- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 0f0bcb: fix bad merge in #3060
by GitHub 24 Oct '16

24 Oct '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 0f0bcb6a088f669a5c1272d238bbe79e29002742 https://github.com/galaxyproject/galaxy/commit/0f0bcb6a088f669a5c1272d238bb… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-10-24 (Mon, 24 Oct 2016) Changed paths: M Makefile Log Message: ----------- fix bad merge in #3060 Commit: 00c48e4878a0b22ce7045692d67d72af7d540215 https://github.com/galaxyproject/galaxy/commit/00c48e4878a0b22ce7045692d67d… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-10-24 (Mon, 24 Oct 2016) Changed paths: M Makefile Log Message: ----------- remove the rest of the badle merged target Commit: 05be84ba47c0932a393cb9925ae10db4fae27396 https://github.com/galaxyproject/galaxy/commit/05be84ba47c0932a393cb9925ae1… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-10-24 (Mon, 24 Oct 2016) Changed paths: M Makefile Log Message: ----------- Merge pull request #3087 from martenson/fix-makefile fix bad merge in #3060 Compare: https://github.com/galaxyproject/galaxy/compare/5662a6a5c6fd...05be84ba47c0

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[galaxyproject/galaxy] e4b376: Change remaining __all__ from list to tuple
by GitHub 24 Oct '16

24 Oct '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e4b3766c1b8798ab20a00c98d10f7bbf29da16ab https://github.com/galaxyproject/galaxy/commit/e4b3766c1b8798ab20a00c98d10f… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-10-18 (Tue, 18 Oct 2016) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M lib/galaxy/auth/providers/alwaysreject.py M lib/galaxy/auth/providers/ldap_ad.py M lib/galaxy/auth/providers/localdb.py M lib/galaxy/auth/providers/pam_auth.py M lib/galaxy/datatypes/checkers.py M lib/galaxy/datatypes/dataproviders/__init__.py M lib/galaxy/datatypes/metadata.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/deferred/data_transfer.py M lib/galaxy/jobs/deferred/manual_data_transfer.py M lib/galaxy/jobs/deferred/pacific_biosciences_smrt_portal.py M lib/galaxy/jobs/metrics/collectl/cli.py M lib/galaxy/jobs/metrics/collectl/processes.py M lib/galaxy/jobs/metrics/collectl/subsystems.py M lib/galaxy/jobs/metrics/instrumenters/collectl.py M lib/galaxy/jobs/metrics/instrumenters/core.py M lib/galaxy/jobs/metrics/instrumenters/cpuinfo.py M lib/galaxy/jobs/metrics/instrumenters/env.py M lib/galaxy/jobs/metrics/instrumenters/meminfo.py M lib/galaxy/jobs/metrics/instrumenters/uname.py M lib/galaxy/jobs/runners/cli.py M lib/galaxy/jobs/runners/condor.py M lib/galaxy/jobs/runners/drmaa.py M lib/galaxy/jobs/runners/godocker.py M lib/galaxy/jobs/runners/kubernetes.py M lib/galaxy/jobs/runners/local.py M lib/galaxy/jobs/runners/pbs.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/jobs/runners/slurm.py M lib/galaxy/jobs/runners/state_handlers/resubmit.py M lib/galaxy/jobs/runners/tasks.py M lib/galaxy/jobs/runners/util/__init__.py M lib/galaxy/jobs/runners/util/drmaa/__init__.py M lib/galaxy/jobs/runners/util/job_script/__init__.