- galaxy-commits - lists.galaxyproject.org

[galaxyproject/usegalaxy-playbook] 3a64a1: Update test to 75d64893489d56e1a7b80165bacdeb2a877...
by GitHub 10 Nov '15

10 Nov '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 3a64a116b0c62704b3b1ad227ebc0638dad3f6c1 https://github.com/galaxyproject/usegalaxy-playbook/commit/3a64a116b0c62704… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-11-10 (Tue, 10 Nov 2015) Changed paths: M stage/group_vars/all.yml Log Message: ----------- Update test to 75d64893489d56e1a7b80165bacdeb2a8777875c.

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[galaxyproject/galaxy] 36797b: Add changed static files.
by GitHub 10 Nov '15

10 Nov '15

Branch: refs/heads/release_15.10 Home: https://github.com/galaxyproject/galaxy Commit: 36797b3195c84b416710029d86cf7b7a24c1faf0 https://github.com/galaxyproject/galaxy/commit/36797b3195c84b416710029d86cf… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2015-11-10 (Tue, 10 Nov 2015) Changed paths: M static/maps/mvc/library/library-folderrow-view.js.map M static/scripts/mvc/library/library-folderrow-view.js Log Message: ----------- Add changed static files. Commit: ad016460dc2799e95ff26fdd0a69bf605f78358b https://github.com/galaxyproject/galaxy/commit/ad016460dc2799e95ff26fdd0a69… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2015-11-10 (Tue, 10 Nov 2015) Changed paths: M client/galaxy/scripts/mvc/library/library-folderrow-view.js Log Message: ----------- Fix import of history datasets into library. Commit: 5603a96aecb29c7065206d8797205f49f2ed32b6 https://github.com/galaxyproject/galaxy/commit/5603a96aecb29c7065206d879720… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-11-10 (Tue, 10 Nov 2015) Changed paths: M client/galaxy/scripts/mvc/library/library-folderrow-view.js M static/maps/mvc/library/library-folderrow-view.js.map M static/scripts/mvc/library/library-folderrow-view.js Log Message: ----------- Merge pull request #1054 from martenson/fix-datalib-hist-import [15.10] Fix datalib hist import Compare: https://github.com/galaxyproject/galaxy/compare/7e6df4f46fe0...5603a96aecb2

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[galaxyproject/galaxy] a956ca: Fix import of history datasets into library.
by GitHub 10 Nov '15

10 Nov '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a956cac4196e0e0c58b45b2efbc79256e4962e0e https://github.com/galaxyproject/galaxy/commit/a956cac4196e0e0c58b45b2efbc7… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2015-11-10 (Tue, 10 Nov 2015) Changed paths: M client/galaxy/scripts/mvc/library/library-folderrow-view.js Log Message: ----------- Fix import of history datasets into library. Commit: 4f824cb920e36d2b79250bdd327e59a771b4587c https://github.com/galaxyproject/galaxy/commit/4f824cb920e36d2b79250bdd327e… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2015-11-10 (Tue, 10 Nov 2015) Changed paths: M static/maps/mvc/library/library-folderrow-view.js.map M static/scripts/mvc/library/library-folderrow-view.js Log Message: ----------- Add changed static files. Commit: 75d64893489d56e1a7b80165bacdeb2a8777875c https://github.com/galaxyproject/galaxy/commit/75d64893489d56e1a7b80165bacd… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-11-10 (Tue, 10 Nov 2015) Changed paths: M client/galaxy/scripts/mvc/library/library-folderrow-view.js M static/maps/mvc/library/library-folderrow-view.js.map M static/scripts/mvc/library/library-folderrow-view.js Log Message: ----------- Merge pull request #1049 from mvdbeek/library_add_from_history Fix import of history datasets into library. Compare: https://github.com/galaxyproject/galaxy/compare/39ff0e9d767a...75d64893489d

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[galaxyproject/usegalaxy-playbook] 528420: Banner regarding Corral downtime
by GitHub 10 Nov '15

10 Nov '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 5284203b28f443f7b9403319ee22f792f6e621bc https://github.com/galaxyproject/usegalaxy-playbook/commit/5284203b28f443f7… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-11-10 (Tue, 10 Nov 2015) Changed paths: M production/group_vars/galaxyservers.yml Log Message: ----------- Banner regarding Corral downtime

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[galaxyproject/galaxy] ad2045: Fix output to print values and not hash key
by GitHub 10 Nov '15

