxy/commit/cdadaa436ccf89ff24c9c7b0935c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-15 (Fri, 15 Apr 2016) Changed paths: M test/base/interactor.py Log Message: ----------- Merge pull request #2173 from jmchilton/single_user Fix running tool tests if remote user middleware is enabled. Compare: https://github.com/galaxyproject/galaxy/compare/58f510fda94d...cdadaa436ccf

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[galaxyproject/usegalaxy-playbook] 7c3c7e: Jetstream fixes for Test's job conf
by GitHub 15 Apr '16

15 Apr '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 7c3c7e4b22b1853e1a671cb569242d163088964d https://github.com/galaxyproject/usegalaxy-playbook/commit/7c3c7e4b22b1853e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-04-15 (Fri, 15 Apr 2016) Changed paths: M templates/galaxy/test.galaxyproject.org/config/job_conf.xml.j2 Log Message: ----------- Jetstream fixes for Test's job conf

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[galaxyproject/galaxy] e193e4: Place $headers before integrity_check
by GitHub 15 Apr '16

15 Apr '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: e193e46e30d84d7f844a2941f72ed65af11f69b3 https://github.com/galaxyproject/galaxy/commit/e193e46e30d84d7f844a2941f72e… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-04-15 (Fri, 15 Apr 2016) Changed paths: M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh Log Message: ----------- Place $headers before integrity_check PBS needs the resource selection (which will be filled in using $headers) to appear before anything else (except the shebang), so this changes the order. Commit: 434321915a61f53cd668170da076251a8c15889f https://github.com/galaxyproject/galaxy/commit/434321915a61f53cd668170da076… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-04-15 (Fri, 15 Apr 2016) Changed paths: M lib/galaxy/jobs/runners/util/job_script/CLUSTER_SLOTS_STATEMENT.sh Log Message: ----------- Use "$NCPUS" if defined to set GALAXY_SLOTS On our PBS cluster we do not have $PBS_NCPUS, and $PBS_NODEFILE contains the hostname of the nodes the task runs on. But we do have "$NCPUS" with the correct number of CPUS. Commit: 8e72b3095bacdac90a6fa7dea6125f489826bcfd https://github.com/galaxyproject/galaxy/commit/8e72b3095bacdac90a6fa7dea612… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-04-15 (Fri, 15 Apr 2016) Changed paths: M lib/galaxy/jobs/runners/util/job_script/CLUSTER_SLOTS_STATEMENT.sh M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh Log Message: ----------- Merge pull request #2174 from mvdbeek/reorder_job_template [16.01] Backport #2146 #2145 Compare: https://github.com/galaxyproject/galaxy/compare/18c00899a30c...8e72b3095bac

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[galaxyproject/galaxy] cde04a: markupsafe.escape() in Python2 does not work on st...
by GitHub 15 Apr '16