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/util/__init__.py M lib/galaxy/util/checkers.py M lib/galaxy/util/hash_util.py M lib/galaxy/util/json.py M lib/galaxy/util/object_wrapper.py M lib/galaxy/util/pastescript/loadwsgi.py M lib/galaxy/util/properties.py M lib/galaxy/util/topsort.py M lib/galaxy/web/__init__.py M lib/galaxy/web/buildapp.py M lib/galaxy/web/framework/__init__.py M lib/galaxy/web/framework/middleware/error.py M lib/galaxy/web/framework/middleware/static.py M lib/galaxy/webapps/galaxy/api/tours.py M lib/galaxy/webapps/galaxy/controllers/userskeys.py M lib/galaxy/webapps/reports/__init__.py M lib/galaxy/webapps/tool_shed/__init__.py M lib/galaxy/webapps/tool_shed/controllers/user.py M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/util/workflow_util.py M scripts/db_shell.py M test/api/test_histories.py M test/api/test_libraries.py M test/unit/tools/test_tool_dependency_description.py Log Message: ----------- Change remaining __all__ from list to tuple Also fix import order and Python3 compatibility. Commit: 5662a6a5c6fd7166b9f5092308e3ff2ca2bb3738 https://github.com/galaxyproject/galaxy/commit/5662a6a5c6fd7166b9f5092308e3… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-10-24 (Mon, 24 Oct 2016) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M lib/galaxy/auth/providers/alwaysreject.py M lib/galaxy/auth/providers/ldap_ad.py M lib/galaxy/auth/providers/localdb.py M lib/galaxy/auth/providers/pam_auth.py M lib/galaxy/datatypes/checkers.py M lib/galaxy/datatypes/dataproviders/__init__.py M lib/galaxy/datatypes/metadata.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/deferred/data_transfer.py M lib/galaxy/jobs/deferred/manual_data_transfer.py M lib/galaxy/jobs/deferred/pacific_biosciences_smrt_portal.py M lib/galaxy/jobs/metrics/collectl/cli.py M lib/galaxy/jobs/metrics/collectl/processes.py M lib/galaxy/jobs/metrics/collectl/subsystems.py M lib/galaxy/jobs/metrics/instrumenters/collectl.py M lib/galaxy/jobs/metrics/instrumenters/core.py M lib/galaxy/jobs/metrics/instrumenters/cpuinfo.py M lib/galaxy/jobs/metrics/instrumenters/env.py M lib/galaxy/jobs/metrics/instrumenters/meminfo.py M lib/galaxy/jobs/metrics/instrumenters/uname.py M lib/galaxy/jobs/runners/cli.py M lib/galaxy/jobs/runners/condor.py M lib/galaxy/jobs/runners/drmaa.py M lib/galaxy/jobs/runners/godocker.py M lib/galaxy/jobs/runners/kubernetes.py M lib/galaxy/jobs/runners/local.py M lib/galaxy/jobs/runners/pbs.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/jobs/runners/slurm.py M lib/galaxy/jobs/runners/state_handlers/resubmit.py M lib/galaxy/jobs/runners/tasks.py M lib/galaxy/jobs/runners/util/__init__.py M lib/galaxy/jobs/runners/util/drmaa/__init__.py M lib/galaxy/jobs/runners/util/job_script/__init__.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/util/__init__.py M lib/galaxy/util/checkers.py M lib/galaxy/util/hash_util.py M lib/galaxy/util/json.py M lib/galaxy/util/object_wrapper.py M lib/galaxy/util/pastescript/loadwsgi.py M lib/galaxy/util/properties.py M lib/galaxy/util/topsort.py M lib/galaxy/web/__init__.py M lib/galaxy/web/buildapp.py M lib/galaxy/web/framework/__init__.py M lib/galaxy/web/framework/middleware/error.py M lib/galaxy/web/framework/middleware/static.py M lib/galaxy/webapps/galaxy/api/tours.py M lib/galaxy/webapps/galaxy/controllers/userskeys.py M lib/galaxy/webapps/reports/__init__.py M lib/galaxy/webapps/tool_shed/__init__.py M lib/galaxy/webapps/tool_shed/controllers/user.py M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/util/workflow_util.py M scripts/db_shell.py M test/api/test_histories.py M test/api/test_libraries.py M test/unit/tools/test_tool_dependency_description.py Log Message: ----------- Merge pull request #3071 from nsoranzo/fix__all__ Change __all__ from list to tuple [2/2] Compare: https://github.com/galaxyproject/galaxy/compare/a6d52cdbdc83...5662a6a5c6fd

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[galaxyproject/galaxy] 096a7b: fix the incorrect handling of root when prefix is ...
