galaxy-commits October 2016

galaxy-commits@lists.galaxyproject.org

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[galaxyproject/usegalaxy-playbook] ef5103: update MTS
by GitHub 14 Oct '16

14 Oct '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: ef5103c91cffeb3acd129ece6205b7ed43a4383e https://github.com/galaxyproject/usegalaxy-playbook/commit/ef5103c91cffeb3a… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-10-14 (Fri, 14 Oct 2016) Changed paths: M common_roles M production/group_vars/toolshedservers.yml Log Message: ----------- update MTS

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[galaxyproject/galaxy] 600112: remove the communication server check
by GitHub 14 Oct '16

14 Oct '16

Branch: refs/heads/master-toolshed Home: https://github.com/galaxyproject/galaxy Commit: 600112256970c1024b3ba4e6fa57cd61f9fe199d https://github.com/galaxyproject/galaxy/commit/600112256970c1024b3ba4e6fa57… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-10-13 (Thu, 13 Oct 2016) Changed paths: M templates/user/index.mako Log Message: ----------- remove the communication server check from non-galaxy calls Commit: cf0e4e84ce4137334ee6e8c20e56a52070179c4d https://github.com/galaxyproject/galaxy/commit/cf0e4e84ce4137334ee6e8c20e56… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-10-14 (Fri, 14 Oct 2016) Changed paths: M templates/user/index.mako Log Message: ----------- Merge pull request #3053 from martenson/fix-userindex-for-ts [16.07] remove the communication server check Commit: 14dcf65132331170bf86c279b23241b7496d16d3 https://github.com/galaxyproject/galaxy/commit/14dcf65132331170bf86c279b232… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-10-14 (Fri, 14 Oct 2016) Changed paths: M templates/user/index.mako Log Message: ----------- Merge pull request #3056 from galaxyproject/release_16.07 [master-toolshed]merge in release_16.07 Compare: https://github.com/galaxyproject/galaxy/compare/735c682ead5f...14dcf6513233

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[galaxyproject/galaxy] 600112: remove the communication server check
by GitHub 14 Oct '16

14 Oct '16

Branch: refs/heads/release_16.07 Home: https://github.com/galaxyproject/galaxy Commit: 600112256970c1024b3ba4e6fa57cd61f9fe199d https://github.com/galaxyproject/galaxy/commit/600112256970c1024b3ba4e6fa57… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-10-13 (Thu, 13 Oct 2016) Changed paths: M templates/user/index.mako Log Message: ----------- remove the communication server check from non-galaxy calls Commit: cf0e4e84ce4137334ee6e8c20e56a52070179c4d https://github.com/galaxyproject/galaxy/commit/cf0e4e84ce4137334ee6e8c20e56… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-10-14 (Fri, 14 Oct 2016) Changed paths: M templates/user/index.mako Log Message: ----------- Merge pull request #3053 from martenson/fix-userindex-for-ts [16.07] remove the communication server check Compare: https://github.com/galaxyproject/galaxy/compare/3300a73c9db6...cf0e4e84ce41

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[galaxyproject/usegalaxy-playbook] b3aa09: Set Java memory on reserved destinations as well
by GitHub 14 Oct '16

14 Oct '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: b3aa0904fc2c468e6c109ed19817d35bdd1277a4 https://github.com/galaxyproject/usegalaxy-playbook/commit/b3aa0904fc2c468e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-10-14 (Fri, 14 Oct 2016) Changed paths: M templates/galaxy/usegalaxy.org/config/job_conf.xml.j2 Log Message: ----------- Set Java memory on reserved destinations as well

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[galaxyproject/usegalaxy-playbook] 505e87: Correctly set JVM memory size for Java tools
by GitHub 14 Oct '16

14 Oct '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 505e87545af74c1cfd7e276b1d35a53d74ada938 https://github.com/galaxyproject/usegalaxy-playbook/commit/505e87545af74c1c… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-10-14 (Fri, 14 Oct 2016) Changed paths: M templates/galaxy/usegalaxy.org/config/job_conf.xml.j2 Log Message: ----------- Correctly set JVM memory size for Java tools

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[galaxyproject/galaxy] 604dfb: Fix for reruning tool with workflow resume that is...
by GitHub 14 Oct '16

14 Oct '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 604dfb27ce0acba176c059f08642aae7a390ddf0 https://github.com/galaxyproject/galaxy/commit/604dfb27ce0acba176c059f08642… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-10-07 (Fri, 07 Oct 2016) Changed paths: M lib/galaxy/tools/parameters/__init__.py Log Message: ----------- Fix for reruning tool with workflow resume that is part of a collection. The special casing of "__identifier__" that occurs here and elsewhere in the code is less than ideal. Commit: a895c823daaf01c2b1b883dc256452411de9a728 https://github.com/galaxyproject/galaxy/commit/a895c823daaf01c2b1b883dc2564… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-10-14 (Fri, 14 Oct 2016) Changed paths: M lib/galaxy/tools/parameters/__init__.py Log Message: ----------- Merge pull request #3019 from blankenberg/collection-wf-resume-error Fix for rerunning tool with workflow resume that is part of a collection. Compare: https://github.com/galaxyproject/galaxy/compare/28bb83f0ab5e...a895c823daaf

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[galaxyproject/galaxy] 36134b: Added code to adjust top setting of tool search if...
by GitHub 14 Oct '16

