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

[galaxyproject/galaxy] 658070: Fix parsing of message configuration
by GitHub 11 Nov '15

11 Nov '15

Branch: refs/heads/release_15.10 Home: https://github.com/galaxyproject/galaxy Commit: 65807013957c3f845b0b8fd793b52b6d9f057505 https://github.com/galaxyproject/galaxy/commit/65807013957c3f845b0b8fd793b5… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-11-10 (Tue, 10 Nov 2015) Changed paths: M client/galaxy/scripts/galaxy-app-base.js M lib/galaxy/managers/configuration.py M static/maps/galaxy-app-base.js.map M static/scripts/galaxy-app-base.js Log Message: ----------- Fix parsing of message configuration Fix default value Add root to Galaxy object Commit: 6953bdf704f3e140ffc47f849fc54dc3d4c37013 https://github.com/galaxyproject/galaxy/commit/6953bdf704f3e140ffc47f849fc5… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-11-11 (Wed, 11 Nov 2015) Changed paths: M client/galaxy/scripts/galaxy-app-base.js M lib/galaxy/managers/configuration.py M static/maps/galaxy-app-base.js.map M static/scripts/galaxy-app-base.js Log Message: ----------- Merge pull request #1059 from guerler/fix_message_000 [15.10] Fix parsing of message configuration Compare: https://github.com/galaxyproject/galaxy/compare/4f72178a9568...6953bdf704f3

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[galaxyproject/galaxy] fef1e5: Fix job permission handling
by GitHub 11 Nov '15

11 Nov '15

Branch: refs/heads/release_15.10 Home: https://github.com/galaxyproject/galaxy Commit: fef1e548bba39c856f6086f0eb2300e6a50d8559 https://github.com/galaxyproject/galaxy/commit/fef1e548bba39c856f6086f0eb23… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-11-06 (Fri, 06 Nov 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/jobs.py Log Message: ----------- Fix job permission handling Catch unavailable history Fix test Commit: a8147327af2e8a90108d11d7fa93fe4d4893f6ab https://github.com/galaxyproject/galaxy/commit/a8147327af2e8a90108d11d7fa93… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-11-09 (Mon, 09 Nov 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/jobs.py Log Message: ----------- Derive permission from job outputs Remove history manager Use dataset manager Commit: b2723e7467c5fb9722a1c6cb009251b0deaf9bc4 https://github.com/galaxyproject/galaxy/commit/b2723e7467c5fb9722a1c6cb0092… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-11-10 (Tue, 10 Nov 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/jobs.py M test/api/test_jobs.py Log Message: ----------- Disable invalid test case. Add validation criteria. Fix comments Fix comment Commit: 4f72178a9568e35f99a5824d66ce4c6911e50d93 https://github.com/galaxyproject/galaxy/commit/4f72178a9568e35f99a5824d66ce… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-11-11 (Wed, 11 Nov 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/jobs.py M test/api/test_jobs.py Log Message: ----------- Merge pull request #1038 from guerler/fix_imported_rerun_000 [15.10] Fix job rerun for imported histories Compare: https://github.com/galaxyproject/galaxy/compare/c85b0d9b0b2d...4f72178a9568

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[galaxyproject/galaxy] b88864: Fix warning statement
by GitHub 11 Nov '15

11 Nov '15

Branch: refs/heads/release_15.10 Home: https://github.com/galaxyproject/galaxy Commit: b88864586c760e0e644bdc32c5d2349b1613446c https://github.com/galaxyproject/galaxy/commit/b88864586c760e0e644bdc32c5d2… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-11-10 (Tue, 10 Nov 2015) Changed paths: M lib/galaxy/tools/parameters/dynamic_options.py Log Message: ----------- Fix warning statement Commit: c85b0d9b0b2d6853b216ebb691987632a3b6bdc6 https://github.com/galaxyproject/galaxy/commit/c85b0d9b0b2d6853b216ebb69198… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-11-11 (Wed, 11 Nov 2015) Changed paths: M lib/galaxy/tools/parameters/dynamic_options.py Log Message: ----------- Merge pull request #1060 from guerler/fix_assert_000 [15.10] Fix warning statement Compare: https://github.com/galaxyproject/galaxy/compare/5603a96aecb2...c85b0d9b0b2d

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[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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