by GitHub 23 Oct '16

23 Oct '16

Branch: refs/heads/release_16.07 Home: https://github.com/galaxyproject/galaxy Commit: 096a7bf94d799f905013f7052c1bdf87062a45a7 https://github.com/galaxyproject/galaxy/commit/096a7bf94d799f905013f7052c1b… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-10-20 (Thu, 20 Oct 2016) Changed paths: M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-folderrow-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M static/maps/mvc/library/library-dataset-view.js.map M static/maps/mvc/library/library-folderrow-view.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/library/library-dataset-view.js M static/scripts/mvc/library/library-folderrow-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- fix the incorrect handling of root when prefix is in play Commit: 65dc4f22aa7b717109aca6fac7947a84d2bd587a https://github.com/galaxyproject/galaxy/commit/65dc4f22aa7b717109aca6fac794… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-10-23 (Sun, 23 Oct 2016) Changed paths: M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-folderrow-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M static/maps/mvc/library/library-dataset-view.js.map M static/maps/mvc/library/library-folderrow-view.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/library/library-dataset-view.js M static/scripts/mvc/library/library-folderrow-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- Merge pull request #3074 from martenson/fix-libraries-prefix [16.07] Fix libraries prefix Compare: https://github.com/galaxyproject/galaxy/compare/cf0e4e84ce41...65dc4f22aa7b

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[galaxyproject/galaxy] afe5e0: Merge branch 'release_16.01'
by GitHub 23 Oct '16

23 Oct '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: afe5e0446ea3a943eb69616fda84fc9870c3b584 https://github.com/galaxyproject/galaxy/commit/afe5e0446ea3a943eb69616fda84… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-05-10 (Tue, 10 May 2016) Changed paths: M lib/galaxy/jobs/runners/slurm.py M templates/show_params.mako M templates/webapps/galaxy/data_manager/view_job.mako Log Message: ----------- Merge branch 'release_16.01' Commit: f730f2d1abff763d35fa8514762d55f8a863c791 https://github.com/galaxyproject/galaxy/commit/f730f2d1abff763d35fa8514762d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-05-18 (Wed, 18 May 2016) Changed paths: A .ci/first_startup.sh M .ci/flake8_blacklist.txt M .ci/flake8_wrapper.sh M .ci/py3_sources.txt M .gitignore M .travis.yml M Makefile M README.rst M client/GruntFile.js M client/README.md M client/bower.json M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/tool-panel.js M client/galaxy/scripts/galaxy.library.js M client/galaxy/scripts/layout/masthead.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/layout/scratchbook.js R client/galaxy/scripts/libs/handlebars.runtime.js M client/galaxy/scripts/mvc/base-mvc.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-view-edit.js M client/galaxy/scripts/mvc/collection/collection-view.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-edit.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/dataset/states.js M client/galaxy/scripts/mvc/form/form-data.js M client/galaxy/scripts/mvc/form/form-input.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-section.js R client/galaxy/scripts/mvc/form/form-select-content.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/history/copy-dialog.js M client/galaxy/scripts/mvc/history/hda-li-edit.js M client/galaxy/scripts/mvc/history/hda-li.js M client/galaxy/scripts/mvc/history/hda-model.js M client/galaxy/scripts/mvc/history/hdca-li-edit.js M client/galaxy/scripts/mvc/history/hdca-li.js M client/galaxy/scripts/mvc/history/hdca-model.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-structure-view.js M client/galaxy/scripts/mvc/history/history-view-annotated.js M client/galaxy/scripts/mvc/history/history-view-edit-current.js M client/galaxy/scripts/mvc/history/history-view-edit.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/history/job-dag.js M client/galaxy/scripts/mvc/history/multi-panel.js M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-folder-view.js M client/galaxy/scripts/mvc/library/library-folderlist-view.js M client/galaxy/scripts/mvc/library/library-folderrow-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-library-view.js M client/galaxy/scripts/mvc/library/library-librarylist-view.js M client/galaxy/scripts/mvc/library/library-libraryrow-view.js M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js M client/galaxy/scripts/mvc/library/library-model.js M client/galaxy/scripts/mvc/list/list-item.js M client/galaxy/scripts/mvc/list/list-view.