- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] e9ed5b: clarify the bitbucket support
by GitHub 20 Nov '15

20 Nov '15

Branch: refs/heads/release_15.10 Home: https://github.com/galaxyproject/galaxy Commit: e9ed5bfa626765754629af20f1567d7102bac231 https://github.com/galaxyproject/galaxy/commit/e9ed5bfa626765754629af20f156… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-11-20 (Fri, 20 Nov 2015) Changed paths: M doc/source/releases/15.10_announce.rst Log Message: ----------- clarify the bitbucket support Commit: a5aeea0685d5e7d1f4406f9abf69ca3da3add160 https://github.com/galaxyproject/galaxy/commit/a5aeea0685d5e7d1f4406f9abf69… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-11-20 (Fri, 20 Nov 2015) Changed paths: M doc/source/releases/15.10_announce.rst Log Message: ----------- Slight wording tweak Commit: ceb8ee127af9390a2cbd3b6046dc360d98992060 https://github.com/galaxyproject/galaxy/commit/ceb8ee127af9390a2cbd3b6046dc… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-11-20 (Fri, 20 Nov 2015) Changed paths: M doc/source/releases/15.10_announce.rst Log Message: ----------- Merge pull request #11 from dannon/tweak-notes Slight wording tweak Commit: 09db120ad84dcaa851a6ae3dbc351a7a958ce736 https://github.com/galaxyproject/galaxy/commit/09db120ad84dcaa851a6ae3dbc35… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-11-20 (Fri, 20 Nov 2015) Changed paths: M doc/source/releases/15.10_announce.rst Log Message: ----------- Merge pull request #1141 from martenson/tweak-notes [15.10] release notes tweaks Compare: https://github.com/galaxyproject/galaxy/compare/a98e56c9ee53...09db120ad84d

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[galaxyproject/galaxy] bbef5e: Improvements to release notes generation.
by GitHub 20 Nov '15

20 Nov '15

Branch: refs/heads/release_15.10 Home: https://github.com/galaxyproject/galaxy Commit: bbef5ed7373b33eaa30f2e493311413e0cea018b https://github.com/galaxyproject/galaxy/commit/bbef5ed7373b33eaa30f2e493311… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-10-14 (Wed, 14 Oct 2015) Changed paths: M scripts/bootstrap_history.py Log Message: ----------- Improvements to release notes generation. - Add last commit for 15.10 (need to automate finding that). - Generate next release annoucement. - Generate annoucement for this release. - Respect the minor tag. Commit: b7bf42e1b4fae9e4c2e3b246868518992dbcce10 https://github.com/galaxyproject/galaxy/commit/b7bf42e1b4fae9e4c2e3b2468685… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-10-14 (Wed, 14 Oct 2015) Changed paths: A doc/source/releases/15.10.rst M doc/source/releases/15.10_announce.rst A doc/source/releases/16.01_announce.rst Log Message: ----------- Fill in release notes for 15.10. Commit: 4f4526bc303eeb40dae9d71d5dc161bb8b398ae6 https://github.com/galaxyproject/galaxy/commit/4f4526bc303eeb40dae9d71d5dc1… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-10-14 (Wed, 14 Oct 2015) Changed paths: M doc/source/releases/15.10_announce.rst Log Message: ----------- deprecate old Data Libraries Commit: cf16e2c7d39657a13d48615841c192a667428b93 https://github.com/galaxyproject/galaxy/commit/cf16e2c7d39657a13d48615841c1… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-11-20 (Fri, 20 Nov 2015) Changed paths: M doc/source/releases/15.10_announce.rst Log Message: ----------- add bitbucker deprecation notice Commit: 76fc6becd65f829db924e3726ade11dc0735e2ca https://github.com/galaxyproject/galaxy/commit/76fc6becd65f829db924e3726ade… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-11-20 (Fri, 20 Nov 2015) Changed paths: M doc/source/releases/15.10_announce.rst Log Message: ----------- add text highlights Commit: a98e56c9ee53a29f89db9740ad418bad12f32259 https://github.com/galaxyproject/galaxy/commit/a98e56c9ee53a29f89db9740ad41… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-11-20 (Fri, 20 Nov 2015) Changed paths: A doc/source/releases/15.10.rst M doc/source/releases/15.10_announce.rst A doc/source/releases/16.01_announce.rst M scripts/bootstrap_history.py Log Message: ----------- Merge pull request #868 from jmchilton/release_notes [15.10] Release notes Compare: https://github.com/galaxyproject/galaxy/compare/743603b4b720...a98e56c9ee53

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[galaxyproject/infrastructure-playbook] 4f7e0a: Fix missing library/ directory
by GitHub 20 Nov '15

20 Nov '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 4f7e0ac5bb70e0624470f7f56c3c687dacfd51eb https://github.com/galaxyproject/infrastructure-playbook/commit/4f7e0ac5bb7… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-11-20 (Fri, 20 Nov 2015) Changed paths: A galaxyenv/library/README A galaxyenv/library/cron.py R library/README R library/cron.py A play-galaxy Log Message: ----------- Fix missing library/ directory Commit: 8a9299e280e58cf92c80943def2ecb0c44dcbc5d https://github.com/galaxyproject/infrastructure-playbook/commit/8a9299e280e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-11-20 (Fri, 20 Nov 2015) Changed paths: M galaxyenv/host_vars/leeroy.galaxyproject.org.yml Log Message: ----------- Merge branch 'master' of github.com:galaxyproject/infrastructure-playbook Compare: https://github.com/galaxyproject/infrastructure-playbook/compare/1654f593b3…

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[galaxyproject/galaxy] cbf5c6: Don't override search url -- this currently affect...
by GitHub 20 Nov '15

20 Nov '15

Branch: refs/heads/release_15.10 Home: https://github.com/galaxyproject/galaxy Commit: cbf5c68ad76d47f74b95df20604b1ae1f787d9d1 https://github.com/galaxyproject/galaxy/commit/cbf5c68ad76d47f74b95df20604b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-11-20 (Fri, 20 Nov 2015) Changed paths: M templates/webapps/galaxy/root/index.mako Log Message: ----------- Don't override search url -- this currently affects main where Help->Search ends up at root.com... Commit: adcf513390e05039acc0ebe761b833686ff7fe13 https://github.com/galaxyproject/galaxy/commit/adcf513390e05039acc0ebe761b8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-11-20 (Fri, 20 Nov 2015) Changed paths: M templates/webapps/galaxy/root/index.mako Log Message: ----------- Simply remove tool_search_url -- it isn't used and it's totally composable. Commit: 743603b4b72078ad251ecd66e37f17f323a71d51 https://github.com/galaxyproject/galaxy/commit/743603b4b72078ad251ecd66e37f… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-11-20 (Fri, 20 Nov 2015) Changed paths: M templates/webapps/galaxy/root/index.mako Log Message: ----------- Merge pull request #1140 from dannon/menufix_2 [15.10] Don't override search url Compare: https://github.com/galaxyproject/galaxy/compare/0fdca7d40a22...743603b4b720

