December 2015 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 4eefd8: Improve startup options related to wheel/dependenc...
by GitHub 23 Dec '15

23 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4eefd885eccd0c42c7a74c8415add3a948a91135 https://github.com/galaxyproject/galaxy/commit/4eefd885eccd0c42c7a74c8415ad… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-12-22 (Tue, 22 Dec 2015) Changed paths: A lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt M run.sh M run_tests.sh M scripts/common_startup.sh Log Message: ----------- Improve startup options related to wheel/dependency/virtualenv management. Drop hard requirement on lzo (doubt anyone other than usegalaxy.org is using it, but it will be added as a extras option for bxlab/bx-python for anyone who is). Fixes #1150 Commit: 9934a45134283d307814058fa09e4b26d3d8452f https://github.com/galaxyproject/galaxy/commit/9934a45134283d307814058fa09e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-12-22 (Tue, 22 Dec 2015) Changed paths: M tox.ini Log Message: ----------- Run tox/Travis with --no-create-venv instead of --skip-venv Commit: 26d7e97ed7b4eaa845bf86fd4991b1fbf4a3ead0 https://github.com/galaxyproject/galaxy/commit/26d7e97ed7b4eaa845bf86fd4991… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-12-23 (Wed, 23 Dec 2015) Changed paths: A lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt M run.sh M run_tests.sh M scripts/common_startup.sh M tox.ini Log Message: ----------- Merge pull request #1389 from natefoo/wheel-startup-option-improvements Improve startup options related to wheel/dependency/virtualenv management. Compare: https://github.com/galaxyproject/galaxy/compare/ded904cb1258...26d7e97ed7b4

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[galaxyproject/galaxy] 630ac3: Python 3 fixes and galaxy-lib updates from planemo...
by GitHub 23 Dec '15

23 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 630ac3658f3c64bd9a9abe5757cce0ed01cad229 https://github.com/galaxyproject/galaxy/commit/630ac3658f3c64bd9a9abe5757cc… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-22 (Tue, 22 Dec 2015) Changed paths: M lib/galaxy/exceptions/error_codes.py M lib/galaxy/tools/deps/commands.py M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/lint.py M lib/galaxy/tools/linters/inputs.py M lib/galaxy/tools/linters/stdio.py M lib/galaxy/tools/parser/output_objects.py M lib/galaxy/tools/parser/yaml.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/panel.py M lib/galaxy/util/__init__.py M lib/galaxy/util/heartbeat.py M lib/galaxy/util/json.py M lib/galaxy/util/xml_macros.py Log Message: ----------- Python 3 fixes and galaxy-lib updates from planemo. (Minus changes for conda which - should be merged as their own PR obviously.) Commit: ded904cb12580723b192fe571cf2a4f20ec16619 https://github.com/galaxyproject/galaxy/commit/ded904cb12580723b192fe571cf2… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-12-23 (Wed, 23 Dec 2015) Changed paths: M lib/galaxy/exceptions/error_codes.py M lib/galaxy/tools/deps/commands.py M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/lint.py M lib/galaxy/tools/linters/inputs.py M lib/galaxy/tools/linters/stdio.py M lib/galaxy/tools/parser/output_objects.py M lib/galaxy/tools/parser/yaml.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/panel.py M lib/galaxy/util/__init__.py M lib/galaxy/util/heartbeat.py M lib/galaxy/util/json.py M lib/galaxy/util/xml_macros.py Log Message: ----------- Merge pull request #1388 from jmchilton/py3_2 Python 3 fixes and galaxy-lib updates from planemo. Compare: https://github.com/galaxyproject/galaxy/compare/61cba6c9429f...ded904cb1258

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[galaxyproject/usegalaxy-playbook] bde12c: install Macs2 and diffbind on Main
by GitHub 22 Dec '15

22 Dec '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: bde12ca35ca13fdfb137fe64b4808a1b45b75356 https://github.com/galaxyproject/usegalaxy-playbook/commit/bde12ca35ca13fdf… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-12-22 (Tue, 22 Dec 2015) Changed paths: M files/galaxy/usegalaxy.org/var/integrated_tool_panel.xml M files/galaxy/usegalaxy.org/var/shed_tool_conf.xml Log Message: ----------- install Macs2 and diffbind on Main

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[galaxyproject/usegalaxy-playbook] 3c547e: update Main mutable confs
by GitHub 22 Dec '15

22 Dec '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 3c547ee6691f03eb4a6c7094d5c8360412b418e3 https://github.com/galaxyproject/usegalaxy-playbook/commit/3c547ee6691f03eb… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-12-22 (Tue, 22 Dec 2015) Changed paths: M files/galaxy/usegalaxy.org/var/integrated_tool_panel.xml M files/galaxy/usegalaxy.org/var/shed_tool_conf.xml M files/galaxy/usegalaxy.org/var/shed_tool_data_table_conf.xml Log Message: ----------- update Main mutable confs

