galaxy-commits January 2016

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[galaxyproject/galaxy] c8b005: Add a requirements file suitable for use with `con...
by GitHub 26 Jan '16

26 Jan '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: c8b0057349be9a683e295c073f66163f47c257e7 https://github.com/galaxyproject/galaxy/commit/c8b0057349be9a683e295c073f66… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-01-21 (Thu, 21 Jan 2016) Changed paths: A lib/galaxy/dependencies/conda-requirements.txt Log Message: ----------- Add a requirements file suitable for use with `conda {create,install} --file`. Commit: 1486af0ef90a186b5648f737af32e84640263857 https://github.com/galaxyproject/galaxy/commit/1486af0ef90a186b5648f737af32… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-01-26 (Tue, 26 Jan 2016) Changed paths: A lib/galaxy/dependencies/conda-environment.txt R lib/galaxy/dependencies/conda-requirements.txt Log Message: ----------- Rename conda-requirements.txt to conda-environment.txt since it is not a requirements file, include instructions on how to install remaining dependencies from pip. Commit: c2d94c43bbd5929d4773e859dc1f5d8e436b0ee8 https://github.com/galaxyproject/galaxy/commit/c2d94c43bbd5929d4773e859dc1f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-26 (Tue, 26 Jan 2016) Changed paths: A lib/galaxy/dependencies/conda-environment.txt Log Message: ----------- Merge pull request #1560 from natefoo/conda-interop [16.01] Add a requirements file suitable for use with `conda {create,install} --file` Compare: https://github.com/galaxyproject/galaxy/compare/35f90da20ca2...c2d94c43bbd5

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[galaxyproject/galaxy] eca2c3: Failing test case to exhibit #1514.
by GitHub 26 Jan '16