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[galaxyproject/galaxy] ed992b: A large assortment of escaping fixes to primarily ...
by GitHub 20 Nov '15

20 Nov '15

Branch: refs/heads/release_15.07 Home: https://github.com/galaxyproject/galaxy Commit: ed992b3b28c7f6d9d637e82e88305b665733a50b https://github.com/galaxyproject/galaxy/commit/ed992b3b28c7f6d9d637e82e8830… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-11-19 (Thu, 19 Nov 2015) Changed paths: M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/collection/pair-collection-creator.js M client/galaxy/scripts/mvc/dataset/dataset-choice.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/history/history-panel.js M client/galaxy/scripts/mvc/history/multi-panel.js M client/galaxy/scripts/mvc/job/job-li.js M client/galaxy/scripts/mvc/list/list-panel.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/toolshed/scripts/mvc/groups/group-detail-view.js M client/toolshed/scripts/mvc/groups/group-listrow-view.js M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/external_service.py M lib/galaxy/webapps/galaxy/controllers/forms.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/library.py M lib/galaxy/webapps/galaxy/controllers/library_admin.py M lib/galaxy/webapps/galaxy/controllers/request_type.py M lib/galaxy/webapps/galaxy/controllers/requests_admin.py M lib/galaxy/webapps/galaxy/controllers/requests_common.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/galaxy/webapps/reports/controllers/jobs.py M lib/galaxy/webapps/reports/controllers/sample_tracking.py M lib/galaxy/webapps/reports/controllers/workflows.py M lib/tool_shed/grids/admin_grids.py M lib/tool_shed/grids/repository_grids.py M lib/tool_shed/grids/repository_review_grids.py M static/maps/mvc/history/multi-panel.js.map M static/maps/mvc/ui/ui-select-default.js.map M static/scripts/libs/jquery/jquery.dynatree.js M static/scripts/mvc/collection/list-collection-creator.js M static/scripts/mvc/collection/list-of-pairs-collection-creator.js M static/scripts/mvc/collection/pair-collection-creator.js M static/scripts/mvc/dataset/dataset-choice.js M static/scripts/mvc/dataset/dataset-li-edit.js M static/scripts/mvc/dataset/dataset-li.js M static/scripts/mvc/history/history-panel.js M static/scripts/mvc/history/multi-panel.js M static/scripts/mvc/job/job-li.js M static/scripts/mvc/list/list-panel.js M static/scripts/mvc/ui/ui-select-default.js Log Message: ----------- A large assortment of escaping fixes to primarily grids and javascript templating, and one bad-data-ingress fix (copy history name).

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[galaxyproject/galaxy] 05ed24: Fix the bad merge :(
by GitHub 20 Nov '15

20 Nov '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 05ed245353331489ee443ac483b1569dab38f500 https://github.com/galaxyproject/galaxy/commit/05ed245353331489ee443ac483b1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-11-19 (Thu, 19 Nov 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/external_service.py M lib/galaxy/webapps/galaxy/controllers/forms.py M lib/galaxy/webapps/galaxy/controllers/request_type.py M lib/galaxy/webapps/galaxy/controllers/requests_common.py M lib/galaxy/webapps/reports/controllers/jobs.py M lib/galaxy/webapps/reports/controllers/sample_tracking.py M lib/galaxy/webapps/reports/controllers/workflows.py M lib/tool_shed/grids/admin_grids.py M lib/tool_shed/grids/repository_review_grids.py Log Message: ----------- Fix the bad merge :(

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[galaxyproject/galaxy] 05f3da: Fix macro bug with empty CDATA being None instead ...
by GitHub 20 Nov '15

20 Nov '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 05f3da308d6a58dc8528f317fa6ea4ffa1fb7610 https://github.com/galaxyproject/galaxy/commit/05f3da308d6a58dc8528f317fa6e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-11-18 (Wed, 18 Nov 2015) Changed paths: M lib/galaxy/util/xml_macros.py M test/unit/tools/test_tool_loader.py Log Message: ----------- Fix macro bug with empty CDATA being None instead of ''. Fixes galaxyproject/planemo#362 thanks for the report @erasche. Test using the following command: ``` nosetests test/unit/tools/test_tool_loader.py ``` Commit: eb16ba3743a7e42cc9ad43f0d7a3eb926ba60cd8 https://github.com/galaxyproject/galaxy/commit/eb16ba3743a7e42cc9ad43f0d7a3… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-11-18 (Wed, 18 Nov 2015) Changed paths: M lib/galaxy/util/xml_macros.py M test/unit/tools/test_tool_loader.py Log Message: ----------- Merge pull request #1122 from jmchilton/empty_cdata_macro [15.10] Fix macro bug with empty CDATA being None instead of ''. Commit: 0fdca7d40a2297ec29ea9df383578626141fcfa7 https://github.com/galaxyproject/galaxy/commit/0fdca7d40a2297ec29ea9df38357… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-11-19 (Thu, 19 Nov 2015) Changed paths: M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/collection/pair-collection-creator.js M client/galaxy/scripts/mvc/dataset/dataset-choice.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/history/copy-dialog.js M client/galaxy/scripts/mvc/history/history-panel.js M client/galaxy/scripts/mvc/history/multi-panel.js M client/galaxy/scripts/mvc/job/job-li.js M client/galaxy/scripts/mvc/list/list-panel.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/toolshed/scripts/mvc/groups/group-detail-view.js M client/toolshed/scripts/mvc/groups/group-listrow-view.js M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/external_service.py M lib/galaxy/webapps/galaxy/controllers/forms.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/library.py M lib/galaxy/webapps/galaxy/controllers/library_admin.py M lib/galaxy/webapps/galaxy/controllers/request_type.py M lib/galaxy/webapps/galaxy/controllers/requests_admin.py M lib/galaxy/webapps/galaxy/controllers/requests_common.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/galaxy/webapps/reports/controllers/jobs.py M lib/galaxy/webapps/reports/controllers/sample_tracking.py M lib/galaxy/webapps/reports/controllers/workflows.py M lib/tool_shed/grids/admin_grids.py M lib/tool_shed/grids/repository_grids.py M lib/tool_shed/grids/repository_review_grids.py M static/maps/mvc/history/copy-dialog.js.map M static/maps/mvc/ui/ui-select-default.js.map M static/scripts/libs/jquery/jquery.dynatree.js M static/scripts/mvc/collection/list-collection-creator.js M static/scripts/mvc/collection/list-of-pairs-collection-creator.js M static/scripts/mvc/collection/pair-collection-creator.js M static/scripts/mvc/dataset/dataset-choice.js M static/scripts/mvc/dataset/dataset-li-edit.js M static/scripts/mvc/dataset/dataset-li.js M static/scripts/mvc/history/copy-dialog.js M static/scripts/mvc/history/history-panel.js M static/scripts/mvc/history/multi-panel.js M static/scripts/mvc/job/job-li.js M static/scripts/mvc/list/list-panel.js M static/scripts/mvc/ui/ui-select-default.js Log Message: ----------- A large assortment of escaping fixes to primarily grids and javascript templating, and one bad-data-ingress fix (copy history name). Commit: f61ec1c3c01b51fe3449a583e1966cc3dff099f2 https://github.com/galaxyproject/galaxy/commit/f61ec1c3c01b51fe3449a583e196… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-11-19 (Thu, 19 Nov 2015) Changed paths: M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/collection/pair-collection-creator.js M client/galaxy/scripts/mvc/dataset/dataset-choice.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/history/copy-dialog.js M client/galaxy/scripts/mvc/history/history-panel.js M client/galaxy/scripts/mvc/history/multi-panel.js M client/galaxy/scripts/mvc/job/job-li.js M client/galaxy/scripts/mvc/list/list-panel.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/toolshed/scripts/mvc/groups/group-detail-view.js M client/toolshed/scripts/mvc/groups/group-listrow-view.js M lib/galaxy/util/xml_macros.py M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/external_service.py M lib/galaxy/webapps/galaxy/controllers/forms.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/library.py M lib/galaxy/webapps/galaxy/controllers/library_admin.py M lib/galaxy/webapps/galaxy/controllers/request_type.py M lib/galaxy/webapps/galaxy/controllers/requests_admin.py M lib/galaxy/webapps/galaxy/controllers/requests_common.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/galaxy/webapps/reports/controllers/jobs.py M lib/galaxy/webapps/reports/controllers/sample_tracking.py M lib/galaxy/webapps/reports/controllers/workflows.py M lib/tool_shed/grids/admin_grids.py M lib/tool_shed/grids/repository_grids.py M lib/tool_shed/grids/repository_review_grids.py M static/maps/galaxy-app-base.js.map M static/maps/mvc/history/copy-dialog.js.map M static/maps/mvc/ui/ui-select-default.js.map M static/scripts/mvc/collection/list-collection-creator.js M static/scripts/mvc/collection/list-of-pairs-collection-creator.js M static/scripts/mvc/collection/pair-collection-creator.js M static/scripts/mvc/dataset/dataset-choice.js M static/scripts/mvc/dataset/dataset-li-edit.js M static/scripts/mvc/dataset/dataset-li.js M static/scripts/mvc/history/copy-dialog.js M static/scripts/mvc/history/history-panel.js M static/scripts/mvc/history/multi-panel.js M static/scripts/mvc/job/job-li.js M static/scripts/mvc/list/list-panel.js M static/scripts/mvc/ui/ui-select-default.js M test/unit/tools/test_tool_loader.py Log Message: ----------- Merge and rebuild client Compare: https://github.com/galaxyproject/galaxy/compare/96b17bd8560f...f61ec1c3c01b