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[galaxyproject/usegalaxy-playbook] a9ea64: update Main mutable confs, installed bunch of samt...
by GitHub 22 Dec '15

22 Dec '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: a9ea64b85243ac2485ba4a93ab30b59d29cae841 https://github.com/galaxyproject/usegalaxy-playbook/commit/a9ea64b85243ac24… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-12-22 (Tue, 22 Dec 2015) Changed paths: M files/galaxy/usegalaxy.org/var/integrated_tool_panel.xml M files/galaxy/usegalaxy.org/var/shed_tool_conf.xml M files/galaxy/usegalaxy.org/var/shed_tool_data_table_conf.xml Log Message: ----------- update Main mutable confs, installed bunch of samtools

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[galaxyproject/usegalaxy-playbook] 4f20ec: update MTS
by GitHub 22 Dec '15

22 Dec '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 4f20ecc148d2bf3f22a6694bcd1277393353b2a6 https://github.com/galaxyproject/usegalaxy-playbook/commit/4f20ecc148d2bf3f… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-12-22 (Tue, 22 Dec 2015) Changed paths: M production/group_vars/toolshedservers.yml Log Message: ----------- update MTS

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[galaxyproject/galaxy] b5ad20: Refactor UI component out of AbstractToolBox.
by GitHub 22 Dec '15

22 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b5ad20401b28e29b727c1212be5443d7dd9c2dad https://github.com/galaxyproject/galaxy/commit/b5ad20401b28e29b727c1212be54… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-18 (Fri, 18 Dec 2015) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Refactor UI component out of AbstractToolBox. If it belongs in the base class ToolBox which is more concerned with Galaxy-spcifics like UI, AbstractToolBox is suppose to be an abstract description of a toolbox - it is about data management. Commit: 536b4e2a2038d889486bbf0836341e03d737f53c https://github.com/galaxyproject/galaxy/commit/536b4e2a2038d889486bbf083634… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-18 (Fri, 18 Dec 2015) Changed paths: M lib/galaxy/util/__init__.py M lib/tool_shed/util/common_util.py Log Message: ----------- Improve some random tool shed code. Commit: 75e7276e5e9c43ec6f09f68adea2870b3a6917dc https://github.com/galaxyproject/galaxy/commit/75e7276e5e9c43ec6f09f68adea2… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-18 (Fri, 18 Dec 2015) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/lineages/tool_shed.py Log Message: ----------- Eliminate sqlalchemy and tool shed dependencies from AbstractToolBox. Provide an extension point instead that allows Galaxy's ToolBox class to provide the functionality that required these dependencies. And optionally load ToolVersion class required for reasoning about tool shed logic. Commit: 61cba6c9429fe790da19f843d8e2b0d415459b4c https://github.com/galaxyproject/galaxy/commit/61cba6c9429fe790da19f843d8e2… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-22 (Tue, 22 Dec 2015) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/lineages/tool_shed.py M lib/galaxy/util/__init__.py M lib/tool_shed/util/common_util.py Log Message: ----------- Merge pull request #1367 from jmchilton/toolbox_refactor_0 Refactor AbstractToolbox toward reuse outside Galaxy Compare: https://github.com/galaxyproject/galaxy/compare/f874d559b7db...61cba6c9429f

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[galaxyproject/galaxy] f042fe: Attempt to fix transiently failing API tests.
by GitHub 22 Dec '15

