galaxy-commits March 2016

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[galaxyproject/galaxy] 975c6f: Much more friendly route mapping.
by GitHub 25 Mar '16

25 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 975c6f5eae19a7f37a828c1d0648f00b2366449a https://github.com/galaxyproject/galaxy/commit/975c6f5eae19a7f37a828c1d0648… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-22 (Tue, 22 Mar 2016) Changed paths: M lib/galaxy/web/framework/base.py M lib/galaxy/web/framework/middleware/statsd.py Log Message: ----------- Much more friendly route mapping. Commit: 84044f9a5f3c5db74ff65eae2544bd61f047f108 https://github.com/galaxyproject/galaxy/commit/84044f9a5f3c5db74ff65eae2544… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-25 (Fri, 25 Mar 2016) Changed paths: M lib/galaxy/web/framework/base.py M lib/galaxy/web/framework/middleware/statsd.py Log Message: ----------- Merge pull request #2002 from dannon/statswork Much more friendly route mapping. Compare: https://github.com/galaxyproject/galaxy/compare/6aaec509edf2...84044f9a5f3c

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[galaxyproject/galaxy] e1fcbc: change default size of fa in iconspans
by GitHub 25 Mar '16

25 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e1fcbc7a208464f9b2a3e6d5eac05bfacd414d38 https://github.com/galaxyproject/galaxy/commit/e1fcbc7a208464f9b2a3e6d5eac0… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-23 (Wed, 23 Mar 2016) Changed paths: M client/galaxy/style/less/library.less M static/style/blue/base.css M static/style/blue/library.css Log Message: ----------- change default size of fa in iconspans leave as is for the globe icon Commit: 6aaec509edf261ddbe866df0030762c4f0d9943e https://github.com/galaxyproject/galaxy/commit/6aaec509edf261ddbe866df00307… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-25 (Fri, 25 Mar 2016) Changed paths: M client/galaxy/style/less/library.less M static/style/blue/base.css M static/style/blue/library.css Log Message: ----------- Merge pull request #2000 from martenson/fix-lib-icons libraries: change default size of fa in iconspans Compare: https://github.com/galaxyproject/galaxy/compare/0f099b75b608...6aaec509edf2

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[galaxyproject/galaxy] dc49a9: Fix unbound error that is possible if using tool b...
by GitHub 25 Mar '16

25 Mar '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: dc49a9cbc1b24fb4abd1c5b98eba433218a3042d https://github.com/galaxyproject/galaxy/commit/dc49a9cbc1b24fb4abd1c5b98eba… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-24 (Thu, 24 Mar 2016) Changed paths: M lib/galaxy/tools/execute.py Log Message: ----------- Fix unbound error that is possible if using tool bursting. Commit: 8accc56132ff5863ff4d0e3127d9aa5c8fc419d4 https://github.com/galaxyproject/galaxy/commit/8accc56132ff5863ff4d0e3127d9… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-25 (Fri, 25 Mar 2016) Changed paths: M lib/galaxy/tools/execute.py Log Message: ----------- Merge pull request #2009 from jmchilton/execute_params_fix [16.01] Fix unbound error that is possible if using tool bursting. Compare: https://github.com/galaxyproject/galaxy/compare/dede9459b019...8accc56132ff

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[galaxyproject/galaxy] b51bdd: Basepanels don't have Galaxy object, causing failu...
by GitHub 24 Mar '16

24 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b51bdd06b189baccab235def65d15a69c761ac28 https://github.com/galaxyproject/galaxy/commit/b51bdd06b189baccab235def65d1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-23 (Wed, 23 Mar 2016) Changed paths: M templates/base/base_panels.mako Log Message: ----------- Basepanels don't have Galaxy object, causing failures in views like published tracks, etc., when resource urls are generated incorrectly Commit: dede9459b019ceb1212f4f152b4108632f892384 https://github.com/galaxyproject/galaxy/commit/dede9459b019ceb1212f4f152b41… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-23 (Wed, 23 Mar 2016) Changed paths: M templates/base/base_panels.mako Log Message: ----------- Merge pull request #2003 from dannon/trackster_debugging [16.01] Fix shared viz (and other base_panels.mako displays) early URL generation. Commit: 0f099b75b608264bf67d7d88c858cfbd96f3225c https://github.com/galaxyproject/galaxy/commit/0f099b75b608264bf67d7d88c858… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-24 (Thu, 24 Mar 2016) Changed paths: M templates/base/base_panels.mako Log Message: ----------- Merge branch 'release_16.01' into dev Compare: https://github.com/galaxyproject/galaxy/compare/86d2b29026fc...0f099b75b608

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[galaxyproject/galaxy] c1fe8a: Fix inconsistency in update state handling for too...
by GitHub 24 Mar '16

24 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c1fe8aac0a646b2bed0b3dbfbf0cd75b595f1690 https://github.com/galaxyproject/galaxy/commit/c1fe8aac0a646b2bed0b3dbfbf0c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-03-23 (Wed, 23 Mar 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/workflow/modules.py Log Message: ----------- Fix inconsistency in update state handling for tool modules Commit: eaf8f4ed5056317f19950fef5e5340217fd0e809 https://github.com/galaxyproject/galaxy/commit/eaf8f4ed5056317f19950fef5e53… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-03-23 (Wed, 23 Mar 2016) Changed paths: M lib/galaxy/tools/parameters/__init__.py Log Message: ----------- Extend doc tests for parameter handling Commit: 86d2b29026fc4176070d3ef5150a4f0f0ff86829 https://github.com/galaxyproject/galaxy/commit/86d2b29026fc4176070d3ef5150a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-24 (Thu, 24 Mar 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/workflow/modules.py Log Message: ----------- Merge pull request #1993 from guerler/revise_parameters_000 Fix inconsistency in update state handling for tool modules Compare: https://github.com/galaxyproject/galaxy/compare/0a77851b9b9d...86d2b29026fc