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[galaxyproject/galaxy] 0fdca7: A large assortment of escaping fixes to primarily ...
by GitHub 20 Nov '15

20 Nov '15

Branch: refs/heads/release_15.10 Home: https://github.com/galaxyproject/galaxy Commit: 0fdca7d40a2297ec29ea9df383578626141fcfa7 https://github.com/galaxyproject/galaxy/commit/0fdca7d40a2297ec29ea9df38357… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-11-19 (Thu, 19 Nov 2015) Changed paths: M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/collection/pair-collection-creator.js M client/galaxy/scripts/mvc/dataset/dataset-choice.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/history/copy-dialog.js M client/galaxy/scripts/mvc/history/history-panel.js M client/galaxy/scripts/mvc/history/multi-panel.js M client/galaxy/scripts/mvc/job/job-li.js M client/galaxy/scripts/mvc/list/list-panel.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/toolshed/scripts/mvc/groups/group-detail-view.js M client/toolshed/scripts/mvc/groups/group-listrow-view.js M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/external_service.py M lib/galaxy/webapps/galaxy/controllers/forms.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/library.py M lib/galaxy/webapps/galaxy/controllers/library_admin.py M lib/galaxy/webapps/galaxy/controllers/request_type.py M lib/galaxy/webapps/galaxy/controllers/requests_admin.py M lib/galaxy/webapps/galaxy/controllers/requests_common.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/galaxy/webapps/reports/controllers/jobs.py M lib/galaxy/webapps/reports/controllers/sample_tracking.py M lib/galaxy/webapps/reports/controllers/workflows.py M lib/tool_shed/grids/admin_grids.py M lib/tool_shed/grids/repository_grids.py M lib/tool_shed/grids/repository_review_grids.py M static/maps/mvc/history/copy-dialog.js.map M static/maps/mvc/ui/ui-select-default.js.map M static/scripts/libs/jquery/jquery.dynatree.js M static/scripts/mvc/collection/list-collection-creator.js M static/scripts/mvc/collection/list-of-pairs-collection-creator.js M static/scripts/mvc/collection/pair-collection-creator.js M static/scripts/mvc/dataset/dataset-choice.js M static/scripts/mvc/dataset/dataset-li-edit.js M static/scripts/mvc/dataset/dataset-li.js M static/scripts/mvc/history/copy-dialog.js M static/scripts/mvc/history/history-panel.js M static/scripts/mvc/history/multi-panel.js M static/scripts/mvc/job/job-li.js M static/scripts/mvc/list/list-panel.js M static/scripts/mvc/ui/ui-select-default.js Log Message: ----------- A large assortment of escaping fixes to primarily grids and javascript templating, and one bad-data-ingress fix (copy history name).

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[galaxyproject/galaxy] 704144: Don't let $input hang cheetah evaluation...
by GitHub 19 Nov '15

19 Nov '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 704144c16936e6ddedee9d509ee4361f50f152f2 https://github.com/galaxyproject/galaxy/commit/704144c16936e6ddedee9d509ee4… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-11-18 (Wed, 18 Nov 2015) Changed paths: M lib/galaxy/tools/evaluation.py Log Message: ----------- Don't let $input hang cheetah evaluation... If $input is undefined. The Python input command was being used and causing Galaxy to hang during evaluation. Commit: 0ff8a21891f7780dd30f81047cb5f8112c924b4a https://github.com/galaxyproject/galaxy/commit/0ff8a21891f7780dd30f81047cb5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-11-18 (Wed, 18 Nov 2015) Changed paths: M lib/galaxy/tools/evaluation.py A test/functional/tools/cheetah_problem_unbound_var.xml A test/functional/tools/cheetah_problem_unbound_var_input.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Add example tools demonstrating cheetah problem (unbound variable). Refine default override of input to raise an exception instead of just throwing in a dummy string. Commit: 7dedb3ff18f06b123ac9d64ac1d9b42948ba903c https://github.com/galaxyproject/galaxy/commit/7dedb3ff18f06b123ac9d64ac1d9… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-11-18 (Wed, 18 Nov 2015) Changed paths: A test/functional/tools/cheetah_problem_syntax_error.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Add another cheetah syntax error example... ... ensure the test framework run the tool, detects that there is an error, and handles things appropriately. Commit: 96b17bd8560f938ee9d3244b6cf5b198864c44ce https://github.com/galaxyproject/galaxy/commit/96b17bd8560f938ee9d3244b6cf5… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-11-19 (Thu, 19 Nov 2015) Changed paths: M lib/galaxy/tools/evaluation.py A test/functional/tools/cheetah_problem_syntax_error.xml A test/functional/tools/cheetah_problem_unbound_var.xml A test/functional/tools/cheetah_problem_unbound_var_input.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #1117 from jmchilton/input_hang Don't let $input hang cheetah evaluation... Compare: https://github.com/galaxyproject/galaxy/compare/81f842743d0c...96b17bd8560f