26 Jan '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: eca2c3bcee2c9f05dee062c60607251a589a93fd https://github.com/galaxyproject/galaxy/commit/eca2c3bcee2c9f05dee062c60607… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-19 (Tue, 19 Jan 2016) Changed paths: M test/api/test_workflows.py A test/functional/tools/for_workflows/1.bam A test/functional/tools/for_workflows/mapper.xml A test/functional/tools/for_workflows/pileup.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Failing test case to exhibit #1514. Commit: f1394d250db103eda0bc88044eaa92f54f56476c https://github.com/galaxyproject/galaxy/commit/f1394d250db103eda0bc88044eaa… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-19 (Tue, 19 Jan 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/validation.py Log Message: ----------- Fix #1514. Prior to PR #1302 workflows wouldn't validate call validate at all on inputs. 1302 was perhaps an over correction that causes validate to be called on datasets that aren't yet READY but require metadata. This rolls that back somewhat, other parameters will still validate - but validation asserting the existence of metadata won't get called in workflows. This is still not ideal but after 1302 and this - we are still in a better, more secure place than beforehand. One might argue that since we need to introduce a new validation point (right before a job is scheduled and set to QUEUED) - that we would be better off rolling back #1302 entirely. I've considered that, but I still think it is better to fail fast on the other problems, also I would rather call the validation code too many times than not enough and it would be very late in the release cycle for such a change. Commit: 3f51101527fee096761a4c22ee8841e64b98f7a6 https://github.com/galaxyproject/galaxy/commit/3f51101527fee096761a4c22ee88… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-20 (Wed, 20 Jan 2016) Changed paths: M lib/galaxy/jobs/actions/post.py M test/api/test_workflows.py M test/api/workflows_format_2/converter.py Log Message: ----------- Attempt to fix #1531. I was unable to reproduce #1531 in testing, but if the problem is something to do with stale state the following sledge hammer should fix it. Runt the new test case with: ./run_tests.sh -api test/api/test_workflows.py:WorkflowsApiTestCase.test_delete_intermediate_datasets_pja_1 Commit: cd95635197eddaeee55be88f96543dc3a97e9343 https://github.com/galaxyproject/galaxy/commit/cd95635197eddaeee55be88f9654… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-20 (Wed, 20 Jan 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Fix #1538. Displaying subcollection mapping in tool forms was broken with #1308 - this fixes that I believe. Commit: bbff72e0ce9876b495971d20223780f1244d1f03 https://github.com/galaxyproject/galaxy/commit/bbff72e0ce9876b495971d202237… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-01-20 (Wed, 20 Jan 2016) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view.js M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Fix upgrade messages Commit: 035a67d0b5a1deeb54592937150a9ae82fab997e https://github.com/galaxyproject/galaxy/commit/035a67d0b5a1deeb54592937150a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-01-21 (Thu, 21 Jan 2016) Changed paths: M client/galaxy/scripts/mvc/form/form-select-content.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M static/maps/mvc/form/form-select-content.js.map M static/maps/mvc/ui/ui-select-default.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/form/form-select-content.js M static/scripts/mvc/ui/ui-select-default.js Log Message: ----------- Keep track of hidden datasets Commit: 1b43e8d68ffd44780f552e2472010d02dbc274b6 https://github.com/galaxyproject/galaxy/commit/1b43e8d68ffd44780f552e247201… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-21 (Thu, 21 Jan 2016) Changed paths: M lib/galaxy/tools/special_tools.py Log Message: ----------- Logging fix. Commit: 093f1f2712eeaa3c4a23952e2488a9a7a6731b17 https://github.com/galaxyproject/galaxy/commit/093f1f2712eeaa3c4a23952e2488… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-21 (Thu, 21 Jan 2016) Changed paths: M lib/galaxy/datatypes/interval.py Log Message: ----------- Make sciex sniffer tighter. Otherwise a bed file easily could sniff as sciex. Commit: 58d75f4bc2e4e52b9f4541d20c1253e49735a22f https://github.com/galaxyproject/galaxy/commit/58d75f4bc2e4e52b9f4541d20c12… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-21 (Thu, 21 Jan 2016) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view.js M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Merge pull request #1550 from guerler/fix_upgrade_000 [16.01] Fix upgrade messages Commit: a00faba4fefabd1e28f3ce58603c9f99abf9a4f8 https://github.com/galaxyproject/galaxy/commit/a00faba4fefabd1e28f3ce58603c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-21 (Thu, 21 Jan 2016) Changed paths: M client/galaxy/scripts/mvc/form/form-select-content.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M static/maps/mvc/form/form-select-content.js.map M static/maps/mvc/ui/ui-select-default.