galaxy-commits March 2016

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[galaxyproject/galaxy] a10934: Fix repeat prefix
by GitHub 04 Mar '16

04 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a10934741dc53b545effdbd407f6b05584bc64de https://github.com/galaxyproject/galaxy/commit/a10934741dc53b545effdbd407f6… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-03-03 (Thu, 03 Mar 2016) Changed paths: M lib/galaxy/tools/parameters/__init__.py Log Message: ----------- Fix repeat prefix Commit: 84daaec66e875055e5513619e9fa4c7368bda229 https://github.com/galaxyproject/galaxy/commit/84daaec66e875055e5513619e9fa… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-04 (Fri, 04 Mar 2016) Changed paths: M lib/galaxy/tools/parameters/__init__.py Log Message: ----------- Merge pull request #1848 from guerler/fix_prefix_000 Fix repeat prefix Compare: https://github.com/galaxyproject/galaxy/compare/6da3c56ec9e6...84daaec66e87

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[galaxyproject/galaxy] 1c73b8: also update rrda when repairing or updating a repo...
by GitHub 04 Mar '16

04 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1c73b8c1a335881d2b1573cc954d1c0ed1438c65 https://github.com/galaxyproject/galaxy/commit/1c73b8c1a335881d2b1573cc954d… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-03-03 (Thu, 03 Mar 2016) Changed paths: M lib/tool_shed/galaxy_install/repair_repository_manager.py M lib/tool_shed/galaxy_install/update_repository_manager.py Log Message: ----------- also update rrda when repairing or updating a repository Commit: 887e2577c98244a223cbc8ef0523fa8d1a4ae352 https://github.com/galaxyproject/galaxy/commit/887e2577c98244a223cbc8ef0523… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-03-04 (Fri, 04 Mar 2016) Changed paths: M lib/tool_shed/util/shed_util_common.py Log Message: ----------- Add logging before removing outdated dependencies Commit: 6da3c56ec9e6e644847eee417e2b3f4b5b5078c0 https://github.com/galaxyproject/galaxy/commit/6da3c56ec9e6e644847eee417e2b… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-04 (Fri, 04 Mar 2016) Changed paths: M lib/tool_shed/galaxy_install/repair_repository_manager.py M lib/tool_shed/galaxy_install/update_repository_manager.py M lib/tool_shed/util/shed_util_common.py Log Message: ----------- Merge pull request #1850 from mvdbeek/old_rrda_fix also update rrda when repairing or updating a repository Compare: https://github.com/galaxyproject/galaxy/compare/45bffbcd1915...6da3c56ec9e6

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[galaxyproject/galaxy] 26d556: Update more scripts to respect GALAXY_VIRTUAL_ENV.
by GitHub 03 Mar '16

03 Mar '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: 26d5561b4ff48eb770970bee5f2ba49d425e9902 https://github.com/galaxyproject/galaxy/commit/26d5561b4ff48eb770970bee5f2b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-03 (Thu, 03 Mar 2016) Changed paths: M manage_tools.sh M run_reports.sh M run_tool_shed.sh Log Message: ----------- Update more scripts to respect GALAXY_VIRTUAL_ENV. Drop explicit sourcing in run_reports and run_tool_shed since they source common_startup. Commit: 97793ab81ab5601466fa89bba7b3250118e95de4 https://github.com/galaxyproject/galaxy/commit/97793ab81ab5601466fa89bba7b3… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-03 (Thu, 03 Mar 2016) Changed paths: M manage_tools.sh M run_reports.sh M run_tool_shed.sh Log Message: ----------- Merge pull request #1847 from jmchilton/more_virtualenv_fixes [16.01] Update more scripts to respect GALAXY_VIRTUAL_ENV. Compare: https://github.com/galaxyproject/galaxy/compare/0fbd22c9a306...97793ab81ab5

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[galaxyproject/galaxy] 8dd247: Minor followup to 1846
by GitHub 03 Mar '16

