galaxy-commits December 2015

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[galaxyproject/galaxy] f969ea: Fix qunit shim to match base_panels.mako shim.
by GitHub 04 Dec '15

04 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f969eabf268a2e07235083d37168ae9887f87876 https://github.com/galaxyproject/galaxy/commit/f969eabf268a2e07235083d37168… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-04 (Fri, 04 Dec 2015) Changed paths: M test/qunit/test-common.js Log Message: ----------- Fix qunit shim to match base_panels.mako shim. QUnit tests of things with underscore require statements would not work without this change. Commit: 5c87d07e0f535ed3367bbd463fb16bc0d83d7cf9 https://github.com/galaxyproject/galaxy/commit/5c87d07e0f535ed3367bbd463fb1… Author: carlfeberhard <carlfeberhard(a)users.noreply.github.com> Date: 2015-12-04 (Fri, 04 Dec 2015) Changed paths: M test/qunit/test-common.js Log Message: ----------- Merge pull request #1233 from jmchilton/underscore_shim Fix qunit shim to match base_panels.mako shim. Compare: https://github.com/galaxyproject/galaxy/compare/74f7b9003680...5c87d07e0f53

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[galaxyproject/usegalaxy-playbook] a30639: Increase Pulsar AMQP ack republish time to 3 minut...
by GitHub 04 Dec '15

04 Dec '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: a306396df1daa8474dcef64036e541d134c45021 https://github.com/galaxyproject/usegalaxy-playbook/commit/a306396df1daa847… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-12-04 (Fri, 04 Dec 2015) Changed paths: M production/host_vars/login5.stampede.tacc.utexas.edu.yml M stage/host_vars/greenfield.psc.xsede.org.yml M stage/host_vars/login5.stampede.tacc.utexas.edu.yml M templates/galaxy/test.galaxyproject.org/config/job_conf.xml.j2 M templates/galaxy/usegalaxy.org/config/job_conf.xml.j2 Log Message: ----------- Increase Pulsar AMQP ack republish time to 3 minutes (default is 30 seconds)

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[galaxyproject/galaxy] 102eee: Replacement should be applied only to first occurr...
by GitHub 04 Dec '15

04 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 102eeef2d7045fa5b8706497f04817cb2f75813a https://github.com/galaxyproject/galaxy/commit/102eeef2d7045fa5b8706497f048… Author: Takao Nakaguchi <takao.nakaguchi(a)gmail.com> Date: 2015-12-04 (Fri, 04 Dec 2015) Changed paths: M lib/tool_shed/galaxy_install/migrate/check.py Log Message: ----------- Replacement should be applied only to first occurrence. Commit: 74f7b900368030e425f79f835e2093102dbed5ba https://github.com/galaxyproject/galaxy/commit/74f7b900368030e425f79f835e20… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-04 (Fri, 04 Dec 2015) Changed paths: M lib/tool_shed/galaxy_install/migrate/check.py Log Message: ----------- Merge pull request #1230 from openlangrid/dev Replacement should be applied only to first occurrence. Compare: https://github.com/galaxyproject/galaxy/compare/600338dac7b0...74f7b9003680

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[galaxyproject/galaxy] 0c8a73: Export GALAXY_TEST_DBURI as GALAXY_CONFIG_OVERRIDE...
by GitHub 04 Dec '15

04 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 0c8a738a35d8c28b18dba6da92ec702096c1554a https://github.com/galaxyproject/galaxy/commit/0c8a738a35d8c28b18dba6da92ec… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-12-04 (Fri, 04 Dec 2015) Changed paths: M run_tests.sh Log Message: ----------- Export GALAXY_TEST_DBURI as GALAXY_CONFIG_OVERRIDE_DATABASE_CONNECTION before installing wheels. Fix #1205. As test/docker/base/run_test_wrapper.sh does. Commit: 600338dac7b0dad7f514f1b9a3c7c123dd63c379 https://github.com/galaxyproject/galaxy/commit/600338dac7b0dad7f514f1b9a3c7… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-12-04 (Fri, 04 Dec 2015) Changed paths: M run_tests.sh Log Message: ----------- Merge pull request #1231 from nsoranzo/dev_tests_conditional_wheels Export GALAXY_TEST_DBURI as GALAXY_CONFIG_OVERRIDE_DATABASE_CONNECTION before installing wheels. Compare: https://github.com/galaxyproject/galaxy/compare/fcabc5242ca8...600338dac7b0