10 Nov '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ad20452340d052570c1b3203259d10e1ad94a236 https://github.com/galaxyproject/galaxy/commit/ad20452340d052570c1b3203259d… Author: Eric Enns <eric.enns(a)phac-aspc.gc.ca> Date: 2015-10-09 (Fri, 09 Oct 2015) Changed paths: M tools/stats/gsummary.py Log Message: ----------- Fix output to print values and not hash key Commit: ad4458a458d7ccb5238094ab3d1967072b5a0b76 https://github.com/galaxyproject/galaxy/commit/ad4458a458d7ccb5238094ab3d19… Author: Eric Enns <eric.enns(a)phac-aspc.gc.ca> Date: 2015-10-09 (Fri, 09 Oct 2015) Changed paths: M tools/stats/gsummary.py Log Message: ----------- Revert to previous changes if using rpy2 Commit: 0ec1b17794d53ae1a535b00f13d955c62f702a94 https://github.com/galaxyproject/galaxy/commit/0ec1b17794d53ae1a535b00f13d9… Author: Eric Enns <eric.enns(a)phac-aspc.gc.ca> Date: 2015-10-14 (Wed, 14 Oct 2015) Changed paths: M tools/stats/gsummary.py Log Message: ----------- Update list comprehension to go through headings instead of summary so that we output in the order we want. Commit: 50c27ace2c6eb260b88aafac72997cfa06ca6c13 https://github.com/galaxyproject/galaxy/commit/50c27ace2c6eb260b88aafac7299… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-10-14 (Wed, 14 Oct 2015) Changed paths: M tools/stats/gsummary.py Log Message: ----------- Merge pull request #885 from ericenns/fix_gsummary_in_release_15.07 [15.07] Fix gsummary in release 15.07 Commit: 0911287df7a5d7e810d83bbcd1e4cb1f849314d7 https://github.com/galaxyproject/galaxy/commit/0911287df7a5d7e810d83bbcd1e4… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-10-14 (Wed, 14 Oct 2015) Changed paths: M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M static/maps/mvc/collection/list-of-pairs-collection-creator.js.map M static/scripts/mvc/collection/list-of-pairs-collection-creator.js Log Message: ----------- UI, list of pairs collection creator: create regexp from filters for name creation Commit: dc9c2e4b7569726263fac8ab06cefb889c2b8af5 https://github.com/galaxyproject/galaxy/commit/dc9c2e4b7569726263fac8ab06ce… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-10-22 (Thu, 22 Oct 2015) Changed paths: M client/galaxy/scripts/mvc/grid/grid-model.js M client/galaxy/scripts/mvc/grid/grid-view.js M static/maps/mvc/grid/grid-view.js.map M static/scripts/mvc/grid/grid-view.js Log Message: ----------- Fix grid batch operations. This should correctly display and request confirmation for batch operations (such as delete a set of <GalaxyObjects> which is scary without a confirmation). It also fixes it to where grid bulk operations actually work in IE. Commit: 7bcbf140936bfc9d25b8e6bed8a0bc14270b0cf2 https://github.com/galaxyproject/galaxy/commit/7bcbf140936bfc9d25b8e6bed8a0… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-10-27 (Tue, 27 Oct 2015) Changed paths: M client/galaxy/scripts/mvc/grid/grid-model.js M client/galaxy/scripts/mvc/grid/grid-view.js M static/maps/mvc/grid/grid-view.js.map M static/scripts/mvc/grid/grid-view.js Log Message: ----------- Merge pull request #978 from dannon/graft_to_stable [15.10] Fix grid bulk operations Commit: 3b133d0d9206f6162494b3f5aa4c04581368480e https://github.com/galaxyproject/galaxy/commit/3b133d0d9206f6162494b3f5aa4c… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-28 (Wed, 28 Oct 2015) Changed paths: M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M static/maps/mvc/collection/list-of-pairs-collection-creator.js.map M static/scripts/mvc/collection/list-of-pairs-collection-creator.js Log Message: ----------- Merge pull request #917 from carlfeberhard/release_15.10 [15.10] UI, list of pairs collection creator: create regexp from filters for … Commit: d20677bb640de726574ae7f3e8d86739a8702cb5 https://github.com/galaxyproject/galaxy/commit/d20677bb640de726574ae7f3e8d8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-10-29 (Thu, 29 Oct 2015) Changed paths: M lib/galaxy/web/framework/webapp.py Log Message: ----------- Fix Remote User failures due to apache null headers. Commit: 3b8edf6aebfb10d1b52b57701eb4cb07558e9c9e https://github.com/galaxyproject/galaxy/commit/3b8edf6aebfb10d1b52b57701eb4… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-11-03 (Tue, 03 Nov 2015) Changed paths: M lib/galaxy/web/framework/webapp.py Log Message: ----------- Merge pull request #1003 from dannon/remote_user_apache_fix [15.10] Fix Remote User failures due to apache null headers. Commit: 57d6c9872c21f0bddfde04b170e8e8021d20ff71 https://github.com/galaxyproject/galaxy/commit/57d6c9872c21f0bddfde04b170e8… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-11-09 (Mon, 09 Nov 2015) Changed paths: M tools/stats/gsummary.py Log Message: ----------- Merge remote-tracking branch 'jmchilton/release_15.07' into release_15.10 Commit: dc534bb258d7a9aaf262784acdb9893339ca43c0 https://github.com/galaxyproject/galaxy/commit/dc534bb258d7a9aaf262784acdb9… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-11-09 (Mon, 09 Nov 2015) Changed paths: M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M lib/galaxy/web/framework/webapp.py M static/maps/mvc/collection/list-of-pairs-collection-creator.js.map M static/scripts/mvc/collection/list-of-pairs-collection-creator.js M tools/stats/gsummary.py Log Message: ----------- Merge branch 'release_15.10' into dev Conflicts: client/galaxy/scripts/mvc/grid/grid-view.js static/maps/mvc/collection/list-of-pairs-collection-creator.js.map static/scripts/mvc/collection/list-of-pairs-collection-creator.js Commit: 2934c2f3bd2aba6bad02d18f687b4410362738ed https://github.com/galaxyproject/galaxy/commit/2934c2f3bd2aba6bad02d18f687b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-11-09 (Mon, 09 Nov 2015) Changed paths: M tools/stats/gsummary.py Log Message: ----------- Lint fix for 15.10 to dev merge. Commit: 39ff0e9d767a7a4089546d76b0747d4373ea97c9 https://github.com/galaxyproject/galaxy/commit/39ff0e9d767a7a4089546d76b074… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-11-10 (Tue, 10 Nov 2015) Changed paths: M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M lib/galaxy/web/framework/webapp.py M static/maps/mvc/collection/list-of-pairs-collection-creator.js.map M static/scripts/mvc/collection/list-of-pairs-collection-creator.js M tools/stats/gsummary.py Log Message: ----------- Merge pull request #1044 from jmchilton/release_15.10_to_dev Bring 15.10 (and 15.07) fixes into dev. Compare: https://github.com/galaxyproject/galaxy/compare/6dfacb6fe648...39ff0e9d767a

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[galaxyproject/galaxy] e074e2: Downgrade WebError. This fixes the interactive de...
by GitHub 10 Nov '15