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tool-form-workflow.js M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/scripts/mvc/tool/tools.js M client/galaxy/scripts/mvc/tours.js M client/galaxy/scripts/mvc/ui/ui-list.js M client/galaxy/scripts/mvc/ui/ui-misc.js A client/galaxy/scripts/mvc/ui/ui-select-content.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/scripts/mvc/upload/default/default-row.js M client/galaxy/scripts/mvc/upload/upload-settings.js M client/galaxy/scripts/mvc/user/user-model.js M client/galaxy/scripts/mvc/user/user-quotameter.js M client/galaxy/scripts/mvc/workflow/workflow-canvas.js M client/galaxy/scripts/mvc/workflow/workflow-view-node.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/scripts/onload.js R client/galaxy/scripts/templates/compiled/panel_section.js R client/galaxy/scripts/templates/compiled/tool_form.js R client/galaxy/scripts/templates/compiled/tool_link.js R client/galaxy/scripts/templates/compiled/tool_search.js R client/galaxy/scripts/templates/panel_section.handlebars R client/galaxy/scripts/templates/tool_form.handlebars R client/galaxy/scripts/templates/tool_link.handlebars R client/galaxy/scripts/templates/tool_search.handlebars M client/galaxy/scripts/utils/utils.js M client/galaxy/style/less/base.less M client/galaxy/style/less/library.less A client/galaxy/style/less/tour.less M client/galaxy/style/less/ui.less M client/galaxy/style/less/upload.less M client/grunt-tasks/install-libs.js M client/grunt-tasks/style.js R client/grunt-tasks/templates.js A client/grunt-tasks/webpack.js M client/package.json M client/webpack.config.js M config/datatypes_conf.xml.sample M 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static/scripts/mvc/dataset/data.js M templates/webapps/galaxy/history/grid.mako A test/unit/datatypes/test_data.py Log Message: ----------- Merge branch 'release_16.04' Commit: 5dfdf90dd09a53e9bc5108f22e439fae961102d5 https://github.com/galaxyproject/galaxy/commit/5dfdf90dd09a53e9bc5108f22e43… Author: anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-07-30 (Sat, 30 Jul 2016) Changed paths: M config/galaxy.ini.sample A config/plugins/plugin1.xml A config/plugins/plugin2.xml A config/plugins/webhooks/plugin1/config/plugin1.yaml A config/plugins/webhooks/plugin2/config/plugin2.yml M lib/galaxy/app.py M lib/galaxy/config.py A lib/galaxy/webapps/galaxy/api/webhooks.py A lib/galaxy/webhooks/__init__.py Log Message: ----------- add Webhooks draft Commit: 9551343c605f3f8895f75f7ba0fc295ee678ae1a https://github.com/galaxyproject/galaxy/commit/9551343c605f3f8895f75f7ba0fc… Author: anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-07-30 (Sat, 30 Jul 2016) Changed paths: R 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Author: anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-08-18 (Thu, 18 Aug 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form.js A client/galaxy/scripts/mvc/tool/tool-webhooks.js M config/plugins/webhooks/plugin2/config/plugin2.yml A config/plugins/webhooks/plugin2/static/style.css M lib/galaxy/webapps/galaxy/api/webhooks.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webhooks/__init__.py M static/maps/mvc/tool/tool-form.js.map A static/maps/mvc/tool/tool-webhooks.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/tool/tool-form.js A static/scripts/mvc/tool/tool-webhooks.js Log Message: ----------- add very basic plugin system (for tools) Commit: d01677618058a9ac7cb3758a4f6f1c3484790012 https://github.com/galaxyproject/galaxy/commit/d01677618058a9ac7cb3758a4f6f… Author: anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-08-19 (Fri, 19 Aug 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-webhooks.js R config/plugins/webhooks/plugin2/config/plugin2.yml R config/plugins/webhooks/plugin2/static/style.css A config/plugins/webhooks/xkcd/config/xkcd.yml A config/plugins/webhooks/xkcd/static/script.js A config/plugins/webhooks/xkcd/static/styles.css M lib/galaxy/webhooks/__init__.py M static/maps/mvc/tool/tool-webhooks.