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[galaxyproject/galaxy] af36ca: add BAM iobio visualisation as Interactive Environ...
by GitHub 19 Nov '15

19 Nov '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: af36ca6d9467932036d19a448ca4c74affffae9a https://github.com/galaxyproject/galaxy/commit/af36ca6d9467932036d19a448ca4… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2015-11-19 (Thu, 19 Nov 2015) Changed paths: A config/plugins/interactive_environments/bam_iobio/config/bam_iobio.ini.sample A config/plugins/interactive_environments/bam_iobio/config/bam_iobio.xml A config/plugins/interactive_environments/bam_iobio/static/js/bam_iobio.js A config/plugins/interactive_environments/bam_iobio/templates/bam_iobio.mako M config/plugins/interactive_environments/common/templates/ie.mako M config/plugins/interactive_environments/ipython/config/ipython.ini.sample M config/plugins/interactive_environments/ipython/static/js/ipython.js M config/plugins/interactive_environments/rstudio/static/js/rstudio.js M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- add BAM iobio visualisation as Interactive Environment Commit: 5188b4179063b3cc57c5c983d48a5fb62387d2b3 https://github.com/galaxyproject/galaxy/commit/5188b4179063b3cc57c5c983d48a… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2015-11-19 (Thu, 19 Nov 2015) Changed paths: M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- make travis happy Commit: 81f842743d0c42522f7f80b603eccbc78d697a3c https://github.com/galaxyproject/galaxy/commit/81f842743d0c42522f7f80b603ec… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-11-19 (Thu, 19 Nov 2015) Changed paths: A config/plugins/interactive_environments/bam_iobio/config/bam_iobio.ini.sample A config/plugins/interactive_environments/bam_iobio/config/bam_iobio.xml A config/plugins/interactive_environments/bam_iobio/static/js/bam_iobio.js A config/plugins/interactive_environments/bam_iobio/templates/bam_iobio.mako M config/plugins/interactive_environments/common/templates/ie.mako M config/plugins/interactive_environments/ipython/config/ipython.ini.sample M config/plugins/interactive_environments/ipython/static/js/ipython.js M config/plugins/interactive_environments/rstudio/static/js/rstudio.js M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Merge pull request #1131 from bgruening/IE_iobio Add BAM iobio visualisation as Interactive Environment Compare: https://github.com/galaxyproject/galaxy/compare/5191c2136a91...81f842743d0c

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[galaxyproject/infrastructure-playbook] 1654f5: install proper legacy node
by GitHub 19 Nov '15

19 Nov '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 1654f593b3914429f1a48a618f64f641ec10a94c https://github.com/galaxyproject/infrastructure-playbook/commit/1654f593b39… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-11-19 (Thu, 19 Nov 2015) Changed paths: M galaxyenv/host_vars/leeroy.galaxyproject.org.yml Log Message: ----------- install proper legacy node

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[galaxyproject/infrastructure-playbook] 3e0e46: Update common roles
by GitHub 19 Nov '15

19 Nov '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 3e0e465b377ee162fb229aaed31289dd54a9ac60 https://github.com/galaxyproject/infrastructure-playbook/commit/3e0e465b377… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-11-19 (Thu, 19 Nov 2015) Changed paths: M common_roles Log Message: ----------- Update common roles Commit: 93e257eddb50eddac81d4ed157e56cdd36e30d63 https://github.com/galaxyproject/infrastructure-playbook/commit/93e257eddb5… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-11-19 (Thu, 19 Nov 2015) Changed paths: M galaxyenv/playbook.yml M taccenv/playbook.yml Log Message: ----------- Handle renamed files role Commit: d646f4f68d73a71512ce193459ad92e062b5a9f1 https://github.com/galaxyproject/infrastructure-playbook/commit/d646f4f68d7… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-11-19 (Thu, 19 Nov 2015) Changed paths: A galaxyenv/files/orval/rsyncd.xml M galaxyenv/host_vars/orval.galaxyproject.org.yml Log Message: ----------- Make orval serve packages over rsync Compare: https://github.com/galaxyproject/infrastructure-playbook/compare/a03d2b5c15…

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[galaxyproject/infrastructure-playbook] a03d2b: jenkins is dead, long live jenkins
by GitHub 19 Nov '15

19 Nov '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: a03d2b5c15aa7c645ef2a8d2fce464567b53a56f https://github.com/galaxyproject/infrastructure-playbook/commit/a03d2b5c15a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-11-19 (Thu, 19 Nov 2015) Changed paths: A galaxyenv/host_vars/leeroy.galaxyproject.org.yml R galaxyenv/host_vars/n2.galaxyproject.org.yml M galaxyenv/host_vars/westvleteren.galaxyproject.org.yml M galaxyenv/inventory M galaxyenv/secret_group_vars/all.yml A galaxyenv/secret_host_vars/leeroy.galaxyproject.org.yml R galaxyenv/secret_host_vars/n2.galaxyproject.org.yml M galaxyenv/secret_host_vars/orval.galaxyproject.org.yml M galaxyenv/secret_host_vars/westvleteren.galaxyproject.org.yml M roles/linuxbrew/tasks/main.yml Log Message: ----------- jenkins is dead, long live jenkins

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[galaxyproject/galaxy] a3fee0: Style: fix state-success-bg change that was not re...
by GitHub 19 Nov '15

19 Nov '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a3fee086c6dee9a688ffb7da13f71c1210cb76da https://github.com/galaxyproject/galaxy/commit/a3fee086c6dee9a688ffb7da13f7… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-11-19 (Thu, 19 Nov 2015) Changed paths: M client/galaxy/style/less/galaxy_bootstrap/variables.less Log Message: ----------- Style: fix state-success-bg change that was not reverted during 5fd4daf Commit: 5191c2136a9131005533faff4b0c1267f1ce35c1 https://github.com/galaxyproject/galaxy/commit/5191c2136a9131005533faff4b0c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-11-19 (Thu, 19 Nov 2015) Changed paths: M client/galaxy/style/less/galaxy_bootstrap/variables.less Log Message: ----------- Merge pull request #1129 from carlfeberhard/fix.styles Style: fix state-success-bg change that was not reverted during 5fd4daf Compare: https://github.com/galaxyproject/galaxy/compare/d2bab13fa92a...5191c2136a91

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[galaxyproject/galaxy] b25b8c: Revise and fix waiting for tool tests.
by GitHub 19 Nov '15

19 Nov '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b25b8c3f243e87a196a6cb0fa23328ee7c7e26f7 https://github.com/galaxyproject/galaxy/commit/b25b8c3f243e87a196a6cb0fa233… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-11-18 (Wed, 18 Nov 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: d2bab13fa92a87a3c4959d782ba0bf061ecf07db https://github.com/galaxyproject/galaxy/commit/d2bab13fa92a87a3c4959d782ba0… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2015-11-19 (Thu, 19 Nov 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: ----------- Merge pull request #1119 from jmchilton/maxseconds Revise and fix waiting for tool tests. Compare: https://github.com/galaxyproject/galaxy/compare/7ab070e9df6e...d2bab13fa92a