10 Nov '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e074e28807f62544212adb79a2dd8fefa39c9cda https://github.com/galaxyproject/galaxy/commit/e074e28807f62544212adb79a2dd… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-11-02 (Mon, 02 Nov 2015) Changed paths: M lib/galaxy/dependencies/conditional-requirements.txt M lib/galaxy/dependencies/requirements.txt Log Message: ----------- Downgrade WebError. This fixes the interactive debugger (for now -- to be replaced w/ werkzeug eventually) Commit: b5c4a3de7060e7c5a77414cc4d638e1eae0a31d9 https://github.com/galaxyproject/galaxy/commit/b5c4a3de7060e7c5a77414cc4d63… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-11-02 (Mon, 02 Nov 2015) Changed paths: M lib/galaxy/dependencies/requirements.txt Log Message: ----------- Remove weberror/pygments from unconditional dependencies list Commit: d4ca44c898d173b9a32c3bdc7c7cce313ecbfa73 https://github.com/galaxyproject/galaxy/commit/d4ca44c898d173b9a32c3bdc7c7c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-11-09 (Mon, 09 Nov 2015) Changed paths: M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conditional-requirements.txt Log Message: ----------- Add pygments back, since it's a dependency of a conditional dependency. Commit: 063390097e23e0f9c8d956ca8a4e493e41b3b38b https://github.com/galaxyproject/galaxy/commit/063390097e23e0f9c8d956ca8a4e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-11-09 (Mon, 09 Nov 2015) Changed paths: M .ci/flake8_wrapper.sh M client/galaxy/scripts/galaxy-app-base.js M client/galaxy/scripts/galaxy.panels.js M client/galaxy/scripts/libs/jquery/select2.js M client/galaxy/scripts/mvc/app/app-analysis.js M client/galaxy/scripts/mvc/app/app-view.js M client/galaxy/scripts/mvc/base-mvc.js M client/galaxy/scripts/mvc/citation/citation-model.js M client/galaxy/scripts/mvc/collection/collection-li-edit.js M client/galaxy/scripts/mvc/collection/collection-li.js M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/collection/collection-panel.js 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.js M client/galaxy/scripts/mvc/dataset/dataset-list.js M client/galaxy/scripts/mvc/dataset/dataset-model.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-repeat.js M client/galaxy/scripts/mvc/form/form-select-content.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/grid/grid-template.js M client/galaxy/scripts/mvc/history/history-content-model.js M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/history-panel.js M client/galaxy/scripts/mvc/history/history-structure-view.js M client/galaxy/scripts/mvc/history/multi-panel.js M client/galaxy/scripts/mvc/job/job-model.js M client/galaxy/scripts/mvc/list/list-item.js M client/galaxy/scripts/mvc/list/list-panel.js M client/galaxy/scripts/mvc/tags.js M client/galaxy/scripts/mvc/tools/tools-form-base.js M client/galaxy/scripts/mvc/tools/tools-form-workflow.js M client/galaxy/scripts/mvc/tools/tools-jobs.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/scripts/mvc/upload/upload-button.js M client/galaxy/scripts/mvc/user/user-model.js M client/galaxy/scripts/mvc/user/user-quotameter.js M client/galaxy/scripts/mvc/visualization/visualization-model.js M client/galaxy/scripts/templates/compiled/tool_link.js M client/galaxy/scripts/templates/tool_link.handlebars M client/galaxy/scripts/utils/add-logging.js M client/galaxy/scripts/utils/deferred.js M client/galaxy/scripts/utils/metrics-logger.js M client/galaxy/scripts/utils/uploadbox.js M client/galaxy/style/less/base.less M client/galaxy/style/less/bootstrap.less M client/galaxy/style/less/ui.less M client/galaxy/style/less/upload.less M config/plugins/visualizations/charts/static/build-app.js M config/plugins/visualizations/charts/static/charts/jqplot/boxplot/wrapper.js M config/plugins/visualizations/charts/static/charts/nvd3/pie/wrapper.js M config/plugins/visualizations/charts/static/charts/tools.js M config/plugins/visualizations/charts/static/views/group.js M config/plugins/visualizations/charts/static/views/viewport.js M lib/galaxy/app.py M lib/galaxy/config.py M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conditional-requirements.txt M lib/galaxy/dependencies/requirements.txt M lib/galaxy/model/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/search/__init__.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/util/__init__.py M lib/galaxy/webapps/galaxy/api/library_contents.py M lib/galaxy/webapps/galaxy/controllers/requests_common.py M lib/galaxy/webapps/reports/app.py M lib/galaxy/webapps/tool_shed/app.py M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py M lib/tool_shed/galaxy_install/tool_migration_manager.py M lib/tool_shed/util/common_util.py M lib/tool_shed/util/hg_util.py M run.sh A scripts/check_eggs.py A scripts/fetch_eggs.py M static/maps/galaxy-app-base.js.map M static/maps/libs/jquery/select2.js.map M static/maps/mvc/app/app-analysis.js.map M static/maps/mvc/app/app-view.js.map M static/maps/mvc/base-mvc.js.map M static/maps/mvc/citation/citation-model.js.map M static/maps/mvc/collection/collection-model.js.map M static/maps/mvc/collection/collection-panel.js.map M static/maps/mvc/collection/list-collection-creator.js.map M static/maps/mvc/collection/list-of-pairs-collection-creator.js.map M static/maps/mvc/collection/pair-collection-creator.js.map M static/maps/mvc/dataset/dataset-choice.js.map M static/maps/mvc/dataset/dataset-li.js.map M static/maps/mvc/dataset/dataset-list.js.map M static/maps/mvc/dataset/dataset-model.js.map M static/maps/mvc/form/form-parameters.js.map M static/maps/mvc/form/form-repeat.js.map M static/maps/mvc/form/form-select-content.js.map M static/maps/mvc/form/form-view.js.map M static/maps/mvc/grid/grid-template.js.map M static/maps/mvc/history/history-content-model.js.map M static/maps/mvc/history/history-contents.js.map M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/history-panel.js.map M static/maps/mvc/history/history-structure-view.js.map M static/maps/mvc/history/multi-panel.js.map M static/maps/mvc/job/job-model.js.map M static/maps/mvc/list/list-item.js.map M static/maps/mvc/list/list-panel.js.map M static/maps/mvc/tags.js.map M static/maps/mvc/tools/tools-form-base.js.map M static/maps/mvc/tools/tools-form-workflow.js.map M static/maps/mvc/tools/tools-jobs.js.map M static/maps/mvc/ui/ui-select-default.js.map M static/maps/mvc/upload/upload-button.js.map M static/maps/mvc/user/user-model.js.map M static/maps/mvc/user/user-quotameter.js.map M static/maps/mvc/visualization/visualization-model.js.map M static/maps/templates/compiled/tool_link.js.map M static/maps/utils/add-logging.js.map M static/maps/utils/deferred.js.map M static/maps/utils/metrics-logger.js.map M static/maps/utils/uploadbox.js.map M static/scripts/galaxy-app-base.js M static/scripts/galaxy.panels.js M static/scripts/libs/jquery/select2.js M static/scripts/mvc/app/app-analysis.js M static/scripts/mvc/base-mvc.js M static/scripts/mvc/citation/citation-model.js M static/scripts/mvc/collection/collection-model.js M static/scripts/mvc/collection/collection-panel.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.js M static/scripts/mvc/dataset/dataset-list.js M static/scripts/mvc/dataset/dataset-model.js M static/scripts/mvc/form/form-parameters.js M static/scripts/mvc/form/form-repeat.js M static/scripts/mvc/form/form-select-content.js M static/scripts/mvc/form/form-view.js M static/scripts/mvc/grid/grid-template.js M static/scripts/mvc/history/history-content-model.js M static/scripts/mvc/history/history-contents.js M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/history-panel.js M static/scripts/mvc/history/history-structure-view.js M static/scripts/mvc/history/multi-panel.js M static/scripts/mvc/job/job-model.js M static/scripts/mvc/list/list-item.js M static/scripts/mvc/list/list-panel.js M static/scripts/mvc/tools/tools-form-base.js M static/scripts/mvc/tools/tools-form-workflow.js M static/scripts/mvc/tools/tools-jobs.js M static/scripts/mvc/ui/ui-select-default.js M static/scripts/mvc/upload/upload-button.js M static/scripts/mvc/user/user-model.js M static/scripts/mvc/user/user-quotameter.js M static/scripts/templates/compiled/tool_link.js M static/scripts/utils/add-logging.js M static/scripts/utils/deferred.js M static/scripts/utils/metrics-logger.js M static/scripts/utils/uploadbox.js M static/style/blue/base.css M templates/galaxy_client_app.mako M test/api/helpers.py M test/qunit/tests/galaxy-app-base.js M tools/filters/wig_to_bigwig.xml Log Message: ----------- Merge and resolve conflicts Commit: 6dfacb6fe648097c94fb32db2df5e643cdcc45e1 https://github.com/galaxyproject/galaxy/commit/6dfacb6fe648097c94fb32db2df5… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-11-10 (Tue, 10 Nov 2015) Changed paths: M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conditional-requirements.txt M lib/galaxy/dependencies/requirements.txt Log Message: ----------- Merge pull request #1017 from dannon/weberror_downgrade Downgrade WebError. Compare: https://github.com/galaxyproject/galaxy/compare/1333f8037572...6dfacb6fe648