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[galaxyproject/usegalaxy-playbook] 51b1d2: Update test to fcabc5242ca8fc6b1e7533ade17e2a8e3d2...
by GitHub 04 Dec '15

04 Dec '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 51b1d23743fbcd531f3cbc677515d2f5b4cc8e42 https://github.com/galaxyproject/usegalaxy-playbook/commit/51b1d23743fbcd53… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-12-04 (Fri, 04 Dec 2015) Changed paths: M stage/group_vars/all.yml Log Message: ----------- Update test to fcabc5242ca8fc6b1e7533ade17e2a8e3d27fe82

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[galaxyproject/galaxy] 6e185f: Allowed for capitailsed packgae name such as R
by GitHub 04 Dec '15

04 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 6e185fa208c27564b4cd2db5e31f55bf58c6eb4e https://github.com/galaxyproject/galaxy/commit/6e185fa208c27564b4cd2db5e31f… Author: Christian-B <github(a)brenn.co.uk> Date: 2015-11-23 (Mon, 23 Nov 2015) Changed paths: M lib/galaxy/tools/deps/resolvers/unlinked_tool_shed_packages.py Log Message: ----------- Allowed for capitailsed packgae name such as R Commit: fcabc5242ca8fc6b1e7533ade17e2a8e3d27fe82 https://github.com/galaxyproject/galaxy/commit/fcabc5242ca8fc6b1e7533ade17e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-04 (Fri, 04 Dec 2015) Changed paths: M lib/galaxy/tools/deps/resolvers/unlinked_tool_shed_packages.py Log Message: ----------- Merge pull request #1160 from Christian-B/unlinked_dependencies Allowed for capitalised package names such as R Compare: https://github.com/galaxyproject/galaxy/compare/11c46f4f35f3...fcabc5242ca8

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[galaxyproject/galaxy] 51cd41: Fix ScIdx sniff method to handle first line commen...
by GitHub 04 Dec '15