15 Apr '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: cde04ad52d40b5d7b26a0c636d9d24bf6adbdc92 https://github.com/galaxyproject/galaxy/commit/cde04ad52d40b5d7b26a0c636d9d… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-04-12 (Tue, 12 Apr 2016) Changed paths: M lib/galaxy/web/framework/helpers/grids.py Log Message: ----------- markupsafe.escape() in Python2 does not work on str containing non-ASCII characters. Fix #2135. Commit: 34900f87f5bc52bc84efe866371588004a049ebf https://github.com/galaxyproject/galaxy/commit/34900f87f5bc52bc84efe8663715… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-04-14 (Thu, 14 Apr 2016) Changed paths: M tools/stats/grouping.py M tools/stats/grouping.xml Log Message: ----------- Fix grouping tool broken in 7347d75a4a36d42f8060e11d708291d796b266a5 / fd85979a8651e0907bebce05cdfb59d77f0d0f64, and enhance performance when removing lines. Commit: 18c00899a30cd162cd0bb3a251a49cff2143d3a3 https://github.com/galaxyproject/galaxy/commit/18c00899a30cd162cd0bb3a251a4… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-14 (Thu, 14 Apr 2016) Changed paths: M lib/galaxy/web/framework/helpers/grids.py Log Message: ----------- Merge pull request #2138 from nsoranzo/release_16.01_fix_for_2135 [16.01] markupsafe.escape() in Python2 does not work on str containing non-ASCII characters Commit: 7f101b8da8d09121a302a6707610434e1e2d3cdf https://github.com/galaxyproject/galaxy/commit/7f101b8da8d09121a302a6707610… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-04-14 (Thu, 14 Apr 2016) Changed paths: M tools/stats/grouping.py M tools/stats/grouping.xml Log Message: ----------- Merge pull request #2166 from blankenberg/release_16.04 [16.04] Fix grouping tool and enhance performance when removing lines. Commit: 7488e3b7be059eb5759020b148c6bff369a15ea6 https://github.com/galaxyproject/galaxy/commit/7488e3b7be059eb5759020b148c6… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-04-15 (Fri, 15 Apr 2016) Changed paths: M lib/galaxy/web/framework/helpers/grids.py Log Message: ----------- Merge branch 'release_16.01' into release_16.04 Conflicts: lib/galaxy/web/framework/helpers/grids.py Commit: 58f510fda94d12a1041460a603ac56dd7f0f1928 https://github.com/galaxyproject/galaxy/commit/58f510fda94d12a1041460a603ac… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-04-15 (Fri, 15 Apr 2016) Changed paths: M lib/galaxy/web/framework/helpers/grids.py M tools/stats/grouping.py M tools/stats/grouping.xml Log Message: ----------- Merge branch 'release_16.04' into dev Compare: https://github.com/galaxyproject/galaxy/compare/88db9e6a0f0b...58f510fda94d

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[galaxyproject/galaxy] cde04a: markupsafe.escape() in Python2 does not work on st...
by GitHub 15 Apr '16

15 Apr '16

Branch: refs/heads/release_16.04 Home: https://github.com/galaxyproject/galaxy Commit: cde04ad52d40b5d7b26a0c636d9d24bf6adbdc92 https://github.com/galaxyproject/galaxy/commit/cde04ad52d40b5d7b26a0c636d9d… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-04-12 (Tue, 12 Apr 2016) Changed paths: M lib/galaxy/web/framework/helpers/grids.py Log Message: ----------- markupsafe.escape() in Python2 does not work on str containing non-ASCII characters. Fix #2135. Commit: 18c00899a30cd162cd0bb3a251a49cff2143d3a3 https://github.com/galaxyproject/galaxy/commit/18c00899a30cd162cd0bb3a251a4… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-14 (Thu, 14 Apr 2016) Changed paths: M lib/galaxy/web/framework/helpers/grids.py Log Message: ----------- Merge pull request #2138 from nsoranzo/release_16.01_fix_for_2135 [16.01] markupsafe.escape() in Python2 does not work on str containing non-ASCII characters Commit: 7488e3b7be059eb5759020b148c6bff369a15ea6 https://github.com/galaxyproject/galaxy/commit/7488e3b7be059eb5759020b148c6… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-04-15 (Fri, 15 Apr 2016) Changed paths: M lib/galaxy/web/framework/helpers/grids.py Log Message: ----------- Merge branch 'release_16.01' into release_16.04 Conflicts: lib/galaxy/web/framework/helpers/grids.py Compare: https://github.com/galaxyproject/galaxy/compare/7f101b8da8d0...7488e3b7be05

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[galaxyproject/infrastructure-playbook] f9bc82: Rename partition on Jetstream to multi
by GitHub 14 Apr '16

14 Apr '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: f9bc8286d623204da6d929035cf078887eece83d https://github.com/galaxyproject/infrastructure-playbook/commit/f9bc8286d62… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-04-14 (Thu, 14 Apr 2016) Changed paths: M jetstreamiuenv/templates/slurm/slurm.conf.j2 M jetstreamtaccenv/templates/slurm/slurm.conf.j2 Log Message: ----------- Rename partition on Jetstream to multi

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galaxy-commits April 2016