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[galaxyproject/galaxy] 54382e: Added gitignore rules to ignore custom tool-data
by GitHub 10 Nov '15

10 Nov '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 54382e8c2f0e6a3e54d7968b999708dcb8bd0998 https://github.com/galaxyproject/galaxy/commit/54382e8c2f0e6a3e54d7968b9997… Author: youri <y.hoogstrate(a)erasmusmc.nl> Date: 2015-11-09 (Mon, 09 Nov 2015) Changed paths: M .gitignore Log Message: ----------- Added gitignore rules to ignore custom tool-data Commit: 1333f803757215a77a988bf211e315744ec00024 https://github.com/galaxyproject/galaxy/commit/1333f803757215a77a988bf211e3… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-11-10 (Tue, 10 Nov 2015) Changed paths: M .gitignore Log Message: ----------- Merge pull request #1048 from yhoogstrate/tool_data_gitignore Added gitignore rules to ignore custom tool-data Compare: https://github.com/galaxyproject/galaxy/compare/daccea42bdbd...1333f8037572

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[galaxyproject/galaxy] ad2045: Fix output to print values and not hash key
by GitHub 09 Nov '15

09 Nov '15

Branch: refs/heads/release_15.10 Home: https://github.com/galaxyproject/galaxy Commit: ad20452340d052570c1b3203259d10e1ad94a236 https://github.com/galaxyproject/galaxy/commit/ad20452340d052570c1b3203259d… Author: Eric Enns <eric.enns(a)phac-aspc.gc.ca> Date: 2015-10-09 (Fri, 09 Oct 2015) Changed paths: M tools/stats/gsummary.py Log Message: ----------- Fix output to print values and not hash key Commit: ad4458a458d7ccb5238094ab3d1967072b5a0b76 https://github.com/galaxyproject/galaxy/commit/ad4458a458d7ccb5238094ab3d19… Author: Eric Enns <eric.enns(a)phac-aspc.gc.ca> Date: 2015-10-09 (Fri, 09 Oct 2015) Changed paths: M tools/stats/gsummary.py Log Message: ----------- Revert to previous changes if using rpy2 Commit: 0ec1b17794d53ae1a535b00f13d955c62f702a94 https://github.com/galaxyproject/galaxy/commit/0ec1b17794d53ae1a535b00f13d9… Author: Eric Enns <eric.enns(a)phac-aspc.gc.ca> Date: 2015-10-14 (Wed, 14 Oct 2015) Changed paths: M tools/stats/gsummary.py Log Message: ----------- Update list comprehension to go through headings instead of summary so that we output in the order we want. Commit: 50c27ace2c6eb260b88aafac72997cfa06ca6c13 https://github.com/galaxyproject/galaxy/commit/50c27ace2c6eb260b88aafac7299… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-10-14 (Wed, 14 Oct 2015) Changed paths: M tools/stats/gsummary.py Log Message: ----------- Merge pull request #885 from ericenns/fix_gsummary_in_release_15.07 [15.07] Fix gsummary in release 15.07 Commit: 57d6c9872c21f0bddfde04b170e8e8021d20ff71 https://github.com/galaxyproject/galaxy/commit/57d6c9872c21f0bddfde04b170e8… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-11-09 (Mon, 09 Nov 2015) Changed paths: M tools/stats/gsummary.py Log Message: ----------- Merge remote-tracking branch 'jmchilton/release_15.07' into release_15.10 Commit: 7e6df4f46fe0eed8328b57543b069911e4988d02 https://github.com/galaxyproject/galaxy/commit/7e6df4f46fe0eed8328b57543b06… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-11-09 (Mon, 09 Nov 2015) Changed paths: M tools/stats/gsummary.py Log Message: ----------- Merge pull request #1043 from jmchilton/release_15.10-forward-port [15.10] Forward port 15.07 fix to 15.10. Compare: https://github.com/galaxyproject/galaxy/compare/3b8edf6aebfb...7e6df4f46fe0

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[galaxyproject/galaxy] 76bcfa: Fix log comments
by GitHub 09 Nov '15

09 Nov '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 76bcfaa0ff85fe996ee2afccfb85e01f154e75b3 https://github.com/galaxyproject/galaxy/commit/76bcfaa0ff85fe996ee2afccfb85… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-11-07 (Sat, 07 Nov 2015) Changed paths: M client/galaxy/scripts/galaxy-app-base.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-repeat.js M client/galaxy/scripts/mvc/form/form-select-content.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/tools/tools-form-base.js M client/galaxy/scripts/mvc/tools/tools-form-workflow.js M client/galaxy/scripts/mvc/tools/tools-jobs.js M client/galaxy/scripts/utils/deferred.js M client/galaxy/scripts/utils/uploadbox.js M static/maps/galaxy-app-base.js.map M static/maps/mvc/form/form-parameters.js.map M static/maps/mvc/form/form-repeat.js.map M static/maps/mvc/form/form-select-content.js.map M static/maps/mvc/form/form-view.js.map M static/maps/mvc/tools/tools-form-base.js.map M static/maps/mvc/tools/tools-form-workflow.js.map M static/maps/mvc/tools/tools-jobs.js.map M static/maps/utils/deferred.js.map M static/maps/utils/uploadbox.js.map M static/scripts/galaxy-app-base.js M static/scripts/mvc/form/form-parameters.js M static/scripts/mvc/form/form-repeat.js M static/scripts/mvc/form/form-select-content.js M static/scripts/mvc/form/form-view.js M static/scripts/mvc/tools/tools-form-base.js M static/scripts/mvc/tools/tools-form-workflow.js M static/scripts/mvc/tools/tools-jobs.js M static/scripts/utils/deferred.js M static/scripts/utils/uploadbox.js Log Message: ----------- Fix log comments Use emit Fix namespace Fix namespace Remove empty line Check if logger exists Fix comment Redo More Fix yet another log Fix statements More fixes Move emitter Commit: daccea42bdbd545e6ed9d91bd4685036b95410a8 https://github.com/galaxyproject/galaxy/commit/daccea42bdbd545e6ed9d91bd468… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-11-09 (Mon, 09 Nov 2015) Changed paths: M client/galaxy/scripts/galaxy-app-base.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-repeat.js M client/galaxy/scripts/mvc/form/form-select-content.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/tools/tools-form-base.js M client/galaxy/scripts/mvc/tools/tools-form-workflow.js M client/galaxy/scripts/mvc/tools/tools-jobs.js M client/galaxy/scripts/utils/deferred.js M client/galaxy/scripts/utils/uploadbox.js M static/maps/galaxy-app-base.js.map M static/maps/mvc/form/form-parameters.js.map M static/maps/mvc/form/form-repeat.js.map M static/maps/mvc/form/form-select-content.js.map M static/maps/mvc/form/form-view.js.map M static/maps/mvc/tools/tools-form-base.js.map M static/maps/mvc/tools/tools-form-workflow.js.map M static/maps/mvc/tools/tools-jobs.js.map M static/maps/utils/deferred.js.map M static/maps/utils/uploadbox.js.map M static/scripts/galaxy-app-base.js M static/scripts/mvc/form/form-parameters.js M static/scripts/mvc/form/form-repeat.js M static/scripts/mvc/form/form-select-content.js M static/scripts/mvc/form/form-view.js M static/scripts/mvc/tools/tools-form-base.js M static/scripts/mvc/tools/tools-form-workflow.js M static/scripts/mvc/tools/tools-jobs.js M static/scripts/utils/deferred.js M static/scripts/utils/uploadbox.js Log Message: ----------- Merge pull request #1040 from guerler/revise_logging_000 Fix log statements and link to logger Compare: https://github.com/galaxyproject/galaxy/compare/c36ff5bcc7e8...daccea42bdbd