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[galaxyproject/galaxy] 72faca: Document GIE proxy config for nginx, mention the A...
by GitHub 18 Nov '15

18 Nov '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 72faca1a3a81b6104c776353ee7b4dc03d6ae9be https://github.com/galaxyproject/galaxy/commit/72faca1a3a81b6104c776353ee7b… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-11-18 (Wed, 18 Nov 2015) Changed paths: M doc/source/admin/interactive_environments.rst Log Message: ----------- Document GIE proxy config for nginx, mention the Ansible role. Commit: 7ab070e9df6ebf0658c966942d38779fbc9d16f1 https://github.com/galaxyproject/galaxy/commit/7ab070e9df6ebf0658c966942d38… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-11-18 (Wed, 18 Nov 2015) Changed paths: M doc/source/admin/interactive_environments.rst Log Message: ----------- Merge pull request #1123 from natefoo/ie-docfix Add nginx config for GIE proxy to documentation Compare: https://github.com/galaxyproject/galaxy/compare/f770128915df...7ab070e9df6e

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[galaxyproject/galaxy] e7d535: Fixes #932
by GitHub 18 Nov '15

18 Nov '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e7d5355f7b064fb0eb4063e905d6b32df1ed7a12 https://github.com/galaxyproject/galaxy/commit/e7d5355f7b064fb0eb4063e905d6… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-10-26 (Mon, 26 Oct 2015) Changed paths: M lib/galaxy/datatypes/data.py Log Message: ----------- Fixes #932 But probably at great cost? This seems like basic functionality that I'm changing though a proper HTTPException is obviously the 'right thing to do'(tm) Commit: f770128915df3fa9d8a3a9fe2c4a210fbd9ac2c6 https://github.com/galaxyproject/galaxy/commit/f770128915df3fa9d8a3a9fe2c4a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-11-18 (Wed, 18 Nov 2015) Changed paths: M lib/galaxy/datatypes/data.py Log Message: ----------- Merge pull request #991 from erasche/fix-932 Fixes #932 Compare: https://github.com/galaxyproject/galaxy/compare/e4e44be27b7b...f770128915df

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[galaxyproject/galaxy] bafb8a: Add uniprotxml datatype
by GitHub 18 Nov '15

18 Nov '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: bafb8a9a4d31191a102e5d8c442cbfc82d3ad97e https://github.com/galaxyproject/galaxy/commit/bafb8a9a4d31191a102e5d8c442c… Author: Jim Johnson <jj(a)umn.edu> Date: 2015-10-29 (Thu, 29 Oct 2015) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Add uniprotxml datatype Commit: 4e6c46fa25cd7f23625d2029b57aad0e67bb732a https://github.com/galaxyproject/galaxy/commit/4e6c46fa25cd7f23625d2029b57a… Author: Jim Johnson <jj(a)umn.edu> Date: 2015-10-29 (Thu, 29 Oct 2015) Changed paths: M lib/galaxy/datatypes/proteomics.py Log Message: ----------- Add UniProtXML datatype to proteomics.py Commit: 2a7bba5abaeef0c71c6b86bbbcaf4cdbb0cf7a31 https://github.com/galaxyproject/galaxy/commit/2a7bba5abaeef0c71c6b86bbbcaf… Author: Jim Johnson <jj(a)umn.edu> Date: 2015-11-02 (Mon, 02 Nov 2015) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Add UniProtXML sniffer tag Commit: e4e44be27b7b3ddf778eb95559b4d0f11e4aecb7 https://github.com/galaxyproject/galaxy/commit/e4e44be27b7b3ddf778eb95559b4… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-11-18 (Wed, 18 Nov 2015) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/proteomics.py Log Message: ----------- Merge pull request #1004 from jj-umn/uniprotxml_datatype UniProtXML datatype Compare: https://github.com/galaxyproject/galaxy/compare/7fef50f45fb6...e4e44be27b7b

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[galaxyproject/galaxy] 28065b: Fix the issue where too many datasets are linked t...
by GitHub 18 Nov '15

18 Nov '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 28065b6ee7eaa15a7607c17316050939781b8cff https://github.com/galaxyproject/galaxy/commit/28065b6ee7eaa15a7607c1731605… Author: Jelle Scholtalbers <j.scholtalbers(a)gmail.com> Date: 2015-10-09 (Fri, 09 Oct 2015) Changed paths: M lib/galaxy/web/base/controllers/admin.py Log Message: ----------- Fix the issue where too many datasets are linked to a certain role and the page will not load - or takes too long for the proxy Commit: 7fef50f45fb6484fcb600cfd167e43d1a735a9d2 https://github.com/galaxyproject/galaxy/commit/7fef50f45fb6484fcb600cfd167e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-11-18 (Wed, 18 Nov 2015) Changed paths: M lib/galaxy/web/base/controllers/admin.py Log Message: ----------- Merge pull request #881 from scholtalbers/role-page-fix Fix the issue where too many datasets are linked to a certain role Compare: https://github.com/galaxyproject/galaxy/compare/ee2b34c387d9...7fef50f45fb6

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[galaxyproject/usegalaxy-playbook] 15e3e5: Set $HOME for Galaxy processes.
by GitHub 18 Nov '15