03 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 8dd24734e3fd9dd64bc4bd93736c9ef571930cbf https://github.com/galaxyproject/galaxy/commit/8dd24734e3fd9dd64bc4bd93736c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-03 (Thu, 03 Mar 2016) Changed paths: M client/galaxy/scripts/onload.js M static/maps/onload.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/onload.js Log Message: ----------- Minor followup to 1846 Commit: 45bffbcd19158e6f147398d07d3f691f18d50247 https://github.com/galaxyproject/galaxy/commit/45bffbcd19158e6f147398d07d3f… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2016-03-03 (Thu, 03 Mar 2016) Changed paths: M client/galaxy/scripts/onload.js M static/maps/onload.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/onload.js Log Message: ----------- Merge pull request #1853 from dannon/style_nits Minor style followup to 1846 Compare: https://github.com/galaxyproject/galaxy/compare/02ed07ca82e1...45bffbcd1915

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[galaxyproject/galaxy] 6e13c3: Cherry-picked changes from pull request #1392.
by GitHub 03 Mar '16

03 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 6e13c3999a6d54b40b2910d5ce95da724f133122 https://github.com/galaxyproject/galaxy/commit/6e13c3999a6d54b40b2910d5ce95… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-02-29 (Mon, 29 Feb 2016) Changed paths: M lib/galaxy/web/form_builder.py M lib/galaxy/webapps/tool_shed/api/categories.py M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/buildapp.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/webapps/tool_shed/model/__init__.py M lib/galaxy/webapps/tool_shed/model/mapping.py M lib/tool_shed/util/common_util.py M lib/tool_shed/util/metadata_util.py M lib/tool_shed/util/repository_util.py M lib/tool_shed/util/shed_util_common.py M lib/tool_shed/util/tool_util.py M test/tool_shed/functional/test_1040_install_repository_basic_circular_dependencies.py Log Message: ----------- Cherry-picked changes from pull request #1392. Commit: 3ec58fd1da5f7122752627eef581d5826190bc13 https://github.com/galaxyproject/galaxy/commit/3ec58fd1da5f7122752627eef581… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-02-29 (Mon, 29 Feb 2016) Changed paths: M lib/galaxy/webapps/tool_shed/api/repositories.py Log Message: ----------- Update API endpoint names in code comments. Commit: b15a7ff06df23d7004f670f34638fe9ee5d33f92 https://github.com/galaxyproject/galaxy/commit/b15a7ff06df23d7004f670f34638… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-03-01 (Tue, 01 Mar 2016) Changed paths: M lib/galaxy/webapps/tool_shed/api/categories.py M lib/tool_shed/util/shed_util_common.py Log Message: ----------- Include repository metadata when browsing repositories in a category. Commit: 02ed07ca82e19e20b37e50e9f6294069240d9ed1 https://github.com/galaxyproject/galaxy/commit/02ed07ca82e19e20b37e50e9f629… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-03 (Thu, 03 Mar 2016) Changed paths: M lib/galaxy/web/form_builder.py M lib/galaxy/webapps/tool_shed/api/categories.py M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/buildapp.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/webapps/tool_shed/model/__init__.py M lib/galaxy/webapps/tool_shed/model/mapping.py M lib/tool_shed/util/common_util.py M lib/tool_shed/util/metadata_util.py M lib/tool_shed/util/repository_util.py M lib/tool_shed/util/shed_util_common.py M lib/tool_shed/util/tool_util.py M test/tool_shed/functional/test_1040_install_repository_basic_circular_dependencies.py Log Message: ----------- Merge pull request #1821 from davebx/toolshed_decouple_api Cherry-picked changes from pull request #1392. Compare: https://github.com/galaxyproject/galaxy/compare/779793810d1f...02ed07ca82e1

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[galaxyproject/galaxy] e0ce68: Fix lack of output when discovering large collecti...
by GitHub 03 Mar '16