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[galaxyproject/usegalaxy-playbook] 7372b6: Dropped link to poss for GCC2016 Training Topics.
by GitHub 07 Nov '15

07 Nov '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 7372b6812790e8338eea0ea30d1a71fc623c72e4 https://github.com/galaxyproject/usegalaxy-playbook/commit/7372b6812790e833… Author: tnabtaf <clements(a)galaxyproject.org> Date: 2015-11-07 (Sat, 07 Nov 2015) Changed paths: M templates/galaxy/common/static/welcome.html.j2 Log Message: ----------- Dropped link to poss for GCC2016 Training Topics.

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[galaxyproject/galaxy] dc10ac: Add stub fetch_eggs.py/check_eggs.py for people wh...
by GitHub 07 Nov '15

07 Nov '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: dc10ac7e3ec3bac08eed4e786fa855c7422b8b3c https://github.com/galaxyproject/galaxy/commit/dc10ac7e3ec3bac08eed4e786fa8… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-11-06 (Fri, 06 Nov 2015) Changed paths: A scripts/check_eggs.py A scripts/fetch_eggs.py Log Message: ----------- Add stub fetch_eggs.py/check_eggs.py for people whose build/test/run pipelines may have been running these by hand. Print hopefully helpful information and return 1. Fixes #1030 Commit: c36ff5bcc7e840289e1d6c10610ac1dd90ddee19 https://github.com/galaxyproject/galaxy/commit/c36ff5bcc7e840289e1d6c10610a… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-11-07 (Sat, 07 Nov 2015) Changed paths: A scripts/check_eggs.py A scripts/fetch_eggs.py Log Message: ----------- Merge pull request #1037 from natefoo/smash-eggs-bugfix1 Add stub fetch_eggs.py/check_eggs.py Compare: https://github.com/galaxyproject/galaxy/compare/e2f9cf2dd6cc...c36ff5bcc7e8

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[galaxyproject/galaxy] 168d42: Keep select field open for multi select
by GitHub 06 Nov '15