18 Nov '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 15e3e529e1c9dddbf9d2dc8dde8f1e9c55076f2f https://github.com/galaxyproject/usegalaxy-playbook/commit/15e3e529e1c9dddb… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-11-18 (Wed, 18 Nov 2015) Changed paths: M templates/supervisor/galaxy.conf.j2 Log Message: ----------- Set $HOME for Galaxy processes. Commit: 1cb189cec659569cebbb2053ac62feb79f76c13b https://github.com/galaxyproject/usegalaxy-playbook/commit/1cb189cec659569c… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-11-18 (Wed, 18 Nov 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: ----------- Test mutable configs Commit: 9fe17d3e77e75e7af7ad2394287f2b4050c40fe9 https://github.com/galaxyproject/usegalaxy-playbook/commit/9fe17d3e77e75e7a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-11-18 (Wed, 18 Nov 2015) Changed paths: A roles/galaxyprojectdotorg.interactive_environments/README.md A roles/galaxyprojectdotorg.interactive_environments/defaults/main.yml A roles/galaxyprojectdotorg.interactive_environments/handlers/main.yml A roles/galaxyprojectdotorg.interactive_environments/meta/.galaxy_install_info A roles/galaxyprojectdotorg.interactive_environments/meta/main.yml A roles/galaxyprojectdotorg.interactive_environments/tasks/docker_ssl.yml A roles/galaxyprojectdotorg.interactive_environments/tasks/extract_component.yml A roles/galaxyprojectdotorg.interactive_environments/tasks/install_dependencies.yml A roles/galaxyprojectdotorg.interactive_environments/tasks/main.yml A roles/galaxyprojectdotorg.interactive_environments/tasks/supervisor.yml A roles/galaxyprojectdotorg.interactive_environments/tasks/synchronize_components.yml A roles/galaxyprojectdotorg.interactive_environments/tasks/webserver_conf.yml A roles/galaxyprojectdotorg.interactive_environments/templates/_prefix.j2 A roles/galaxyprojectdotorg.interactive_environments/templates/config.ini.j2 A roles/galaxyprojectdotorg.interactive_environments/templates/ipython_apache.conf.j2 A roles/galaxyprojectdotorg.interactive_environments/templates/ipython_nginx.conf.j2 A roles/galaxyprojectdotorg.interactive_environments/templates/proxy_supervisor.conf.j2 Log Message: ----------- Add the interactive_environments role Commit: 9d483c5c7cfb38539cabd9fecdaca23857cef6e6 https://github.com/galaxyproject/usegalaxy-playbook/commit/9d483c5c7cfb3853… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-11-18 (Wed, 18 Nov 2015) Changed paths: M galaxy.yml A stage/files/interactive_environments/plugins/.ansible_ie_role_current_version A stage/files/interactive_environments/plugins/common/templates/ie.mako A stage/files/interactive_environments/plugins/interactive_environments.dtd A stage/files/interactive_environments/plugins/ipython/config/ipython.ini.sample A stage/files/interactive_environments/plugins/ipython/config/ipython.xml A stage/files/interactive_environments/plugins/ipython/static/js/ipython.js A stage/files/interactive_environments/plugins/ipython/templates/ipython.mako A stage/files/interactive_environments/plugins/ipython/templates/notebook.ipynb A stage/files/interactive_environments/plugins/rstudio/config/rstudio.ini.sample A stage/files/interactive_environments/plugins/rstudio/config/rstudio.xml A stage/files/interactive_environments/plugins/rstudio/static/js/crypto/base64.js A stage/files/interactive_environments/plugins/rstudio/static/js/crypto/jsbn.js A stage/files/interactive_environments/plugins/rstudio/static/js/crypto/prng4.js A stage/files/interactive_environments/plugins/rstudio/static/js/crypto/rng.js A stage/files/interactive_environments/plugins/rstudio/static/js/crypto/rsa.js A stage/files/interactive_environments/plugins/rstudio/static/js/crypto/rstudio.big.js A stage/files/interactive_environments/plugins/rstudio/static/js/crypto/rstudio.min.js A stage/files/interactive_environments/plugins/rstudio/static/js/crypto/rstudio/base64.js A stage/files/interactive_environments/plugins/rstudio/static/js/crypto/rstudio/jsbn.js A stage/files/interactive_environments/plugins/rstudio/static/js/crypto/rstudio/prng4.js A stage/files/interactive_environments/plugins/rstudio/static/js/crypto/rstudio/rng.js A stage/files/interactive_environments/plugins/rstudio/static/js/crypto/rstudio/rsa.js A stage/files/interactive_environments/plugins/rstudio/static/js/crypto/wu/base64.js A stage/files/interactive_environments/plugins/rstudio/static/js/crypto/wu/jsbn.js A stage/files/interactive_environments/plugins/rstudio/static/js/crypto/wu/prng4.js A stage/files/interactive_environments/plugins/rstudio/static/js/crypto/wu/rng.js A stage/files/interactive_environments/plugins/rstudio/static/js/crypto/wu/rsa.js A stage/files/interactive_environments/plugins/rstudio/static/js/rstudio.js A stage/files/interactive_environments/plugins/rstudio/templates/rstudio.mako A stage/files/interactive_environments/proxy/.ansible_ie_role_current_version A stage/files/interactive_environments/proxy/Dockerfile A stage/files/interactive_environments/proxy/README.md A stage/files/interactive_environments/proxy/lib/main.js A stage/files/interactive_environments/proxy/lib/mapper.js A stage/files/interactive_environments/proxy/lib/proxy.js A stage/files/interactive_environments/proxy/package.json M stage/group_vars/all.yml M stage/group_vars/galaxyservers.yml M stage/secret_vars/galaxyservers.yml Log Message: ----------- Update Test and use the interactive_environments role to deploy IPython Commit: ac7af1a513fe1c3f3a121398ebfb912734bd5c1e https://github.com/galaxyproject/usegalaxy-playbook/commit/ac7af1a513fe1c3f… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-11-18 (Wed, 18 Nov 2015) Changed paths: A production/files/interactive_environments/plugins/.ansible_ie_role_current_version A production/files/interactive_environments/plugins/common/templates/ie.mako A production/files/interactive_environments/plugins/interactive_environments.dtd A production/files/interactive_environments/plugins/ipython/config/ipython.ini.sample A production/files/interactive_environments/plugins/ipython/config/ipython.xml A production/files/interactive_environments/plugins/ipython/static/js/ipython.js A production/files/interactive_environments/plugins/ipython/templates/ipython.mako A production/files/interactive_environments/plugins/ipython/templates/notebook.ipynb A production/files/interactive_environments/plugins/rstudio/config/rstudio.ini.sample A production/files/interactive_environments/plugins/rstudio/config/rstudio.xml A production/files/interactive_environments/plugins/rstudio/static/js/crypto/base64.js A production/files/interactive_environments/plugins/rstudio/static/js/crypto/jsbn.js A production/files/interactive_environments/plugins/rstudio/static/js/crypto/prng4.js A production/files/interactive_environments/plugins/rstudio/static/js/crypto/rng.js A production/files/interactive_environments/plugins/rstudio/static/js/crypto/rsa.js A production/files/interactive_environments/plugins/rstudio/static/js/crypto/rstudio.big.js A production/files/interactive_environments/plugins/rstudio/static/js/crypto/rstudio.min.js A production/files/interactive_environments/plugins/rstudio/static/js/crypto/rstudio/base64.js A production/files/interactive_environments/plugins/rstudio/static/js/crypto/rstudio/jsbn.js A production/files/interactive_environments/plugins/rstudio/static/js/crypto/rstudio/prng4.js A production/files/interactive_environments/plugins/rstudio/static/js/crypto/rstudio/rng.js A production/files/interactive_environments/plugins/rstudio/static/js/crypto/rstudio/rsa.js A production/files/interactive_environments/plugins/rstudio/static/js/crypto/wu/base64.js A production/files/interactive_environments/plugins/rstudio/static/js/crypto/wu/jsbn.js A production/files/interactive_environments/plugins/rstudio/static/js/crypto/wu/prng4.js A production/files/interactive_environments/plugins/rstudio/static/js/crypto/wu/rng.js A production/files/interactive_environments/plugins/rstudio/static/js/crypto/wu/rsa.js A production/files/interactive_environments/plugins/rstudio/static/js/rstudio.js A production/files/interactive_environments/plugins/rstudio/templates/rstudio.mako A production/files/interactive_environments/proxy/.ansible_ie_role_current_version A production/files/interactive_environments/proxy/Dockerfile A production/files/interactive_environments/proxy/README.md A production/files/interactive_environments/proxy/lib/main.js A production/files/interactive_environments/proxy/lib/mapper.js A production/files/interactive_environments/proxy/lib/proxy.js A production/files/interactive_environments/proxy/package.json M production/group_vars/all.yml M production/group_vars/galaxyservers.yml M production/host_vars/galaxy-web-01.tacc.utexas.edu.yml M production/secret_vars/galaxyservers.yml Log Message: ----------- Deploy the IPython IE on Main Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/23c400852d03...…