14 Oct '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 36134bca694c9dc6b2584fb661dfbce4ddb793e6 https://github.com/galaxyproject/galaxy/commit/36134bca694c9dc6b2584fb661df… Author: Scott Szakonyi <sszakony(a)nd.edu> Date: 2016-10-14 (Fri, 14 Oct 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tools.js Log Message: ----------- Added code to adjust top setting of tool search if messagebox is visible, issue 2907 Commit: 6312d8052b9668a03b3bb25ea02b9d42ac32de6d https://github.com/galaxyproject/galaxy/commit/6312d8052b9668a03b3bb25ea02b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-10-14 (Fri, 14 Oct 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tools.js M static/maps/mvc/tool/tools.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/tool/tools.js Log Message: ----------- Rebuild cilent. Commit: 28bb83f0ab5e93b5f961f12dac555bf96a9073ea https://github.com/galaxyproject/galaxy/commit/28bb83f0ab5e93b5f961f12dac55… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-10-14 (Fri, 14 Oct 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tools.js M static/maps/mvc/tool/tools.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/tool/tools.js Log Message: ----------- Merge pull request #3055 from dannon/cherrypick_masthead_fix Cherrypick masthead fix Compare: https://github.com/galaxyproject/galaxy/compare/e5913a49e260...28bb83f0ab5e

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[galaxyproject/galaxy] f6d5f3: Fix downloading tool tarball with boolean test inp...
by GitHub 14 Oct '16

14 Oct '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f6d5f3c4a2e51bd6b75a99dc015360e4ca9a6461 https://github.com/galaxyproject/galaxy/commit/f6d5f3c4a2e51bd6b75a99dc0153… Author: Dave B <dave(a)bx.psu.edu> Date: 2016-10-13 (Thu, 13 Oct 2016) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Fix downloading tool tarball with boolean test input values. Commit: e5913a49e260be47ff4f32ae21780264731d98d5 https://github.com/galaxyproject/galaxy/commit/e5913a49e260be47ff4f32ae2178… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-10-14 (Fri, 14 Oct 2016) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge pull request #3047 from galaxyproject/tool_tarball_fix Fix downloading tool tarball with boolean test input values. Compare: https://github.com/galaxyproject/galaxy/compare/d26f46423e5d...e5913a49e260

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[galaxyproject/galaxy] bb4428: Failthrough to using imghdr when PIL does not dete...
by GitHub 14 Oct '16

14 Oct '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: bb4428896839898fb5d0c9b88ae18fc9b705a27b https://github.com/galaxyproject/galaxy/commit/bb4428896839898fb5d0c9b88ae1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-10-13 (Thu, 13 Oct 2016) Changed paths: M lib/galaxy/datatypes/images.py M lib/galaxy/datatypes/util/image_util.py M lib/galaxy/util/checkers.py M tools/data_source/upload.py Log Message: ----------- Failthrough to using imghdr when PIL does not detect an image correctly. Some misc cleanup, avoiding use of system functions as variable names, etc. Commit: cb6e25278c4a59d4ea2edd9ce5e9c757b1ebf7f8 https://github.com/galaxyproject/galaxy/commit/cb6e25278c4a59d4ea2edd9ce5e9… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-10-13 (Thu, 13 Oct 2016) Changed paths: M lib/galaxy/datatypes/images.py M lib/galaxy/datatypes/sequence.py R lib/galaxy/datatypes/util/image_util.py M lib/galaxy/util/checkers.py A lib/galaxy/util/image_util.py M tools/data_source/upload.py Log Message: ----------- Refactoring, because it was bugging me. Commit: ed263bf8a52b37199cc7822126598a75a9984335 https://github.com/galaxyproject/galaxy/commit/ed263bf8a52b37199cc782212659… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-10-13 (Thu, 13 Oct 2016) Changed paths: M lib/galaxy/util/image_util.py Log Message: ----------- import order. Commit: 4bc429776853239961c45c9656c69b3be0ae01bc https://github.com/galaxyproject/galaxy/commit/4bc429776853239961c45c9656c6… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-10-13 (Thu, 13 Oct 2016) Changed paths: M lib/galaxy/util/image_util.py Log Message: ----------- Simplify, strip out passing of image. Commit: d26f46423e5d79dd8d0519d90350389838fece3c https://github.com/galaxyproject/galaxy/commit/d26f46423e5d79dd8d0519d90350… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-10-14 (Fri, 14 Oct 2016) Changed paths: M lib/galaxy/datatypes/images.py M lib/galaxy/datatypes/sequence.py R lib/galaxy/datatypes/util/image_util.py M lib/galaxy/util/checkers.py A lib/galaxy/util/image_util.py M tools/data_source/upload.py Log Message: ----------- Merge pull request #3042 from dannon/image_detection_fixes Image detection fixes Compare: https://github.com/galaxyproject/galaxy/compare/4446ccc98c97...d26f46423e5d

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[galaxyproject/galaxy] b6d447: Fix for displaying parameters to the user, that ha...
by GitHub 13 Oct '16

13 Oct '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b6d4473aa0975f88b2d2cf8aa1372aecfc92919b https://github.com/galaxyproject/galaxy/commit/b6d4473aa0975f88b2d2cf8aa137… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-10-13 (Thu, 13 Oct 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Fix for displaying parameters to the user, that have a False value. Previously, e.g. an integer with a value of 0 would display "Not available.". Commit: 4446ccc98c970f5077080f563585c90b1f84dc3a https://github.com/galaxyproject/galaxy/commit/4446ccc98c970f5077080f563585… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-10-13 (Thu, 13 Oct 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Merge pull request #3045 from blankenberg/value_to_display_text-fix Fix for displaying parameters to the user, that have a False value. Compare: https://github.com/galaxyproject/galaxy/compare/0062eacfdf86...4446ccc98c97

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galaxy-commits October 2016