Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: dd77cdb62576a62ea7e8ce8e31d2d7d78aef7823 https://github.com/galaxyproject/galaxy/commit/dd77cdb62576a62ea7e8ce8e31d2d... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-01-25 (Wed, 25 Jan 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/configuration.py M test/api/test_datatypes.py Log Message: ----------- Add API test for converters after toolbox reload Commit: 78b4f8f7627a63be7ba593109c1ffd36891168ba https://github.com/galaxyproject/galaxy/commit/78b4f8f7627a63be7ba593109c1ff... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-01-25 (Wed, 25 Jan 2017) Changed paths: M lib/galaxy/datatypes/registry.py M lib/galaxy/queue_worker.py Log Message: ----------- Reload converter tools after toolbox reload Commit: 36ecf28adaa3328cac3248dc7e8c3ef79211c204 https://github.com/galaxyproject/galaxy/commit/36ecf28adaa3328cac3248dc7e8c3... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-01-25 (Wed, 25 Jan 2017) Changed paths: M test/api/test_datatypes.py Log Message: ----------- Use CONVERTER_fasta_to_tabular as example converter (thx @jmchilton) Commit: e4999510ee2bc44802b4891a1a09b00489b01a9c https://github.com/galaxyproject/galaxy/commit/e4999510ee2bc44802b4891a1a09b... Author: Daniel Blankenberg <dan.blankenberg@gmail.com> Date: 2017-01-30 (Mon, 30 Jan 2017) Changed paths: M lib/galaxy/datatypes/registry.py M lib/galaxy/queue_worker.py M lib/galaxy/webapps/galaxy/api/configuration.py M test/api/test_datatypes.py Log Message: ----------- Merge pull request #3486 from mvdbeek/converter_reload [16.10] BUG: Reload converter tools after toolbox reload Commit: cc40b9d45514e1388e2d98e676fe5b75b28d6a3e https://github.com/galaxyproject/galaxy/commit/cc40b9d45514e1388e2d98e676fe5... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-01-31 (Tue, 31 Jan 2017) Changed paths: M lib/galaxy/model/mapping.py M lib/galaxy/workflow/scheduling_manager.py Log Message: ----------- This enforces serial workflow scheduling within the context of a particular history. Commit: 749a503534033d3260681b75ad829a640d1c4a3b https://github.com/galaxyproject/galaxy/commit/749a503534033d3260681b75ad829... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-01-31 (Tue, 31 Jan 2017) Changed paths: M config/galaxy.ini.sample Log Message: ----------- Minor typo in sample. Commit: 8be1429dda7e158601371331494501fd6043a5e0 https://github.com/galaxyproject/galaxy/commit/8be1429dda7e15860137133149450... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-01-31 (Tue, 31 Jan 2017) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/workflow/scheduling_manager.py Log Message: ----------- Add configuration for history_local_serial_workflow_scheduling Commit: 2b55fc75ebad92183e78a80b3240f7b978bd448d https://github.com/galaxyproject/galaxy/commit/2b55fc75ebad92183e78a80b3240f... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-01-31 (Tue, 31 Jan 2017) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py Log Message: ----------- Might be more palatable if this is defaulted to false. Commit: 9a7066c4b4c9f3824257cc00695b87ef9a065c0f https://github.com/galaxyproject/galaxy/commit/9a7066c4b4c9f3824257cc00695b8... Author: jvolkening <jdv@base2bio.com> Date: 2017-02-01 (Wed, 01 Feb 2017) Changed paths: M lib/galaxy/tools/verify/asserts/xml.py Log Message: ----------- fix <is_valid_xml> output test assert check Commit: 58241e8dcb71500d399dbe2089f5b20f1eb89b53 https://github.com/galaxyproject/galaxy/commit/58241e8dcb71500d399dbe2089f5b... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-02-01 (Wed, 01 Feb 2017) 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 M static/scripts/bundled/login.bundled.js.map Log Message: ----------- Rebuild client for 17.01 with latest node. Commit: 9dc1bbd3bc4697f5fbf1e183883aba9277058706 https://github.com/galaxyproject/galaxy/commit/9dc1bbd3bc4697f5fbf1e183883ab... Author: Martin Cech <cech.marten@gmail.com> Date: 2017-02-01 (Wed, 01 Feb 2017) 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 M static/scripts/bundled/login.bundled.js.map Log Message: ----------- Merge pull request #3535 from dannon/minor_fix [17.01] Rebuild client for 17.01 with latest node. Commit: 31725972ef9342145effa6ad24d912022afb278c https://github.com/galaxyproject/galaxy/commit/31725972ef9342145effa6ad24d91... Author: Daniel Blankenberg <dan.blankenberg@gmail.com> Date: 2017-02-01 (Wed, 01 Feb 2017) Changed