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/form/form-select-content.js M static/scripts/mvc/ui/ui-select-default.js Log Message: ----------- Merge pull request #1551 from guerler/fix_hidden_rerun_000 [16.01] Keep track of hidden datasets Commit: 17abd4a30d41ff070202c1818ad84c015a642733 https://github.com/galaxyproject/galaxy/commit/17abd4a30d41ff070202c1818ad8… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2016-01-21 (Thu, 21 Jan 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/validation.py M test/api/test_workflows.py A test/functional/tools/for_workflows/1.bam A test/functional/tools/for_workflows/mapper.xml A test/functional/tools/for_workflows/pileup.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #1536 from jmchilton/issue_1514 [16.01] Test case and fix for issue #1514 Commit: 2fc982027cb3de555afbd1650b52dbd84897956a https://github.com/galaxyproject/galaxy/commit/2fc982027cb3de555afbd1650b52… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-01-21 (Thu, 21 Jan 2016) Changed paths: M lib/galaxy/tools/special_tools.py Log Message: ----------- Merge pull request #1553 from jmchilton/logging_fix [16.01] Logging fix. Commit: e48388ef6cca6505d47b3daf3c2e0c4a5041b3f4 https://github.com/galaxyproject/galaxy/commit/e48388ef6cca6505d47b3daf3c2e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-01-21 (Thu, 21 Jan 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Merge pull request #1545 from jmchilton/subcollection_mapping_problem [16.01] Fix #1538. Commit: 8ceb4d8ee495d21a664e3faece1e072a88048494 https://github.com/galaxyproject/galaxy/commit/8ceb4d8ee495d21a664e3faece1e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-01-21 (Thu, 21 Jan 2016) Changed paths: M scripts/common_startup.sh Log Message: ----------- Force --skip-venv if we can detect that Python is Conda Python. Commit: fe96255022f4fdf72f39be959a15993d014a0d38 https://github.com/galaxyproject/galaxy/commit/fe96255022f4fdf72f39be959a15… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-01-21 (Thu, 21 Jan 2016) Changed paths: M scripts/common_startup.sh Log Message: ----------- Merge pull request #1554 from natefoo/conda-interop [16.01] Force --skip-venv if we can detect that Python is Conda Python. Commit: f5fbe1c5020fb432346ce6340833937d13cbf6d0 https://github.com/galaxyproject/galaxy/commit/f5fbe1c5020fb432346ce6340833… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-01-21 (Thu, 21 Jan 2016) Changed paths: M client/galaxy/scripts/mvc/visualization/visualization-model.js M config/plugins/visualizations/charts/Gruntfile.js M config/plugins/visualizations/charts/static/build-app.js M config/plugins/visualizations/charts/templates/charts.mako M config/plugins/visualizations/scatterplot/templates/scatterplot.mako R static/maps/libs/backbone/backbone.js.map M static/maps/mvc/visualization/visualization-model.js.map R static/scripts/libs/backbone/backbone.js M static/scripts/mvc/visualization/visualization-model.js Log Message: ----------- Client: remove older compiled backbone/backbone.js, update scatterplot and charts for same; Visualizations: fix visualization-model url; Scatterplot: fix title bug and Galaxy var Commit: 1b7462644d0352d44b36e2d790d6d10d906e7be4 https://github.com/galaxyproject/galaxy/commit/1b7462644d0352d44b36e2d790d6… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-01-22 (Fri, 22 Jan 2016) Changed paths: M client/galaxy/scripts/mvc/visualization/visualization-model.js M config/plugins/visualizations/charts/Gruntfile.js M config/plugins/visualizations/charts/static/build-app.js M config/plugins/visualizations/charts/templates/charts.mako M config/plugins/visualizations/scatterplot/templates/scatterplot.mako R static/maps/libs/backbone/backbone.js.map M static/maps/mvc/visualization/visualization-model.js.map R static/scripts/libs/backbone/backbone.js M static/scripts/mvc/visualization/visualization-model.js Log Message: ----------- Merge pull request #1558 from carlfeberhard/release_16.01 [16.01] Fix redundant backbone and visualizations Commit: c117d400506e605c41e3837b83d79593733c5af0 https://github.com/galaxyproject/galaxy/commit/c117d400506e605c41e3837b83d7… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-01-26 (Tue, 26 Jan 2016) Changed paths: M lib/galaxy/datatypes/interval.py Log Message: ----------- Merge pull request #1557 from jmchilton/sciex_sniff [16.01] Tighten up ScIdx sniffer. Commit: 35f90da20ca21a8f82d1650c0cf520a064b6bd8a https://github.com/galaxyproject/galaxy/commit/35f90da20ca21a8f82d1650c0cf5… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-01-26 (Tue, 26 Jan 2016) Changed paths: M lib/galaxy/jobs/actions/post.py M test/api/test_workflows.py M test/api/workflows_format_2/converter.py Log Message: ----------- Merge pull request #1542 from jmchilton/did_fix [16.01] Attempt to fix #1531. Commit: 11654a0950ee89f643893de119f55314ac626217 https://github.com/galaxyproject/galaxy/commit/11654a0950ee89f643893de119f5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-26 (Tue, 26 Jan 2016) Changed paths: M lib/galaxy/datatypes/interval.py M lib/galaxy/jobs/actions/post.py M test/api/test_workflows.py M test/api/workflows_format_2/converter.py Log Message: ----------- Merge release_16.01 into dev. Commit: f725e964333d084798410d90a522eadfcdecd540 https://github.com/galaxyproject/galaxy/commit/f725e964333d084798410d90a522… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-26 (Tue, 26 Jan 2016) Changed paths: M lib/galaxy/datatypes/interval.py M lib/galaxy/jobs/actions/post.py M test/api/test_workflows.py M test/api/workflows_format_2/converter.py Log Message: ----------- Merge pull request #1591 from jmchilton/dev_merge_3 Merge 16.01 into dev. Compare: https://github.com/galaxyproject/galaxy/compare/217e38eae30f...f725e964333d