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tool-webhooks.js Log Message: ----------- add first webhook Commit: 08a2d275fa5f8b3713b28be52fcc78eea609a21d https://github.com/galaxyproject/galaxy/commit/08a2d275fa5f8b3713b28be52fcc… Author: anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-08-20 (Sat, 20 Aug 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-webhooks.js A config/plugins/webhooks/phdcomics/config/phdcomics.yaml A config/plugins/webhooks/phdcomics/helper/__init__.py A config/plugins/webhooks/phdcomics/static/script.js A config/plugins/webhooks/phdcomics/static/styles.css R config/plugins/webhooks/plugin1/config/plugin1.yaml M config/plugins/webhooks/xkcd/static/script.js M config/plugins/webhooks/xkcd/static/styles.css M lib/galaxy/webapps/galaxy/api/webhooks.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webhooks/__init__.py M static/maps/mvc/tool/tool-webhooks.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tool-webhooks.js Log Message: ----------- add one more plugin Commit: 3b9d1c96e0ea48e09c17c48fb9da8d1f65bbc791 https://github.com/galaxyproject/galaxy/commit/3b9d1c96e0ea48e09c17c48fb9da… Author: anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-08-20 (Sat, 20 Aug 2016) Changed paths: M client/galaxy/scripts/layout/masthead.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/tool/tool-form.js R client/galaxy/scripts/mvc/tool/tool-webhooks.js A client/galaxy/scripts/mvc/webhooks.js A config/plugins/webhooks/topbar_test/config/topbar_test.yml M lib/galaxy/webhooks/__init__.py M static/maps/layout/menu.js.map M static/maps/mvc/tool/tool-form.js.map A static/maps/mvc/webhooks.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/menu.js M static/scripts/mvc/tool/tool-form.js A static/scripts/mvc/webhooks.js Log Message: ----------- topbar webhooks testing Commit: a4497004ac47a25d6f9cefbfcb08183c5b6b8564 https://github.com/galaxyproject/galaxy/commit/a4497004ac47a25d6f9cefbfcb08… Author: anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-08-20 (Sat, 20 Aug 2016) Changed paths: M config/galaxy.ini.sample A config/plugins/plugin1.xml A config/plugins/plugin2.xml A config/plugins/webhooks/plugin1/config/plugin1.yaml A config/plugins/webhooks/plugin2/config/plugin2.yml M lib/galaxy/app.py M lib/galaxy/config.py A lib/galaxy/webapps/galaxy/api/webhooks.py A lib/galaxy/webhooks/__init__.py Log Message: ----------- add Webhooks draft Commit: 356e7ad3982da9916da927c52dad29e86a1e0ceb https://github.com/galaxyproject/galaxy/commit/356e7ad3982da9916da927c52dad… Author: anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-08-20 (Sat, 20 Aug 2016) Changed paths: R config/plugins/plugin1.xml R config/plugins/plugin2.xml Log Message: ----------- remove extra files Commit: 649bdd2aa947e11ab300152f4d9054be74229020 https://github.com/galaxyproject/galaxy/commit/649bdd2aa947e11ab300152f4d90… Author: anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-08-20 (Sat, 20 Aug 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form.js A client/galaxy/scripts/mvc/tool/tool-webhooks.js M config/plugins/webhooks/plugin2/config/plugin2.yml A config/plugins/webhooks/plugin2/static/style.css M lib/galaxy/webapps/galaxy/api/webhooks.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webhooks/__init__.py M static/maps/mvc/tool/tool-form.js.map A static/maps/mvc/tool/tool-webhooks.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/tool/tool-form.js A static/scripts/mvc/tool/tool-webhooks.js Log Message: ----------- add very basic plugin system (for tools) Commit: 6ea52120840ac0e89aa6b6cfbce414a81a1c42e7 https://github.com/galaxyproject/galaxy/commit/6ea52120840ac0e89aa6b6cfbce4… Author: anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-08-20 (Sat, 20 Aug 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-webhooks.js R config/plugins/webhooks/plugin2/config/plugin2.yml R config/plugins/webhooks/plugin2/static/style.css A config/plugins/webhooks/xkcd/config/xkcd.yml A config/plugins/webhooks/xkcd/static/script.js A config/plugins/webhooks/xkcd/static/styles.css M lib/galaxy/webhooks/__init__.py M static/maps/mvc/tool/tool-webhooks.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tool-webhooks.js Log Message: ----------- add first webhook Commit: 4cbc8a0c0ce1587a52418d91e2918ecdc07cf7ca https://github.com/galaxyproject/galaxy/commit/4cbc8a0c0ce1587a52418d91e291… Author: anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-08-20 (Sat, 20 Aug 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-webhooks.js A config/plugins/webhooks/phdcomics/config/phdcomics.yaml A config/plugins/webhooks/phdcomics/helper/__init__.py A config/plugins/webhooks/phdcomics/static/script.js A config/plugins/webhooks/phdcomics/static/styles.css R config/plugins/webhooks/plugin1/config/plugin1.yaml M config/plugins/webhooks/xkcd/static/script.js M config/plugins/webhooks/xkcd/static/styles.css M lib/galaxy/webapps/galaxy/api/webhooks.