06 Nov '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 168d42acf39196969c48864c9dcb43cb311eb641 https://github.com/galaxyproject/galaxy/commit/168d42acf39196969c48864c9dcb… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-11-03 (Tue, 03 Nov 2015) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-default.js M static/maps/mvc/ui/ui-select-default.js.map M static/scripts/mvc/ui/ui-select-default.js Log Message: ----------- Keep select field open for multi select Commit: f57d91794917ac7ee057585addc1891e81c40fdf https://github.com/galaxyproject/galaxy/commit/f57d91794917ac7ee057585addc1… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-11-03 (Tue, 03 Nov 2015) Changed paths: M client/galaxy/scripts/libs/jquery/select2.js M static/maps/libs/jquery/select2.js.map M static/scripts/libs/jquery/select2.js Log Message: ----------- Patch select2 to avoid resetting highlighted location Keep search term Commit: bbc3e943e73ebb0c8358dcf0d26ac617e68bb57c https://github.com/galaxyproject/galaxy/commit/bbc3e943e73ebb0c8358dcf0d26a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-11-05 (Thu, 05 Nov 2015) Changed paths: M .ci/flake8_blacklist.txt M .ci/flake8_wrapper.sh M .gitignore M client/galaxy/scripts/galaxy-app-base.js M client/galaxy/scripts/galaxy.panels.js M client/galaxy/scripts/mvc/app/app-analysis.js M client/galaxy/scripts/mvc/app/app-view.js M client/galaxy/scripts/mvc/base-mvc.js M client/galaxy/scripts/mvc/citation/citation-model.js M client/galaxy/scripts/mvc/collection/collection-li-edit.js M client/galaxy/scripts/mvc/collection/collection-li.js M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/collection/collection-panel.js 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.js M client/galaxy/scripts/mvc/dataset/dataset-list.js M client/galaxy/scripts/mvc/dataset/dataset-model.js M client/galaxy/scripts/mvc/grid/grid-template.js M client/galaxy/scripts/mvc/history/history-content-model.js M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/history-panel.js M client/galaxy/scripts/mvc/history/history-structure-view.js M client/galaxy/scripts/mvc/history/multi-panel.js M client/galaxy/scripts/mvc/job/job-model.js M client/galaxy/scripts/mvc/list/list-item.js M client/galaxy/scripts/mvc/list/list-panel.js M client/galaxy/scripts/mvc/tags.js M client/galaxy/scripts/mvc/tools/tools-form-base.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/scripts/mvc/upload/upload-button.js M client/galaxy/scripts/mvc/user/user-model.js M client/galaxy/scripts/mvc/user/user-quotameter.js M client/galaxy/scripts/mvc/visualization/visualization-model.js M client/galaxy/scripts/templates/compiled/tool_link.js M client/galaxy/scripts/templates/tool_link.handlebars M client/galaxy/scripts/utils/add-logging.js M client/galaxy/scripts/utils/deferred.js M client/galaxy/scripts/utils/metrics-logger.js M client/galaxy/style/less/base.less M client/galaxy/style/less/bootstrap.less M client/galaxy/style/less/ui.less M client/galaxy/style/less/upload.less M config/plugins/visualizations/charts/static/build-app.js M config/plugins/visualizations/charts/static/charts/jqplot/boxplot/wrapper.js M config/plugins/visualizations/charts/static/charts/nvd3/pie/wrapper.js M config/plugins/visualizations/charts/static/charts/tools.js M config/plugins/visualizations/charts/static/views/group.js M config/plugins/visualizations/charts/static/views/viewport.js M doc/source/lib/galaxy.auth.providers.rst M doc/source/lib/galaxy.datatypes.rst A doc/source/lib/galaxy.dependencies.rst M doc/source/lib/galaxy.eggs.rst M doc/source/lib/galaxy.jobs.runners.rst M doc/source/lib/galaxy.rst M doc/source/lib/galaxy.tools.deps.resolvers.rst M doc/source/lib/galaxy.web.framework.middleware.rst M doc/source/lib/galaxy.webapps.galaxy.controllers.rst M doc/source/lib/galaxy.webapps.reports.controllers.rst M doc/source/lib/galaxy.webapps.rst M doc/source/lib/galaxy.webapps.tool_shed.api.rst M doc/source/lib/modules.rst R doc/source/lib/pkg_resources.rst M lib/galaxy/app.py M lib/galaxy/config.py M lib/galaxy/jobs/metrics/instrumenters/collectl.py A lib/galaxy/jobs/runners/util/drmaa/__init__.py A lib/galaxy/jobs/runners/util/retry.py A lib/galaxy/jobs/runners/util/sudo.py M lib/galaxy/model/__init__.py M lib/galaxy/objectstore/__init__.py M lib/galaxy/objectstore/rods.py M lib/galaxy/objectstore/s3.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/commands.py M lib/galaxy/tools/deps/docker_util.py M lib/galaxy/tools/deps/dockerfiles.py M lib/galaxy/tools/deps/resolvers/modules.py M lib/galaxy/tools/deps/resolvers/tool_shed_packages.py M lib/galaxy/tools/lint.py A lib/galaxy/tools/lint_util.py M lib/galaxy/tools/linters/command.py M lib/galaxy/tools/linters/help.py M lib/galaxy/tools/linters/inputs.py M lib/galaxy/tools/linters/outputs.py A lib/galaxy/tools/linters/stdio.py M lib/galaxy/tools/linters/tests.py M lib/galaxy/tools/linters/top_level.py A lib/galaxy/tools/linters/xml_order.py M lib/galaxy/tools/loader_directory.py M lib/galaxy/tools/search/__init__.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/util/__init__.py M lib/galaxy/util/xml_macros.py M lib/galaxy/webapps/galaxy/api/library_contents.py M lib/galaxy/webapps/galaxy/controllers/requests_common.py M lib/galaxy/webapps/reports/app.py M lib/galaxy/webapps/tool_shed/app.py M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py M lib/pulsar/client/transport/curl.py M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/install_environment.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py M lib/tool_shed/galaxy_install/tool_migration_manager.py M lib/tool_shed/util/common_util.py M lib/tool_shed/util/hg_util.py M run.sh M scripts/tools/maf/check_loc_file.py M static/maps/galaxy-app-base.js.map M static/maps/mvc/app/app-analysis.js.map M static/maps/mvc/app/app-view.js.map M static/maps/mvc/base-mvc.js.map M static/maps/mvc/citation/citation-model.js.map M static/maps/mvc/collection/collection-model.js.map M static/maps/mvc/collection/collection-panel.js.map M static/maps/mvc/collection/list-collection-creator.js.map M static/maps/mvc/collection/list-of-pairs-collection-creator.js.map M static/maps/mvc/collection/pair-collection-creator.js.map M static/maps/mvc/dataset/dataset-choice.js.map M static/maps/mvc/dataset/dataset-li.js.map M static/maps/mvc/dataset/dataset-list.js.map M static/maps/mvc/dataset/dataset-model.js.map M static/maps/mvc/grid/grid-template.js.map M static/maps/mvc/history/history-content-model.js.map M static/maps/mvc/history/history-contents.js.map M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/history-panel.js.map M static/maps/mvc/history/history-structure-view.js.map M static/maps/mvc/history/multi-panel.js.map M static/maps/mvc/job/job-model.js.map M static/maps/mvc/list/list-item.js.map M static/maps/mvc/list/list-panel.js.map M static/maps/mvc/tags.js.map M static/maps/mvc/tools/tools-form-base.js.map M static/maps/mvc/ui/ui-select-default.js.map M static/maps/mvc/upload/upload-button.js.map M static/maps/mvc/user/user-model.js.map M static/maps/mvc/user/user-quotameter.js.map M static/maps/mvc/visualization/visualization-model.js.map M static/maps/templates/compiled/tool_link.js.map M static/maps/utils/add-logging.js.map M static/maps/utils/deferred.js.map M static/maps/utils/metrics-logger.js.map M static/scripts/galaxy-app-base.js M static/scripts/galaxy.panels.js M static/scripts/mvc/app/app-analysis.js M static/scripts/mvc/base-mvc.js M static/scripts/mvc/citation/citation-model.js M static/scripts/mvc/collection/collection-model.js M static/scripts/mvc/collection/collection-panel.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.js M static/scripts/mvc/dataset/dataset-list.js M static/scripts/mvc/dataset/dataset-model.js M static/scripts/mvc/grid/grid-template.js M static/scripts/mvc/history/history-content-model.js M static/scripts/mvc/history/history-contents.js M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/history-panel.js M static/scripts/mvc/history/history-structure-view.js M static/scripts/mvc/history/multi-panel.js M static/scripts/mvc/job/job-model.js M static/scripts/mvc/list/list-item.js M static/scripts/mvc/list/list-panel.js M static/scripts/mvc/tools/tools-form-base.js M static/scripts/mvc/ui/ui-select-default.js M static/scripts/mvc/upload/upload-button.js M static/scripts/mvc/user/user-model.js M static/scripts/mvc/user/user-quotameter.js M static/scripts/templates/compiled/tool_link.js M static/scripts/utils/add-logging.js M static/scripts/utils/deferred.js M static/scripts/utils/metrics-logger.js M static/style/blue/base.css M templates/galaxy_client_app.mako M test/api/helpers.py M test/qunit/tests/galaxy-app-base.js M tools/data_source/data_source.py M tools/evolution/add_scores.py M tools/extract/extract_genomic_dna.py M tools/extract/liftOver_wrapper.py M tools/filters/axt_to_concat_fasta.py M tools/filters/axt_to_fasta.py M tools/filters/axt_to_lav.py M tools/filters/catWrapper.py M tools/filters/gff/extract_GFF_Features.py M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_feature_count.py M tools/filters/gff/sort_gtf.py M tools/filters/gff_to_bed_converter.py M tools/filters/lav_to_bed.py M tools/filters/secure_hash_message_digest.py M tools/filters/wiggle_to_simple.py M tools/genomespace/genomespace_exporter.py M tools/maf/interval2maf.py M tools/maf/interval2maf.xml M tools/maf/interval_maf_to_merged_fasta.py M tools/maf/maf_by_block_number.py M tools/maf/maf_filter.py M tools/maf/maf_limit_size.py M tools/maf/maf_limit_to_species.py M tools/maf/maf_reverse_complement.py M tools/maf/maf_split_by_species.py M tools/maf/maf_stats.py M tools/maf/maf_thread_for_species.py M tools/maf/maf_to_bed.py M tools/maf/maf_to_bed_code.py M tools/maf/maf_to_fasta_concat.py M tools/maf/maf_to_fasta_multiple_sets.py M tools/maf/maf_to_interval.py M tools/maf/vcf_to_maf_customtrack.py M tools/next_gen_conversion/fastq_conversions.py M tools/next_gen_conversion/fastq_gen_conv.py M tools/next_gen_conversion/solid2fastq.py M tools/next_gen_conversion/solid_to_fastq.py M tools/ngs_simulation/ngs_simulation.py M tools/stats/aggregate_scores_in_intervals.py M tools/stats/filtering.py M tools/stats/grouping.py M tools/stats/gsummary.py Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into revise_multiselect_000 Commit: 975a94ce016811ff08eb1e9ac75b4463277e6199 https://github.com/galaxyproject/galaxy/commit/975a94ce016811ff08eb1e9ac75b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-11-05 (Thu, 05 Nov 2015) Changed paths: M static/maps/mvc/ui/ui-select-default.js.map M static/scripts/mvc/ui/ui-select-default.js Log Message: ----------- Pack scripts Commit: e2f9cf2dd6cca01a4fccc92ff746ea00fa1e3dd0 https://github.com/galaxyproject/galaxy/commit/e2f9cf2dd6cca01a4fccc92ff746… Author: carlfeberhard <carlfeberhard(a)users.noreply.github.com> Date: 2015-11-06 (Fri, 06 Nov 2015) Changed paths: M client/galaxy/scripts/libs/jquery/select2.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M static/maps/libs/jquery/select2.js.map M static/maps/mvc/ui/ui-select-default.js.map M static/scripts/libs/jquery/select2.js M static/scripts/mvc/ui/ui-select-default.js Log Message: ----------- Merge pull request #1019 from guerler/revise_multiselect_000 Keep select field open for multi select Compare: https://github.com/galaxyproject/galaxy/compare/1498ca2364ff...e2f9cf2dd6cc