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[galaxyproject/galaxy] 3f5110: Attempt to fix #1531.
by GitHub 26 Jan '16

26 Jan '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: 3f51101527fee096761a4c22ee8841e64b98f7a6 https://github.com/galaxyproject/galaxy/commit/3f51101527fee096761a4c22ee88… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-20 (Wed, 20 Jan 2016) Changed paths: M lib/galaxy/jobs/actions/post.py M test/api/test_workflows.py M test/api/workflows_format_2/converter.py Log Message: ----------- Attempt to fix #1531. I was unable to reproduce #1531 in testing, but if the problem is something to do with stale state the following sledge hammer should fix it. Runt the new test case with: ./run_tests.sh -api test/api/test_workflows.py:WorkflowsApiTestCase.test_delete_intermediate_datasets_pja_1 Commit: 35f90da20ca21a8f82d1650c0cf520a064b6bd8a https://github.com/galaxyproject/galaxy/commit/35f90da20ca21a8f82d1650c0cf5… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-01-26 (Tue, 26 Jan 2016) Changed paths: M lib/galaxy/jobs/actions/post.py M test/api/test_workflows.py M test/api/workflows_format_2/converter.py Log Message: ----------- Merge pull request #1542 from jmchilton/did_fix [16.01] Attempt to fix #1531. Compare: https://github.com/galaxyproject/galaxy/compare/c117d400506e...35f90da20ca2

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[galaxyproject/galaxy] 093f1f: Make sciex sniffer tighter.
by GitHub 26 Jan '16

26 Jan '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: 093f1f2712eeaa3c4a23952e2488a9a7a6731b17 https://github.com/galaxyproject/galaxy/commit/093f1f2712eeaa3c4a23952e2488… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-21 (Thu, 21 Jan 2016) Changed paths: M lib/galaxy/datatypes/interval.py Log Message: ----------- Make sciex sniffer tighter. Otherwise a bed file easily could sniff as sciex. Commit: c117d400506e605c41e3837b83d79593733c5af0 https://github.com/galaxyproject/galaxy/commit/c117d400506e605c41e3837b83d7… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-01-26 (Tue, 26 Jan 2016) Changed paths: M lib/galaxy/datatypes/interval.py Log Message: ----------- Merge pull request #1557 from jmchilton/sciex_sniff [16.01] Tighten up ScIdx sniffer. Compare: https://github.com/galaxyproject/galaxy/compare/1b7462644d03...c117d400506e

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[galaxyproject/galaxy] 55635b: Update ``area/`` list to reflect current areas.
by GitHub 26 Jan '16