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[galaxyproject/galaxy] ab31bd: move text out of icon spans for library dataset vi...
by GitHub 24 Mar '16

24 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ab31bd9f4865c3544a8bb8a4be8c77d41360bbed https://github.com/galaxyproject/galaxy/commit/ab31bd9f4865c3544a8bb8a4be8c… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-24 (Thu, 24 Mar 2016) Changed paths: M client/galaxy/scripts/mvc/library/library-dataset-view.js M static/maps/mvc/library/library-dataset-view.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/library/library-dataset-view.js Log Message: ----------- move text out of icon spans for library dataset view also re-touch the html to be better readable Commit: 0a77851b9b9dba237b529c06d7fcbe3b97ab2b47 https://github.com/galaxyproject/galaxy/commit/0a77851b9b9dba237b529c06d7fc… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-03-24 (Thu, 24 Mar 2016) Changed paths: M client/galaxy/scripts/mvc/library/library-dataset-view.js M static/maps/mvc/library/library-dataset-view.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/library/library-dataset-view.js Log Message: ----------- Merge pull request #2008 from martenson/libtext-from-span libraries: move text out of icon spans for library dataset view Compare: https://github.com/galaxyproject/galaxy/compare/909a5491e505...0a77851b9b9d

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[galaxyproject/galaxy] cfd937: Repack scripts
by GitHub 23 Mar '16

23 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: cfd937a46e8795c4d06deb3325e18d7439390d65 https://github.com/galaxyproject/galaxy/commit/cfd937a46e8795c4d06deb3325e1… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-03-23 (Wed, 23 Mar 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 M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Repack scripts Commit: 909a5491e50521c7374ef4e939e89015afe0ddde https://github.com/galaxyproject/galaxy/commit/909a5491e50521c7374ef4e939e8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-23 (Wed, 23 Mar 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 M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Merge pull request #2004 from guerler/repack_000 Repack js-scripts Compare: https://github.com/galaxyproject/galaxy/compare/3b0743fab272...909a5491e505

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[galaxyproject/galaxy] 93b747: remove deprecated user-facing lib link;
by GitHub 23 Mar '16

23 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 93b7473be87813454753c9c8e58bca297a59ca2e https://github.com/galaxyproject/galaxy/commit/93b7473be87813454753c9c8e58b… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-23 (Wed, 23 Mar 2016) Changed paths: M client/galaxy/scripts/layout/menu.js M static/maps/layout/menu.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/menu.js Log Message: ----------- remove deprecated user-facing lib link; remove 'published' from the menu items for shared elements Commit: 3b0743fab27220824ad14a0579b960ce79b20f0c https://github.com/galaxyproject/galaxy/commit/3b0743fab27220824ad14a0579b9… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2016-03-23 (Wed, 23 Mar 2016) Changed paths: M client/galaxy/scripts/layout/menu.js M static/maps/layout/menu.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/menu.js Log Message: ----------- Merge pull request #1996 from martenson/remove-liblink alter 'shared data' menu Compare: https://github.com/galaxyproject/galaxy/compare/fb549c80d49c...3b0743fab272

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[galaxyproject/galaxy] b51bdd: Basepanels don't have Galaxy object, causing failu...
by GitHub 23 Mar '16

23 Mar '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: b51bdd06b189baccab235def65d15a69c761ac28 https://github.com/galaxyproject/galaxy/commit/b51bdd06b189baccab235def65d1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-23 (Wed, 23 Mar 2016) Changed paths: M templates/base/base_panels.mako Log Message: ----------- Basepanels don't have Galaxy object, causing failures in views like published tracks, etc., when resource urls are generated incorrectly Commit: dede9459b019ceb1212f4f152b4108632f892384 https://github.com/galaxyproject/galaxy/commit/dede9459b019ceb1212f4f152b41… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-23 (Wed, 23 Mar 2016) Changed paths: M templates/base/base_panels.mako Log Message: ----------- Merge pull request #2003 from dannon/trackster_debugging [16.01] Fix shared viz (and other base_panels.mako displays) early URL generation. Compare: https://github.com/galaxyproject/galaxy/compare/21e71a9b46b9...dede9459b019

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[galaxyproject/usegalaxy-playbook] 8af4f9: Add a 32 GB destination, increase the BWA-MEM DM t...
by GitHub 23 Mar '16

23 Mar '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 8af4f9b38a8b14d898700befa0856acecca8c77b https://github.com/galaxyproject/usegalaxy-playbook/commit/8af4f9b38a8b14d8… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-03-23 (Wed, 23 Mar 2016) Changed paths: M files/galaxy/common/dynamic_rules/reserved.py M templates/galaxy/test.galaxyproject.org/config/job_conf.xml.j2 Log Message: ----------- Add a 32 GB destination, increase the BWA-MEM DM to 64GB

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galaxy-commits March 2016