22 Dec '15

Branch: refs/heads/release_15.10 Home: https://github.com/galaxyproject/galaxy Commit: f042fe8548ec4a0f2f29b72d0c34736e2ff524f9 https://github.com/galaxyproject/galaxy/commit/f042fe8548ec4a0f2f29b72d0c34… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-18 (Fri, 18 Dec 2015) Changed paths: M test/api/test_jobs.py Log Message: ----------- Attempt to fix transiently failing API tests. - Fix default timeout of wait_on_state api helper. Had the wrong default specified and might fix this failure: https://jenkins.galaxyproject.org/job/docker-api/229/testReport/junit/api.t… - Modify job search test case to allow a little more time between the history being "ok" and the job, in case there is a timing condition if the HDA is committed first and then job. Also improve the test output in case this isn't the problem. Commit: 93c6d0542124c220e36c1e90d62e3e2aef607e9a https://github.com/galaxyproject/galaxy/commit/93c6d0542124c220e36c1e90d62e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-18 (Fri, 18 Dec 2015) Changed paths: M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/test.py M test/base/twilltestcase.py A test/functional/tools/maxseconds.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Revise and fix waiting for tool tests. - maxseconds on test tag stopped being respected at some point, fix that. - maxseconds on test tag stopped being parsed at some later point, fix that. - Revise default behavior so it can be overridden with yet another testing environment variable GALAXY_TEST_DEFAULT_WAIT. - Add test case to ensure there is no future regression of these behaviors. Commit: ffb973477b02c4bc1cbfa95c7a6247f1d7949fdd https://github.com/galaxyproject/galaxy/commit/ffb973477b02c4bc1cbfa95c7a62… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-18 (Fri, 18 Dec 2015) Changed paths: M scripts/functional_tests.py Log Message: ----------- Do not check for tool migrations when running tests. This is an inappropriate time for the check and causes slow down when running tests. Commit: 641b275aa424421591833f6a3bce3ebd8b358017 https://github.com/galaxyproject/galaxy/commit/641b275aa424421591833f6a3bce… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-18 (Fri, 18 Dec 2015) Changed paths: M test/api/helpers.py M test/api/test_jobs.py Log Message: ----------- Wait on jobs and history in certain API test cases. This strategy proved to work around certain race conditions in tool testing so hopefully it will solve the transiently failing job searching and filtering test cases. Commit: 57a76065a54f63a47874158c121f002308648025 https://github.com/galaxyproject/galaxy/commit/57a76065a54f63a47874158c121f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-18 (Fri, 18 Dec 2015) Changed paths: M test/api/helpers.py Log Message: ----------- Fix missing assertion pointed out @nsoranzo. Lots of other tests would fail if simple uploads aren't working, but it is better to be direct and very explicit about why this particular test is failing. Commit: 2817eabf95a980a250e272c3917e5dcfc24743b2 https://github.com/galaxyproject/galaxy/commit/2817eabf95a980a250e272c3917e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-18 (Fri, 18 Dec 2015) Changed paths: M test/functional/tools/maxseconds.xml Log Message: ----------- Fail maxseconds test tool if sleep is interrupted. Commit: 5d26f589cc475ff95b97ef2dcb34d5a290079e8b https://github.com/galaxyproject/galaxy/commit/5d26f589cc475ff95b97ef2dcb34… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-12-22 (Tue, 22 Dec 2015) Changed paths: M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/test.py M scripts/functional_tests.py M test/api/helpers.py M test/api/test_jobs.py M test/base/twilltestcase.py A test/functional/tools/maxseconds.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #1295 from jmchilton/test_fixes_backport_15_10 [15.10] Backport various testing fixes. Compare: https://github.com/galaxyproject/galaxy/compare/52b66d0dee8c...5d26f589cc47

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[galaxyproject/galaxy] c3580d: Allow installation of different repositories with ...
by GitHub 22 Dec '15

22 Dec '15

Branch: refs/heads/release_15.10 Home: https://github.com/galaxyproject/galaxy Commit: c3580da7b826b42de631017d4d2baf7e6ac3cfdf https://github.com/galaxyproject/galaxy/commit/c3580da7b826b42de631017d4d2b… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2015-12-22 (Tue, 22 Dec 2015) Changed paths: M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py Log Message: ----------- Allow installation of different repositories with the same name in a single install transaction. Commit: 52b66d0dee8c026bfb8858671f900b862837fae5 https://github.com/galaxyproject/galaxy/commit/52b66d0dee8c026bfb8858671f90… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-22 (Tue, 22 Dec 2015) Changed paths: M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py Log Message: ----------- Merge pull request #1385 from martenson/port-marius-ts-fix [15.10] Port marius TS fix Compare: https://github.com/galaxyproject/galaxy/compare/abd51e7f791c...52b66d0dee8c

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[galaxyproject/usegalaxy-playbook] fb80d1: Mutable configs
by GitHub 22 Dec '15

22 Dec '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: fb80d1dfca288948ac9c1a368efe9df8261ad896 https://github.com/galaxyproject/usegalaxy-playbook/commit/fb80d1dfca288948… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-12-22 (Tue, 22 Dec 2015) Changed paths: M files/galaxy/test.galaxyproject.org/var/integrated_tool_panel.xml M files/galaxy/test.galaxyproject.org/var/shed_tool_conf.xml M files/galaxy/test.galaxyproject.org/var/shed_tool_data_table_conf.xml Log Message: ----------- Mutable configs Commit: 0c3eff8d001fccd6fe6e9aa561fee036c414e468 https://github.com/galaxyproject/usegalaxy-playbook/commit/0c3eff8d001fccd6… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-12-22 (Tue, 22 Dec 2015) Changed paths: M files/galaxy/test.galaxyproject.org/config/tool_data_table_conf.xml M files/galaxy/usegalaxy.org/config/tool_data_table_conf.xml Log Message: ----------- Update tool_data_table_conf.xml for liftOver location file -> data table. Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/b77be7583061...…

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