26 Jan '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 55635bff82c12a27c0e31fa44cda70a8ff8beef2 https://github.com/galaxyproject/galaxy/commit/55635bff82c12a27c0e31fa44cda… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-25 (Mon, 25 Jan 2016) Changed paths: M doc/source/project/issues.rst Log Message: ----------- Update ``area/`` list to reflect current areas. Commit: 20f6bce375083d71eeed990615e7d2538cf7ec3f https://github.com/galaxyproject/galaxy/commit/20f6bce375083d71eeed990615e7… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-25 (Mon, 25 Jan 2016) Changed paths: M doc/source/project/issues.rst Log Message: ----------- New areas. Commit: 53c699a4c347b5f6692c398f1c034a6767b782ad https://github.com/galaxyproject/galaxy/commit/53c699a4c347b5f6692c398f1c03… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-25 (Mon, 25 Jan 2016) Changed paths: M doc/source/project/issues.rst Log Message: ----------- Add note about how to modify labels in Galaxy project. Commit: 6c487941d213ac57a83206f6e3c948d8c2b97654 https://github.com/galaxyproject/galaxy/commit/6c487941d213ac57a83206f6e3c9… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-26 (Tue, 26 Jan 2016) Changed paths: M doc/source/project/issues.rst Log Message: ----------- Adjust tooling language based on note from @nsoranzo. Commit: d1dcf25f57762d99f5318dbe26a82a99091933a8 https://github.com/galaxyproject/galaxy/commit/d1dcf25f57762d99f5318dbe26a8… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-01-26 (Tue, 26 Jan 2016) Changed paths: M doc/source/project/issues.rst Log Message: ----------- add plural form Commit: 217e38eae30f216dba0ca9920c76d0510c97c3bd https://github.com/galaxyproject/galaxy/commit/217e38eae30f216dba0ca9920c76… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-01-26 (Tue, 26 Jan 2016) Changed paths: M doc/source/project/issues.rst Log Message: ----------- Merge pull request #1579 from jmchilton/area_tags Clarify area github tags. Compare: https://github.com/galaxyproject/galaxy/compare/b77b096a3881...217e38eae30f

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[galaxyproject/usegalaxy-playbook] 7109a0: Enable bam.io on Test
by GitHub 26 Jan '16

26 Jan '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 7109a04252759a3b9d47da2706da469f2a05602d https://github.com/galaxyproject/usegalaxy-playbook/commit/7109a04252759a3b… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-01-26 (Tue, 26 Jan 2016) Changed paths: M stage/group_vars/galaxyservers.yml Log Message: ----------- Enable bam.io on Test

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[galaxyproject/usegalaxy-playbook] dca40e: Test mutable stuff
by GitHub 26 Jan '16

26 Jan '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: dca40e262baa309afb9204c3d4f225eae4f5382a https://github.com/galaxyproject/usegalaxy-playbook/commit/dca40e262baa309a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-01-26 (Tue, 26 Jan 2016) 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 M stage/files/interactive_environments/plugins/.ansible_ie_role_current_version M stage/files/interactive_environments/proxy/.ansible_ie_role_current_version Log Message: ----------- Test mutable stuff

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[galaxyproject/galaxy] 297345: small spelling error
by GitHub 26 Jan '16

26 Jan '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 29734512abdbaa266da8d9ee39d2829c9c4ab6ee https://github.com/galaxyproject/galaxy/commit/29734512abdbaa266da8d9ee39d2… Author: matthdsm <matthias.desmet(a)ugent.be> Date: 2016-01-26 (Tue, 26 Jan 2016) Changed paths: M config/galaxy.ini.sample Log Message: ----------- small spelling error maxiumum > maximum Commit: b77b096a3881fc841810ce834cf2c06194e4c979 https://github.com/galaxyproject/galaxy/commit/b77b096a3881fc841810ce834cf2… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-26 (Tue, 26 Jan 2016) Changed paths: M config/galaxy.ini.sample Log Message: ----------- Merge pull request #1582 from matthdsm/patch-1 small spelling error Compare: https://github.com/galaxyproject/galaxy/compare/fdb90c729f85...b77b096a3881

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[galaxyproject/galaxy] 807586: Merge release_16.01 into dev.
by GitHub 26 Jan '16