paths: M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Fix conda resolver when conda_auto_init = True and install = False Conda dependencies were being prematurely installed during installation of repositories from the ToolShed (at the point where we are just trying to list already installed dependencies). Commit: a121b889ef584086c96c6b9230198b3e2a04d6f6 https://github.com/galaxyproject/galaxy/commit/a121b889ef584086c96c6b9230198... Author: Eric Rasche <rasche.eric@gmail.com> Date: 2017-02-01 (Wed, 01 Feb 2017) Changed paths: M lib/galaxy/datatypes/sequence.py Log Message: ----------- Only read 6 bytes. Fixes #3529 Commit: c602336cc82fe60c54d10834c26fb8b0eafe81b0 https://github.com/galaxyproject/galaxy/commit/c602336cc82fe60c54d10834c26fb... Author: Daniel Blankenberg <dan.blankenberg@gmail.com> Date: 2017-02-01 (Wed, 01 Feb 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/jobs.py Log Message: ----------- Fix for rerunning a job when the tool does not exist. Commit: 3858528d90c1380ae33c7e6087ee3ee1a9bb85f9 https://github.com/galaxyproject/galaxy/commit/3858528d90c1380ae33c7e6087ee3... Author: Martin Cech <cech.marten@gmail.com> Date: 2017-02-01 (Wed, 01 Feb 2017) Changed paths: M lib/galaxy/datatypes/sequence.py Log Message: ----------- Merge pull request #3537 from jmchilton/backport_genbank_fix [17.01] Backport of fix unbounded readline in genbank datatype Commit: da7fed47445d8d1483eb456f32af19a0b0ff5412 https://github.com/galaxyproject/galaxy/commit/da7fed47445d8d1483eb456f32af1... Author: John Chilton <jmchilton@gmail.com> Date: 2017-02-01 (Wed, 01 Feb 2017) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Fix wiggle to wiggle2simple1 for Python path changes in #3364. Fixes #3539. #minor Commit: 840c3b0fd846ea5fb58fb34378717aeadea7e81a https://github.com/galaxyproject/galaxy/commit/840c3b0fd846ea5fb58fb34378717... Author: John Chilton <jmchilton@gmail.com> Date: 2017-02-01 (Wed, 01 Feb 2017) Changed paths: M test/integration/test_resolvers.py Log Message: ----------- Fix integration test for default Conda mapping. It worked locally simply because I had R already installed on my system globally. Commit: a7cc18d616a2fe020d1946eac91ab248f9a1c995 https://github.com/galaxyproject/galaxy/commit/a7cc18d616a2fe020d1946eac91ab... Author: John Chilton <jmchilton@gmail.com> Date: 2017-02-01 (Wed, 01 Feb 2017) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Fix tools that use Galaxy sequence utilities for #3364. Thanks to @peterjc for reporting and @martenson for grepping. xref #minor #3364 Commit: bb15a431f006dfbe0d9777529300b8e1981fc988 https://github.com/galaxyproject/galaxy/commit/bb15a431f006dfbe0d9777529300b... Author: Martin Cech <cech.marten@gmail.com> Date: 2017-02-01 (Wed, 01 Feb 2017) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge pull request #3540 from jmchilton/wiggle_fix_1701 [17.01] Fix wiggle to wiggle2simple1 for Python path changes in #3364. Commit: da0affd45d4fb5479d0e0adcc4efa147bee41e63 https://github.com/galaxyproject/galaxy/commit/da0affd45d4fb5479d0e0adcc4efa... Author: Martin Cech <cech.marten@gmail.com> Date: 2017-02-01 (Wed, 01 Feb 2017) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge pull request #3542 from jmchilton/more_python_preservation [17.01] Fix tools that use Galaxy sequence utilities for #3364. Commit: 105557ba35317120af7f241aebec99f43c4c8553 https://github.com/galaxyproject/galaxy/commit/105557ba35317120af7f241aebec9... Author: jvolkening <jdv@base2bio.com> Date: 2017-02-01 (Wed, 01 Feb 2017) Changed paths: A test-data/simple.xml A test/functional/tools/is_valid_xml.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- added functional test for <is_valid_xml> Commit: 2322bc1ff59e85fb4f9db281d04b96e124dd73aa https://github.com/galaxyproject/galaxy/commit/2322bc1ff59e85fb4f9db281d04b9... Author: Marius van den Beek <m.vandenbeek@gmail.com> Date: 2017-02-02 (Thu, 02 Feb 2017) Changed paths: M test/integration/test_resolvers.py Log Message: ----------- Merge pull request #3541 from jmchilton/backport_3508 [17.01] Fix integration test for default Conda mapping. Commit: f1062afa55c486a0b35418bf7e7e988136c78cb6 https://github.com/galaxyproject/galaxy/commit/f1062afa55c486a0b35418bf7e7e9... Author: Nicola Soranzo <nsoranzo@tiscali.it> Date: 2017-02-02 (Thu, 02 Feb 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/jobs.py Log Message: ----------- Merge pull request #3538 from blankenberg/fix-rerun-no-tool [17.01] Fix for rerunning a job when the tool does not exist. Commit: 0ce7f6897fe7a037ae9ff9a79c082c56fec0e929 https://github.com/galaxyproject/galaxy/commit/0ce7f6897fe7a037ae9ff9a79c082... Author: Martin Cech <cech.marten@gmail.com> Date: 2017-02-02 (Thu, 02 Feb 2017) Changed paths: M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- add comments from @mvdbeek Commit: 961efb4d9af9ea17fbd0f80b7f07158f2cb971ad https://github.com/galaxyproject/galaxy/commit/961efb4d9af9ea17fbd0f80b7f071... Author: Martin Cech <cech.marten@gmail.com> Date: 2017-02-02 (Thu, 02 Feb 2017) Changed paths: M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Merge pull request #3536 from blankenberg/17.01-conda-fix [17.01] Fix conda resolver when conda_auto_install = True and install = False Commit: f6919651f8225c2d48c7b2ecb667e365d7be7bf7 https://github.com/galaxyproject/galaxy/commit/f6919651f8225c2d48c7b2ecb667e... Author: Nicola Soranzo <nsoranzo@tiscali.it> Date: 2017-02-02 (Thu, 02 Feb 2017) Changed paths: M lib/galaxy/tools/verify/asserts/xml.py A test-data/simple.xml A test/functional/tools/is_valid_xml.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #3530 from jvolkening/release_17.01 fix <is_valid_xml> output test assert check Commit: b6cd80a5b35938847d4b306501a4e1fc7030c441 https://github.com/galaxyproject/galaxy/commit/b6cd80a5b35938847d4b306501a4e... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2017-02-02 (Thu, 02 Feb 2017) Changed paths: M lib/galaxy/datatypes/registry.py M lib/galaxy/queue_worker.py M lib/galaxy/webapps/galaxy/api/configuration.py M test/api/test_datatypes.py Log Message: ----------- Merge branch 'release_16.10' into release_17.01 Commit: 62e6639d4716462dc4c6d5292c362a4ce0ba8a31 https://github.com/galaxyproject/galaxy/commit/62e6639d4716462dc4c6d5292c362... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2017-02-02 (Thu, 02 Feb 2017) Changed paths: M .ci/flake8_lint_include_list.txt M test/api/test_datatypes.py Log Message: ----------- Fix import order Broken in commit dd77cdb62576a62ea7e8ce8e31d2d7d78aef7823 . Need to remove the file from .ci/flake8_lint_include_list.txt because 'base' is not in application-import-names Commit: 409ca0a3c7eec50aaaec15215d380ec098ce4ec1 https://github.com/galaxyproject/galaxy/commit/409ca0a3c7eec50aaaec15215d380... Author: Martin Cech <cech.marten@gmail.com> Date: 2017-02-02 (Thu, 02 Feb 2017) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/model/mapping.py M lib/galaxy/workflow/scheduling_manager.py Log Message: ----------- Merge pull request #3520 from dannon/history_serial_workflow_scheduling [17.01] History-local serial workflow scheduling. Commit: 49970e786fcf2d885b6a81aa61786cba7912f3fe https://github.com/galaxyproject/galaxy/commit/49970e786fcf2d885b6a81aa61786... Author: Marius van den Beek <m.vandenbeek@gmail.com> Date: 2017-02-03 (Fri, 03 Feb 2017) Changed paths: M .ci/flake8_lint_include_list.txt M test/api/test_datatypes.py Log Message: ----------- Merge pull request #3549 from nsoranzo/release_17.01_fix_import_order [17.01] Fix import order Commit: 0b074f3fa55e5e831d761cefe9dadbf2129706a7 https://github.com/galaxyproject/galaxy/commit/0b074f3fa55e5e831d761cefe9dad... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2017-02-03 (Fri, 03 Feb 2017) Changed paths: M .ci/flake8_lint_include_list.txt M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/datatypes/registry.py M lib/galaxy/model/mapping.py M lib/galaxy/queue_worker.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/verify/asserts/xml.py M lib/galaxy/webapps/galaxy/api/configuration.py M lib/galaxy/webapps/galaxy/api/jobs.py M lib/galaxy/workflow/scheduling_manager.py M static/maps/mvc/library/library-dataset-view.js.map M static/maps/mvc/library/library-folderrow-view.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/mvc/library/library-dataset-view.js M static/scripts/mvc/library/library-folderrow-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js A test-data/simple.xml M test/api/test_datatypes.py A test/functional/tools/is_valid_xml.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge branch 'release_17.01' into dev Conflicts: static/scripts/bundled/analysis.bundled.js static/scripts/bundled/analysis.bundled.js.map static/scripts/bundled/libs.bundled.js.map Compare: https://github.com/galaxyproject/galaxy/compare/0219e26085e7...0b074f3fa55e