03 Mar '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: e0ce68cc58a6d6eeb306f5c0445563e71bcc1d12 https://github.com/galaxyproject/galaxy/commit/e0ce68cc58a6d6eeb306f5c04455… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-03 (Thu, 03 Mar 2016) Changed paths: M lib/galaxy/tools/parameters/output_collect.py Log Message: ----------- Fix lack of output when discovering large collections... Example log statement collected for each dataset: ``` galaxy.tools.parameters.output_collect DEBUG 2016-03-03 11:47:31,302 (8) Created dynamic collection dataset for path [/home/john/workspace/galaxy/database/job_working_directory/000/8/oe2_ie2.fq] with element identifier [oe2:ie2] for output [list_output]. ``` Commit: 0fbd22c9a30686afe62de1e1f23ff309dd6374a8 https://github.com/galaxyproject/galaxy/commit/0fbd22c9a30686afe62de1e1f23f… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-03 (Thu, 03 Mar 2016) Changed paths: M lib/galaxy/tools/parameters/output_collect.py Log Message: ----------- Merge pull request #1852 from jmchilton/dataset_collection_log [16.01] Fix lack of log output when discovering large collections... Compare: https://github.com/galaxyproject/galaxy/compare/de70306407c0...0fbd22c9a306

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[galaxyproject/usegalaxy-playbook] 2841ee: remove border around carousel so it matches twitte...
by GitHub 03 Mar '16

03 Mar '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 2841ee2db805198cb43356c92f75bf5090761919 https://github.com/galaxyproject/usegalaxy-playbook/commit/2841ee2db805198c… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-03 (Thu, 03 Mar 2016) Changed paths: M templates/galaxy/common/static/welcome.html.j2 Log Message: ----------- remove border around carousel so it matches twitter borderless widget

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[galaxyproject/galaxy] 159e5f: Do not create text values for failed inputs
by GitHub 03 Mar '16

03 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 159e5fd5d55dac24541189bea24e6f977c10a1d6 https://github.com/galaxyproject/galaxy/commit/159e5fd5d55dac24541189bea24e… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-03-02 (Wed, 02 Mar 2016) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Do not create text values for failed inputs Commit: 779793810d1f742dd1fd161c3eec1695df152d4d https://github.com/galaxyproject/galaxy/commit/779793810d1f742dd1fd161c3eec… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-03 (Thu, 03 Mar 2016) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge pull request #1844 from guerler/fix_text_value_handling_000 Do not create text values for failed inputs Compare: https://github.com/galaxyproject/galaxy/compare/80bcb987c84a...779793810d1f

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[galaxyproject/galaxy] 1220e2: Prevent tours from kicking off within iframes, cau...
by GitHub 03 Mar '16

03 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1220e2e9788026af7b7047720d03f7bb097f5762 https://github.com/galaxyproject/galaxy/commit/1220e2e9788026af7b7047720d03… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-03 (Thu, 03 Mar 2016) Changed paths: M client/galaxy/scripts/onload.js M static/maps/onload.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/onload.js Log Message: ----------- Prevent tours from kicking off within iframes, causing duplicate tour step display. Commit: 80bcb987c84a8331c84db864a557f326594afd91 https://github.com/galaxyproject/galaxy/commit/80bcb987c84a8331c84db864a557… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-03-03 (Thu, 03 Mar 2016) Changed paths: M client/galaxy/scripts/onload.js M static/maps/onload.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/onload.js Log Message: ----------- Merge pull request #1846 from dannon/tour_iframe_bug Prevent tours from kicking off within iframes Compare: https://github.com/galaxyproject/galaxy/compare/9b0c491729de...80bcb987c84a

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[galaxyproject/galaxy] 6968cf: Using node 5.7, 'grunt style' fails with the error...
by GitHub 03 Mar '16

03 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 6968cf0158f6b14ebbeaac3655151b5f67c393de https://github.com/galaxyproject/galaxy/commit/6968cf0158f6b14ebbeaac365515… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-02 (Wed, 02 Mar 2016) Changed paths: M client/grunt-tasks/style.js Log Message: ----------- Using node 5.7, 'grunt style' fails with the error: "ERROR Warning: Cannot delete files outside the current working directory. Use --force to continue. " This re-enables deletion of the temporary file. Commit: 9b0c491729de2945dc78b1766f520160c846c5d3 https://github.com/galaxyproject/galaxy/commit/9b0c491729de2945dc78b1766f52… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-02 (Wed, 02 Mar 2016) Changed paths: M client/grunt-tasks/style.js Log Message: ----------- Merge pull request #1841 from dannon/grunt_style Using node 5.7, 'grunt style' fails with the error: Compare: https://github.com/galaxyproject/galaxy/compare/158732edb6ce...9b0c491729de

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galaxy-commits March 2016