26 Jan '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 807586ace8d90b33b24a9584af73a6a4dc763b34 https://github.com/galaxyproject/galaxy/commit/807586ace8d90b33b24a9584af73… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-26 (Tue, 26 Jan 2016) Changed paths: M client/galaxy/scripts/mvc/form/form-select-content.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/scripts/mvc/visualization/visualization-model.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M config/plugins/visualizations/charts/Gruntfile.js M config/plugins/visualizations/charts/templates/charts.mako M config/plugins/visualizations/scatterplot/templates/scatterplot.mako M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/validation.py M lib/galaxy/tools/special_tools.py M scripts/common_startup.sh R static/maps/libs/backbone/backbone.js.map M static/maps/mvc/form/form-select-content.js.map M static/maps/mvc/ui/ui-select-default.js.map M static/maps/mvc/visualization/visualization-model.js.map M static/maps/mvc/workflow/workflow-view.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 R static/scripts/libs/backbone/backbone.js M static/scripts/mvc/form/form-select-content.js M static/scripts/mvc/ui/ui-select-default.js M static/scripts/mvc/visualization/visualization-model.js M static/scripts/mvc/workflow/workflow-view.js M test/api/test_workflows.py A test/functional/tools/for_workflows/1.bam A test/functional/tools/for_workflows/mapper.xml A test/functional/tools/for_workflows/pileup.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge release_16.01 into dev. Commit: fdb90c729f859dd6a581d71817bc0bfb3a03abd9 https://github.com/galaxyproject/galaxy/commit/fdb90c729f859dd6a581d71817bc… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-26 (Tue, 26 Jan 2016) Changed paths: M client/galaxy/scripts/mvc/form/form-select-content.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/scripts/mvc/visualization/visualization-model.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M config/plugins/visualizations/charts/Gruntfile.js M config/plugins/visualizations/charts/templates/charts.mako M config/plugins/visualizations/scatterplot/templates/scatterplot.mako M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/validation.py M lib/galaxy/tools/special_tools.py M scripts/common_startup.sh R static/maps/libs/backbone/backbone.js.map M static/maps/mvc/form/form-select-content.js.map M static/maps/mvc/ui/ui-select-default.js.map M static/maps/mvc/visualization/visualization-model.js.map M static/maps/mvc/workflow/workflow-view.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 R static/scripts/libs/backbone/backbone.js M static/scripts/mvc/form/form-select-content.js M static/scripts/mvc/ui/ui-select-default.js M static/scripts/mvc/visualization/visualization-model.js M static/scripts/mvc/workflow/workflow-view.js M test/api/test_workflows.py A test/functional/tools/for_workflows/1.bam A test/functional/tools/for_workflows/mapper.xml A test/functional/tools/for_workflows/pileup.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #1583 from jmchilton/dev_merge_2 Merge release_16.01 into dev. Compare: https://github.com/galaxyproject/galaxy/compare/585b93fd1868...fdb90c729f85

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[galaxyproject/galaxy] 06e9cb: remove the until-now-tolerated global side effect
by GitHub 25 Jan '16

25 Jan '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 06e9cb8b6c51ca01de5012da10e8513bccbe0443 https://github.com/galaxyproject/galaxy/commit/06e9cb8b6c51ca01de5012da10e8… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-01-25 (Mon, 25 Jan 2016) Changed paths: M client/galaxy/style/less/tour.less M static/style/blue/base.css Log Message: ----------- remove the until-now-tolerated global side effect Commit: 585b93fd186895d8727c614042029cb166613293 https://github.com/galaxyproject/galaxy/commit/585b93fd186895d8727c61404202… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2016-01-25 (Mon, 25 Jan 2016) Changed paths: M client/galaxy/style/less/tour.less M static/style/blue/base.css Log Message: ----------- Merge pull request #1577 from martenson/restrict-tourpopover-to-tour restrict blue popover to tours Compare: https://github.com/galaxyproject/galaxy/compare/1275dfd09955...585b93fd1868

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