04 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 51cd41be94ea4e5af50201bbd0e85ade21774e69 https://github.com/galaxyproject/galaxy/commit/51cd41be94ea4e5af50201bbd0e8… Author: Greg Von Kuster <ghv2(a)psu.edu> Date: 2015-12-02 (Wed, 02 Dec 2015) Changed paths: M lib/galaxy/datatypes/interval.py Log Message: ----------- Fix ScIdx sniff method to handle first line comment Commit: c04b3a5bb557c836e60c060f68598ea314fc9521 https://github.com/galaxyproject/galaxy/commit/c04b3a5bb557c836e60c060f6859… Author: Greg Von Kuster <ghv2(a)psu.edu> Date: 2015-12-02 (Wed, 02 Dec 2015) Changed paths: M lib/galaxy/datatypes/interval.py Log Message: ----------- Re-add egg imports Commit: 30b13bb1d6e576c4f6e32f4e98b08c9a3a5651eb https://github.com/galaxyproject/galaxy/commit/30b13bb1d6e576c4f6e32f4e98b0… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-12-02 (Wed, 02 Dec 2015) Changed paths: M lib/galaxy/datatypes/interval.py Log Message: ----------- Merge pull request #1203 from gregvonkuster/release_15.10 [15.10] Fix ScIdx sniff method to handle first line comment Commit: a5b7e6cb8e90387a7b9f6acb79b80a2114fa3928 https://github.com/galaxyproject/galaxy/commit/a5b7e6cb8e90387a7b9f6acb79b8… Author: Eric Enns <eric.enns(a)phac-aspc.gc.ca> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Updated tool input collection to only add items from a collection which are being used by the tool and not the entire collection. (Thanks to @markiskander for helping me find this). Commit: ee5a87af2e3d0a76da5df398826478bc4854c599 https://github.com/galaxyproject/galaxy/commit/ee5a87af2e3d0a76da5df3988264… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Fix for updating tool parameter dicts when a new parameter has been added to a section. Fixes issues seen during rerun under mentioned condition. Commit: d83e8d358f1b04683fa20245a66f12a8d881be4e https://github.com/galaxyproject/galaxy/commit/d83e8d358f1b04683fa20245a66f… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge pull request #1215 from blankenberg/rerunfix_15.10 [15.10] Fix for updating tool parameter dicts when a new parameter has been added to a section Commit: c9abc2bc97dbdbe85c82946ca1138a6f6139bb33 https://github.com/galaxyproject/galaxy/commit/c9abc2bc97dbdbe85c82946ca113… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M test/tool_shed/test_data/1440_files/complex_dependency/tool_dependencies.xml Log Message: ----------- Fix for test/tool_shed/functional/test_1440_missing_env_sh_files.py . Properly order the installation of the repositories adding prior_installation_required="True". Otherwise filter_1440 is installed first and ends in INSTALLED status because of the logic of Repository.create_tool_dependency_with_initialized_env_sh_file() method contained in lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py . Commit: 2b697e3c1ae76e4c718ed558e88a3c387d6e35c9 https://github.com/galaxyproject/galaxy/commit/2b697e3c1ae76e4c718ed558e88a… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py Log Message: ----------- Fix detection of missing repository dependencies when reinstalling an updated Tool Shed repository. Fix test/tool_shed/functional/test_1087_install_updated_repository_dependencies.py . Commit: d1684e7c9d9dc42918004dc15bf1e7d039c96088 https://github.com/galaxyproject/galaxy/commit/d1684e7c9d9dc42918004dc15bf1… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Merge pull request #1224 from jmchilton/collection_naming_performance [15.10] Backport #1217 Commit: 516b079ab97d7fc0a40255d03dcaf2cb600a2384 https://github.com/galaxyproject/galaxy/commit/516b079ab97d7fc0a40255d03dca… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M test/tool_shed/test_data/1440_files/complex_dependency/tool_dependencies.xml Log Message: ----------- Merge pull request #1222 from nsoranzo/release_15.10_tool_shed_fixes [15.10] Tool Shed fixes. Commit: 11c46f4f35f3c1cb579198d28402ebacd51e6ec8 https://github.com/galaxyproject/galaxy/commit/11c46f4f35f3c1cb579198d28402… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-12-04 (Fri, 04 Dec 2015) Changed paths: M lib/galaxy/datatypes/interval.py M lib/galaxy/tools/__init__.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M test/tool_shed/test_data/1440_files/complex_dependency/tool_dependencies.xml Log Message: ----------- Merge branch 'master' into dev Compare: https://github.com/galaxyproject/galaxy/compare/e76933b55749...11c46f4f35f3

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[galaxyproject/galaxy] 51cd41: Fix ScIdx sniff method to handle first line commen...
by GitHub 04 Dec '15