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[galaxyproject/galaxy] 8231df: Add 2 missing dependencies of dependencies
by GitHub 06 Nov '15

06 Nov '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 8231df01fac0bf9596cfb6bc3c3586c0baffbe6f https://github.com/galaxyproject/galaxy/commit/8231df01fac0bf9596cfb6bc3c35… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-29 (Thu, 29 Oct 2015) Changed paths: M lib/galaxy/dependencies/requirements.txt Log Message: ----------- Add 2 missing dependencies of dependencies Commit: a2d30648c9a83c776937cd78d9ae470d6a155094 https://github.com/galaxyproject/galaxy/commit/a2d30648c9a83c776937cd78d9ae… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-11-02 (Mon, 02 Nov 2015) Changed paths: M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conditional-requirements.txt Log Message: ----------- Add importlib and ordereddict for Python 2.6. They won't be installed by conditional since they will always be installed as dependencies of kombu in requirements.txt. This should be fixed at some point. Commit: ff3501243978a9c949eb7f0bd9b1443aad17163e https://github.com/galaxyproject/galaxy/commit/ff3501243978a9c949eb7f0bd9b1… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-11-02 (Mon, 02 Nov 2015) Changed paths: M lib/galaxy/dependencies/__init__.py Log Message: ----------- XPath support is not the same on all Python 2.6es Commit: 1498ca2364ff7f64841fea44aa53758dcb880d45 https://github.com/galaxyproject/galaxy/commit/1498ca2364ff7f64841fea44aa53… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-11-06 (Fri, 06 Nov 2015) Changed paths: M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conditional-requirements.txt M lib/galaxy/dependencies/requirements.txt Log Message: ----------- Merge pull request #1006 from natefoo/smash_eggs Add 2 missing dependencies of dependencies Compare: https://github.com/galaxyproject/galaxy/compare/f69c06b6cf6d...1498ca2364ff

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[galaxyproject/galaxy] 4908a5: wig_to_bigwig: Add error message for wrongly forma...
by GitHub 05 Nov '15

05 Nov '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4908a5bab6578137521c13932c799719648f2351 https://github.com/galaxyproject/galaxy/commit/4908a5bab6578137521c13932c79… Author: Jelle Scholtalbers <j.scholtalbers(a)gmail.com> Date: 2015-11-05 (Thu, 05 Nov 2015) Changed paths: M tools/filters/wig_to_bigwig.xml Log Message: ----------- wig_to_bigwig: Add error message for wrongly formatted data Commit: f69c06b6cf6dfa1635743c35901bd1f57b3b4f21 https://github.com/galaxyproject/galaxy/commit/f69c06b6cf6dfa1635743c35901b… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2015-11-05 (Thu, 05 Nov 2015) Changed paths: M tools/filters/wig_to_bigwig.xml Log Message: ----------- Merge pull request #1033 from scholtalbers/wig_to_bigwig_error_msg wig_to_bigwig: Add error message for wrongly formatted data Compare: https://github.com/galaxyproject/galaxy/compare/596247627516...f69c06b6cf6d

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[galaxyproject/usegalaxy-playbook] 9f9961: Test mutable configs
by GitHub 05 Nov '15

05 Nov '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 9f99615b50b892da2d96fb62bf684dbc569ef010 https://github.com/galaxyproject/usegalaxy-playbook/commit/9f99615b50b892da… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-11-05 (Thu, 05 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: e8809829b129803cbbfdf1979dbb6c5219110a87 https://github.com/galaxyproject/usegalaxy-playbook/commit/e8809829b129803c… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-11-05 (Thu, 05 Nov 2015) Changed paths: M files/galaxy/common/dynamic_rules/multi_dynamic_walltime.py M files/galaxy/common/dynamic_rules/reserved.py M templates/galaxy/test.galaxyproject.org/config/job_conf.xml.j2 Log Message: ----------- Add Anton to reserved users, increased reserved job limits on Test Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/5e9e49fcd98c...…

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[galaxyproject/galaxy] 771765: Allow resizing of regular multi-select boxes
by GitHub 05 Nov '15

05 Nov '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 7717659c784085a772565d028c77c73b48a54630 https://github.com/galaxyproject/galaxy/commit/7717659c784085a772565d028c77… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-11-04 (Wed, 04 Nov 2015) Changed paths: M client/galaxy/scripts/galaxy.panels.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/style/less/base.less M client/galaxy/style/less/ui.less M config/plugins/visualizations/charts/static/build-app.js M static/maps/mvc/ui/ui-select-default.js.map M static/scripts/galaxy.panels.js M static/scripts/mvc/ui/ui-select-default.js M static/style/blue/base.css Log Message: ----------- Allow resizing of regular multi-select boxes Remove event handler Add mouse leave event handler Improve visibility and accessibility Fix tag name Style compromise Repack charts Commit: 8a9372b989b35a049ceec721846ae0811a8f8cfe https://github.com/galaxyproject/galaxy/commit/8a9372b989b35a049ceec721846a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-11-04 (Wed, 04 Nov 2015) Changed paths: M client/galaxy/scripts/mvc/grid/grid-template.js M client/galaxy/scripts/mvc/upload/upload-button.js M client/galaxy/style/less/base.less M client/galaxy/style/less/upload.less M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M run.sh M static/maps/mvc/grid/grid-template.js.map M static/maps/mvc/upload/upload-button.js.map M static/scripts/mvc/grid/grid-template.js M static/scripts/mvc/upload/upload-button.js M static/style/blue/base.css M test/api/helpers.py Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into revise_multiselect_001 Commit: 59624762751624c831e0b60a3fde1fdf9d4a78f9 https://github.com/galaxyproject/galaxy/commit/59624762751624c831e0b60a3fde… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-11-05 (Thu, 05 Nov 2015) Changed paths: M client/galaxy/scripts/galaxy.panels.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/style/less/base.less M client/galaxy/style/less/ui.less M config/plugins/visualizations/charts/static/build-app.js M static/maps/mvc/ui/ui-select-default.js.map M static/scripts/galaxy.panels.js M static/scripts/mvc/ui/ui-select-default.js M static/style/blue/base.css Log Message: ----------- Merge pull request #1025 from guerler/revise_multiselect_001 Allow resizing of regular multi-select boxes Compare: https://github.com/galaxyproject/galaxy/compare/afa65f4d9a36...596247627516

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[galaxyproject/infrastructure-playbook] 6d10ce: Whoops, there is no `group_users`.
by GitHub 05 Nov '15

05 Nov '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 6d10ce184dc53a0d427e6a51c0af75613be61a0a https://github.com/galaxyproject/infrastructure-playbook/commit/6d10ce184dc… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-11-05 (Thu, 05 Nov 2015) Changed paths: M galaxyenv/group_vars/starforgebuilders.yml Log Message: ----------- Whoops, there is no `group_users`.