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[galaxyproject/galaxy] fe0f9b: Add BIOM v1 in default datatypes.
by GitHub 18 Nov '15

18 Nov '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: fe0f9ba905f11cfff4407aa574fa761e5eadf2f5 https://github.com/galaxyproject/galaxy/commit/fe0f9ba905f11cfff4407aa574fa… Author: fescudie <fescudie(a)toulouse.inra.fr> Date: 2015-10-20 (Tue, 20 Oct 2015) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/text.py Log Message: ----------- Add BIOM v1 in default datatypes. Commit: e834b6e189ff0e4e17b1cd3ac541f96a44ba1249 https://github.com/galaxyproject/galaxy/commit/e834b6e189ff0e4e17b1cd3ac541… Author: fescudie <fescudie(a)toulouse.inra.fr> Date: 2015-10-20 (Tue, 20 Oct 2015) Changed paths: M lib/galaxy/datatypes/text.py Log Message: ----------- Add BIOM v1 in default datatypes Commit: ee2b34c387d9bb6189c8befaa069887b535d413c https://github.com/galaxyproject/galaxy/commit/ee2b34c387d9bb6189c8befaa069… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-11-18 (Wed, 18 Nov 2015) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/text.py Log Message: ----------- Merge pull request #950 from fescudie/dev Add BIOM v1 in default datatypes. Compare: https://github.com/galaxyproject/galaxy/compare/c252987b4c5f...ee2b34c387d9

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[galaxyproject/galaxy] 05f3da: Fix macro bug with empty CDATA being None instead ...
by GitHub 18 Nov '15

18 Nov '15

Branch: refs/heads/release_15.10 Home: https://github.com/galaxyproject/galaxy Commit: 05f3da308d6a58dc8528f317fa6ea4ffa1fb7610 https://github.com/galaxyproject/galaxy/commit/05f3da308d6a58dc8528f317fa6e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-11-18 (Wed, 18 Nov 2015) Changed paths: M lib/galaxy/util/xml_macros.py M test/unit/tools/test_tool_loader.py Log Message: ----------- Fix macro bug with empty CDATA being None instead of ''. Fixes galaxyproject/planemo#362 thanks for the report @erasche. Test using the following command: ``` nosetests test/unit/tools/test_tool_loader.py ``` Commit: eb16ba3743a7e42cc9ad43f0d7a3eb926ba60cd8 https://github.com/galaxyproject/galaxy/commit/eb16ba3743a7e42cc9ad43f0d7a3… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-11-18 (Wed, 18 Nov 2015) Changed paths: M lib/galaxy/util/xml_macros.py M test/unit/tools/test_tool_loader.py Log Message: ----------- Merge pull request #1122 from jmchilton/empty_cdata_macro [15.10] Fix macro bug with empty CDATA being None instead of ''. Compare: https://github.com/galaxyproject/galaxy/compare/73f46f4e0814...eb16ba3743a7

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[galaxyproject/galaxy] 937f99: Fix API installation of tool_dependencies
by GitHub 18 Nov '15

18 Nov '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 937f99b851e2078152c851a0b552c00b99167747 https://github.com/galaxyproject/galaxy/commit/937f99b851e2078152c851a0b552… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2015-11-15 (Sun, 15 Nov 2015) Changed paths: M lib/galaxy/webapps/tool_shed/api/repositories.py Log Message: ----------- Fix API installation of tool_dependencies This should fix an installation issue with tool_dependencies via the API. Tool dependency repositories to not have any tools specified and with this no metadata associated. It was broken in https://github.com/galaxyproject/galaxy/commit/bb6a784f13ff3f91762244d44884… So I think this should be part of 15.10. Thanks to Greg for fixing this one. Commit: 040118aae35da2c72fbf6332b32e8f3e0025a341 https://github.com/galaxyproject/galaxy/commit/040118aae35da2c72fbf6332b32e… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-11-16 (Mon, 16 Nov 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/remote_files.py Log Message: ----------- Encode unicode string before passing to hashlib.sha1(). Fixes #673. Commit: 3ffa607c15a70a532a7d21a0b3b1a46171e53171 https://github.com/galaxyproject/galaxy/commit/3ffa607c15a70a532a7d21a0b3b1… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-11-17 (Tue, 17 Nov 2015) Changed paths: M client/galaxy/scripts/galaxy.menu.js M static/maps/galaxy.menu.js.map M static/scripts/galaxy.menu.js Log Message: ----------- Deprecate old library UI in the "Shared Data" menu. Commit: e61e30cde549c448375b555aadfc85b235b4871a https://github.com/galaxyproject/galaxy/commit/e61e30cde549c448375b555aadfc… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-11-17 (Tue, 17 Nov 2015) Changed paths: M lib/galaxy/webapps/tool_shed/api/repositories.py Log Message: ----------- Merge pull request #1100 from martenson/fix-ts-api-install [15.10] Fix API installation of tool_dependencies Commit: 05e66827d40151c0cd1729299fa82a510138359e https://github.com/galaxyproject/galaxy/commit/05e66827d40151c0cd1729299fa8… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-11-17 (Tue, 17 Nov 2015) Changed paths: M client/galaxy/scripts/galaxy.menu.js M static/maps/galaxy.menu.js.map M static/scripts/galaxy.menu.js Log Message: ----------- Merge pull request #1112 from nsoranzo/release_15.10_data_libraries_beta [15.10] Deprecate old library UI in the "Shared Data" menu. Commit: 27dc31ace9a4e3a28ab2416c8f9cdbe4735c7063 https://github.com/galaxyproject/galaxy/commit/27dc31ace9a4e3a28ab2416c8f9c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-11-17 (Tue, 17 Nov 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/remote_files.py Log Message: ----------- Merge pull request #1106 from nsoranzo/release_15.07_library_import_utf8 [15.07] Encode unicode string before passing to hashlib.sha1(). Commit: 73f46f4e08141f78927056fa3e4709d0ab323972 https://github.com/galaxyproject/galaxy/commit/73f46f4e08141f78927056fa3e47… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-11-18 (Wed, 18 Nov 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/remote_files.py Log Message: ----------- Merge branch 'release_15.07' into release_15.10 Commit: c252987b4c5febb7fa10db3c7359449f325fc9ca https://github.com/galaxyproject/galaxy/commit/c252987b4c5febb7fa10db3c7359… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-11-18 (Wed, 18 Nov 2015) Changed paths: M client/galaxy/scripts/galaxy.menu.js M lib/galaxy/webapps/galaxy/api/remote_files.py M static/maps/galaxy.menu.js.map M static/scripts/galaxy.menu.js Log Message: ----------- Merge branch 'master' into dev Compare: https://github.com/galaxyproject/galaxy/compare/3d933edd32dd...c252987b4c5f