04 Dec '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/galaxy Commit: 51cd41be94ea4e5af50201bbd0e85ade21774e69 https://github.com/galaxyproject/galaxy/commit/51cd41be94ea4e5af50201bbd0e8… Author: Greg Von Kuster <ghv2(a)psu.edu> Date: 2015-12-02 (Wed, 02 Dec 2015) Changed paths: M lib/galaxy/datatypes/interval.py Log Message: ----------- Fix ScIdx sniff method to handle first line comment Commit: c04b3a5bb557c836e60c060f68598ea314fc9521 https://github.com/galaxyproject/galaxy/commit/c04b3a5bb557c836e60c060f6859… Author: Greg Von Kuster <ghv2(a)psu.edu> Date: 2015-12-02 (Wed, 02 Dec 2015) Changed paths: M lib/galaxy/datatypes/interval.py Log Message: ----------- Re-add egg imports Commit: 30b13bb1d6e576c4f6e32f4e98b08c9a3a5651eb https://github.com/galaxyproject/galaxy/commit/30b13bb1d6e576c4f6e32f4e98b0… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-12-02 (Wed, 02 Dec 2015) Changed paths: M lib/galaxy/datatypes/interval.py Log Message: ----------- Merge pull request #1203 from gregvonkuster/release_15.10 [15.10] Fix ScIdx sniff method to handle first line comment Commit: a5b7e6cb8e90387a7b9f6acb79b80a2114fa3928 https://github.com/galaxyproject/galaxy/commit/a5b7e6cb8e90387a7b9f6acb79b8… Author: Eric Enns <eric.enns(a)phac-aspc.gc.ca> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Updated tool input collection to only add items from a collection which are being used by the tool and not the entire collection. (Thanks to @markiskander for helping me find this). Commit: ee5a87af2e3d0a76da5df398826478bc4854c599 https://github.com/galaxyproject/galaxy/commit/ee5a87af2e3d0a76da5df3988264… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Fix for updating tool parameter dicts when a new parameter has been added to a section. Fixes issues seen during rerun under mentioned condition. Commit: d83e8d358f1b04683fa20245a66f12a8d881be4e https://github.com/galaxyproject/galaxy/commit/d83e8d358f1b04683fa20245a66f… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge pull request #1215 from blankenberg/rerunfix_15.10 [15.10] Fix for updating tool parameter dicts when a new parameter has been added to a section Commit: c9abc2bc97dbdbe85c82946ca1138a6f6139bb33 https://github.com/galaxyproject/galaxy/commit/c9abc2bc97dbdbe85c82946ca113… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M test/tool_shed/test_data/1440_files/complex_dependency/tool_dependencies.xml Log Message: ----------- Fix for test/tool_shed/functional/test_1440_missing_env_sh_files.py . Properly order the installation of the repositories adding prior_installation_required="True". Otherwise filter_1440 is installed first and ends in INSTALLED status because of the logic of Repository.create_tool_dependency_with_initialized_env_sh_file() method contained in lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py . Commit: 2b697e3c1ae76e4c718ed558e88a3c387d6e35c9 https://github.com/galaxyproject/galaxy/commit/2b697e3c1ae76e4c718ed558e88a… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py Log Message: ----------- Fix detection of missing repository dependencies when reinstalling an updated Tool Shed repository. Fix test/tool_shed/functional/test_1087_install_updated_repository_dependencies.py . Commit: d1684e7c9d9dc42918004dc15bf1e7d039c96088 https://github.com/galaxyproject/galaxy/commit/d1684e7c9d9dc42918004dc15bf1… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Merge pull request #1224 from jmchilton/collection_naming_performance [15.10] Backport #1217 Commit: 516b079ab97d7fc0a40255d03dcaf2cb600a2384 https://github.com/galaxyproject/galaxy/commit/516b079ab97d7fc0a40255d03dca… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M test/tool_shed/test_data/1440_files/complex_dependency/tool_dependencies.xml Log Message: ----------- Merge pull request #1222 from nsoranzo/release_15.10_tool_shed_fixes [15.10] Tool Shed fixes. Compare: https://github.com/galaxyproject/galaxy/compare/da2cc588e5a5...516b079ab97d

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[galaxyproject/galaxy] 6735c9: replace the readthedocs badge,
by GitHub 03 Dec '15

03 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 6735c9deceadba39c0a2b34b076f37440c087fc3 https://github.com/galaxyproject/galaxy/commit/6735c9deceadba39c0a2b34b076f… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M README.rst Log Message: ----------- replace the readthedocs badge, we cannot use it until https://github.com/rtfd/readthedocs.org/issues/1767 is resolved Commit: e76933b55749c619c4debf4e62cd1f4d7e3cb7e1 https://github.com/galaxyproject/galaxy/commit/e76933b55749c619c4debf4e62cd… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M README.rst Log Message: ----------- Merge pull request #1229 from martenson/remove-readthecdocs-badge replace the readthedocs badge, Compare: https://github.com/galaxyproject/galaxy/compare/9a1fc647a380...e76933b55749

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[galaxyproject/galaxy]
by GitHub 03 Dec '15

03 Dec '15

Branch: refs/heads/revert-1222-release_15.10_tool_shed_fixes Home: https://github.com/galaxyproject/galaxy

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galaxy-commits December 2015