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[galaxyproject/infrastructure-playbook] c77875: Update common roles
by GitHub 05 Nov '15

05 Nov '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: c77875df48b1416c2e4d6b930365ae5224b6a865 https://github.com/galaxyproject/infrastructure-playbook/commit/c77875df48b… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-11-05 (Thu, 05 Nov 2015) Changed paths: M common_roles Log Message: ----------- Update common roles Commit: 4f4646c9b1494a1bc62f80773d88cda51201b609 https://github.com/galaxyproject/infrastructure-playbook/commit/4f4646c9b14… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-11-05 (Thu, 05 Nov 2015) Changed paths: A galaxyenv/group_vars/starforgebuilders.yml R galaxyenv/host_vars/mjolnir0.galaxyproject.org.yml M galaxyenv/inventory Log Message: ----------- Install docker on starforge builder Compare: https://github.com/galaxyproject/infrastructure-playbook/compare/bde9fa7aea…

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[galaxyproject/infrastructure-playbook] bde9fa: Use pam_mkhomedir if using ldap and an alternate h...
by GitHub 05 Nov '15

05 Nov '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: bde9fa7aea45f6f30726ccdab12f314f9f63e809 https://github.com/galaxyproject/infrastructure-playbook/commit/bde9fa7aea4… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-11-05 (Thu, 05 Nov 2015) Changed paths: M galaxyenv/host_vars/mjolnir0.galaxyproject.org.yml A roles/ldap/files/pam-config-mkhomedir M roles/ldap/handlers/main.yml M roles/ldap/tasks/nss.yml Log Message: ----------- Use pam_mkhomedir if using ldap and an alternate home directory is specified

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[galaxyproject/infrastructure-playbook] 2115d6: Update common roles and adjust for changed apt_rep...
by GitHub 04 Nov '15

04 Nov '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 2115d6f4e69a392e0fb3bb82b96396ede4d02bc1 https://github.com/galaxyproject/infrastructure-playbook/commit/2115d6f4e69… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-11-04 (Wed, 04 Nov 2015) Changed paths: M common_roles M galaxyenv/host_vars/n2.galaxyproject.org.yml Log Message: ----------- Update common roles and adjust for changed apt_repository format Commit: 2d8dbb4bc0513bd2fa0b8b97ec533eeadb7c60f9 https://github.com/galaxyproject/infrastructure-playbook/commit/2d8dbb4bc05… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-11-04 (Wed, 04 Nov 2015) Changed paths: M common_roles Log Message: ----------- Update common roles again Compare: https://github.com/galaxyproject/infrastructure-playbook/compare/d6751dc6b5…

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[galaxyproject/infrastructure-playbook] d6751d: Bring the kerberos, ldap, and nfs roles over from ...
by GitHub 04 Nov '15

04 Nov '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: d6751dc6b5e6eb1fea81689ca7a66a709d562ffc https://github.com/galaxyproject/infrastructure-playbook/commit/d6751dc6b5e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-11-04 (Wed, 04 Nov 2015) Changed paths: M galaxyenv/group_vars/baseenv.yml A galaxyenv/group_vars/liteenv.yml M galaxyenv/host_vars/mjolnir0.galaxyproject.org.yml M galaxyenv/inventory M playbook.yml A roles/kerberos/defaults/main.yml A roles/kerberos/tasks/auth.yml A roles/kerberos/tasks/k5login.yml A roles/kerberos/tasks/main.yml A roles/kerberos/templates/krb5.conf.j2 A roles/ldap/files/debian-nsswitch.conf A roles/ldap/handlers/main.yml A roles/ldap/tasks/main.yml A roles/ldap/tasks/nss.yml A roles/ldap/templates/ldap.conf.j2 A roles/ldap/vars/debian_family.yml A roles/ldap/vars/default.yml A roles/ldap/vars/ubuntu.yml A roles/nfs/defaults/main.yml A roles/nfs/files/default-nfs-common A roles/nfs/handlers/main.yml A roles/nfs/tasks/ldap.yml A roles/nfs/tasks/main.yml A roles/nfs/templates/default-autofs.j2 A roles/nfs/templates/idmapd.conf.j2 Log Message: ----------- Bring the kerberos, ldap, and nfs roles over from the private playbook and combine them into a "lite" env for galaxy hosts that does the auth and ldap stuff but without afs. Make mjolnir0 use the lite env.

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[galaxyproject/usegalaxy-playbook] 5e9e49: Readme formatting
by GitHub 04 Nov '15

04 Nov '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 5e9e49fcd98c1aa2b5bfd2071fe015bc64084846 https://github.com/galaxyproject/usegalaxy-playbook/commit/5e9e49fcd98c1aa2… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-11-04 (Wed, 04 Nov 2015) Changed paths: M README.md Log Message: ----------- Readme formatting

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[galaxyproject/usegalaxy-playbook] eec6b5: Add instructions on how to restart Galaxy Test aft...
by GitHub 04 Nov '15

04 Nov '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: eec6b5ce1909efc3ae2fa1aa1287035603134307 https://github.com/galaxyproject/usegalaxy-playbook/commit/eec6b5ce1909efc3… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-11-04 (Wed, 04 Nov 2015) Changed paths: M README.md Log Message: ----------- Add instructions on how to restart Galaxy Test after an update.

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[galaxyproject/usegalaxy-playbook] f36a35: Add sanitize_whitelist for both servers in mutable...
by GitHub 04 Nov '15

04 Nov '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: f36a35849b6213d134156dfc7f2741a207fa9c54 https://github.com/galaxyproject/usegalaxy-playbook/commit/f36a35849b6213d1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-11-04 (Wed, 04 Nov 2015) Changed paths: M stage/group_vars/galaxyservers.yml Log Message: ----------- Add sanitize_whitelist for both servers in mutable configs.

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[galaxyproject/usegalaxy-playbook] 24d737: Mutable configs.
by GitHub 04 Nov '15

04 Nov '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 24d737b54cfdad8038760704dac68fb7509833b4 https://github.com/galaxyproject/usegalaxy-playbook/commit/24d737b54cfdad80… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-11-04 (Wed, 04 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: ----------- Mutable configs.

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