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[galaxyproject/galaxy] d824cc: In interactive environments, the /import volume ca...
by GitHub 18 Nov '15

18 Nov '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/galaxy Commit: d824cca31fcebe97b8c7cfd1040eecbb9e5f03d3 https://github.com/galaxyproject/galaxy/commit/d824cca31fcebe97b8c7cfd1040e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-11-12 (Thu, 12 Nov 2015) Changed paths: M config/plugins/interactive_environments/ipython/config/ipython.ini.sample M config/plugins/interactive_environments/ipython/templates/ipython.mako M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- In interactive environments, the /import volume can now be made conditional. Also, fix a bug when using a proxy for the node proxy and cookie_path is / Commit: c4351413265796dacc15b8e3fc7382b8514f5b59 https://github.com/galaxyproject/galaxy/commit/c4351413265796dacc15b8e3fc73… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-11-13 (Fri, 13 Nov 2015) Changed paths: M config/plugins/interactive_environments/ipython/config/ipython.ini.sample Log Message: ----------- Built image tag differs from intended. Commit: 64b084067c73cea1de455e4816d73101c3752165 https://github.com/galaxyproject/galaxy/commit/64b084067c73cea1de455e4816d7… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-11-13 (Fri, 13 Nov 2015) Changed paths: M config/plugins/interactive_environments/ipython/config/ipython.ini.sample M config/plugins/interactive_environments/ipython/templates/ipython.mako M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Merge pull request #1076 from natefoo/ie-conditional-import-volume [15.10] Fix a bug in IEs when proxying the proxy Commit: 75e7e4c2cf7a0cb18b8096c8119e4b0cb207e2a3 https://github.com/galaxyproject/galaxy/commit/75e7e4c2cf7a0cb18b8096c8119e… Author: Dave B <dave(a)bx.psu.edu> Date: 2015-11-14 (Sat, 14 Nov 2015) Changed paths: M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py Log Message: ----------- Fix 500 error when attempting to update installed repository. Commit: 7150983aab78e4ceb71f8ad2592369523899d768 https://github.com/galaxyproject/galaxy/commit/7150983aab78e4ceb71f8ad25923… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-11-14 (Sat, 14 Nov 2015) Changed paths: M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py Log Message: ----------- Merge pull request #1093 from martenson/release_15.10 [15.10] Fix 500 error when attempting to update installed repository. Commit: 937f99b851e2078152c851a0b552c00b99167747 https://github.com/galaxyproject/galaxy/commit/937f99b851e2078152c851a0b552… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2015-11-15 (Sun, 15 Nov 2015) Changed paths: M lib/galaxy/webapps/tool_shed/api/repositories.py Log Message: ----------- Fix API installation of tool_dependencies This should fix an installation issue with tool_dependencies via the API. Tool dependency repositories to not have any tools specified and with this no metadata associated. It was broken in https://github.com/galaxyproject/galaxy/commit/bb6a784f13ff3f91762244d44884… So I think this should be part of 15.10. Thanks to Greg for fixing this one. Commit: 040118aae35da2c72fbf6332b32e8f3e0025a341 https://github.com/galaxyproject/galaxy/commit/040118aae35da2c72fbf6332b32e… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-11-16 (Mon, 16 Nov 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/remote_files.py Log Message: ----------- Encode unicode string before passing to hashlib.sha1(). Fixes #673. Commit: 3ffa607c15a70a532a7d21a0b3b1a46171e53171 https://github.com/galaxyproject/galaxy/commit/3ffa607c15a70a532a7d21a0b3b1… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-11-17 (Tue, 17 Nov 2015) Changed paths: M client/galaxy/scripts/galaxy.menu.js M static/maps/galaxy.menu.js.map M static/scripts/galaxy.menu.js Log Message: ----------- Deprecate old library UI in the "Shared Data" menu. Commit: e61e30cde549c448375b555aadfc85b235b4871a https://github.com/galaxyproject/galaxy/commit/e61e30cde549c448375b555aadfc… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-11-17 (Tue, 17 Nov 2015) Changed paths: M lib/galaxy/webapps/tool_shed/api/repositories.py Log Message: ----------- Merge pull request #1100 from martenson/fix-ts-api-install [15.10] Fix API installation of tool_dependencies Commit: 05e66827d40151c0cd1729299fa82a510138359e https://github.com/galaxyproject/galaxy/commit/05e66827d40151c0cd1729299fa8… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-11-17 (Tue, 17 Nov 2015) Changed paths: M client/galaxy/scripts/galaxy.menu.js M static/maps/galaxy.menu.js.map M static/scripts/galaxy.menu.js Log Message: ----------- Merge pull request #1112 from nsoranzo/release_15.10_data_libraries_beta [15.10] Deprecate old library UI in the "Shared Data" menu. Commit: 27dc31ace9a4e3a28ab2416c8f9cdbe4735c7063 https://github.com/galaxyproject/galaxy/commit/27dc31ace9a4e3a28ab2416c8f9c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-11-17 (Tue, 17 Nov 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/remote_files.py Log Message: ----------- Merge pull request #1106 from nsoranzo/release_15.07_library_import_utf8 [15.07] Encode unicode string before passing to hashlib.sha1(). Commit: 73f46f4e08141f78927056fa3e4709d0ab323972 https://github.com/galaxyproject/galaxy/commit/73f46f4e08141f78927056fa3e47… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-11-18 (Wed, 18 Nov 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/remote_files.py Log Message: ----------- Merge branch 'release_15.07' into release_15.10 Compare: https://github.com/galaxyproject/galaxy/compare/a3034ab6d99d...73f46f4e0814

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[galaxyproject/galaxy] 040118: Encode unicode string before passing to hashlib.sh...
by GitHub 18 Nov '15

18 Nov '15

Branch: refs/heads/release_15.10 Home: https://github.com/galaxyproject/galaxy Commit: 040118aae35da2c72fbf6332b32e8f3e0025a341 https://github.com/galaxyproject/galaxy/commit/040118aae35da2c72fbf6332b32e… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-11-16 (Mon, 16 Nov 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/remote_files.py Log Message: ----------- Encode unicode string before passing to hashlib.sha1(). Fixes #673. Commit: 27dc31ace9a4e3a28ab2416c8f9cdbe4735c7063 https://github.com/galaxyproject/galaxy/commit/27dc31ace9a4e3a28ab2416c8f9c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-11-17 (Tue, 17 Nov 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/remote_files.py Log Message: ----------- Merge pull request #1106 from nsoranzo/release_15.07_library_import_utf8 [15.07] Encode unicode string before passing to hashlib.sha1(). Commit: 73f46f4e08141f78927056fa3e4709d0ab323972 https://github.com/galaxyproject/galaxy/commit/73f46f4e08141f78927056fa3e47… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-11-18 (Wed, 18 Nov 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/remote_files.py Log Message: ----------- Merge branch 'release_15.07' into release_15.10 Compare: https://github.com/galaxyproject/galaxy/compare/05e66827d401...73f46f4e0814

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