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webhooks/__init__.py M static/maps/mvc/tool/tool-webhooks.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tool-webhooks.js Log Message: ----------- add one more plugin Commit: d2b58c80993c42b3add50a0266d4b8f9ca269a6d https://github.com/galaxyproject/galaxy/commit/d2b58c80993c42b3add50a0266d4… Author: anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-08-20 (Sat, 20 Aug 2016) Changed paths: M client/galaxy/scripts/layout/masthead.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/tool/tool-form.js R client/galaxy/scripts/mvc/tool/tool-webhooks.js A client/galaxy/scripts/mvc/webhooks.js A config/plugins/webhooks/topbar_test/config/topbar_test.yml M lib/galaxy/webhooks/__init__.py M static/maps/layout/menu.js.map M static/maps/mvc/tool/tool-form.js.map A static/maps/mvc/webhooks.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/menu.js M static/scripts/mvc/tool/tool-form.js A static/scripts/mvc/webhooks.js Log Message: ----------- topbar webhooks testing Commit: 763aa1026dc6071cab0687859d5d764ac9f438ed https://github.com/galaxyproject/galaxy/commit/763aa1026dc6071cab0687859d5d… Author: anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-08-20 (Sat, 20 Aug 2016) Log Message: ----------- Merge branch 'feature/plugin-system' of github.com:bgruening/galaxy into feature/plugin-system Commit: bec41c889def0b012ec809d5e3e97fe2bc006492 https://github.com/galaxyproject/galaxy/commit/bec41c889def0b012ec809d5e3e9… Author: anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-08-20 (Sat, 20 Aug 2016) Changed paths: M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/scripts/mvc/webhooks.js A config/plugins/webhooks/masthead_test/config/masthead_test.yml M config/plugins/webhooks/phdcomics/config/phdcomics.yaml R config/plugins/webhooks/topbar_test/config/topbar_test.yml M config/plugins/webhooks/xkcd/config/xkcd.yml M lib/galaxy/webhooks/__init__.py M static/maps/layout/menu.js.map M static/maps/mvc/tool/tool-form.js.map M static/maps/mvc/webhooks.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/menu.js M static/scripts/mvc/tool/tool-form.js M static/scripts/mvc/webhooks.js Log Message: ----------- renamings and fixes Commit: ddc9c647b2d2d910bdcc31579d0d1c1f54b6bdab https://github.com/galaxyproject/galaxy/commit/ddc9c647b2d2d910bdcc31579d0d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-08-25 (Thu, 25 Aug 2016) Changed paths: M .ci/first_startup.sh A .ci/flake8_lint_include_list.txt A .ci/flake8_wrapper_imports.sh M .ci/py3_sources.txt M .gitignore M .travis.yml M CONTRIBUTORS.md M Makefile M README.rst R buildbot_setup.sh M client/README.md M client/bower.json A client/galaxy/scripts/layout/generic-nav-view.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/layout/scratchbook.js M client/galaxy/scripts/libs/backbone.js M client/galaxy/scripts/libs/bootstrap-tour.js M client/galaxy/scripts/libs/d3.js M client/galaxy/scripts/libs/jquery/jquery.js M client/galaxy/scripts/libs/jquery/jquery.migrate.js M client/galaxy/scripts/libs/raven.js M client/galaxy/scripts/libs/require.js R client/galaxy/scripts/libs/tracekit.js M client/galaxy/scripts/libs/underscore.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/dataset/dataset-model.js M client/galaxy/scripts/mvc/form/form-data.js M client/galaxy/scripts/mvc/form/form-input.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-section.js M client/galaxy/scripts/mvc/form/form-view.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-view-annotated.js M client/galaxy/scripts/mvc/history/history-view-edit-current.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/tool/tool-form.js R client/galaxy/scripts/mvc/tool/tool-template.js M client/galaxy/scripts/mvc/tool/tools.js M client/galaxy/scripts/mvc/ui/popup-menu.js M client/galaxy/scripts/mvc/ui/ui-buttons.js M client/galaxy/scripts/mvc/ui/ui-drilldown.js M client/galaxy/scripts/mvc/ui/ui-frames.js M client/galaxy/scripts/mvc/ui/ui-list.js M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/mvc/ui/ui-options.js M client/galaxy/scripts/mvc/ui/ui-portlet.js M client/galaxy/scripts/mvc/ui/ui-select-content.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/scripts/mvc/ui/ui-select.js M client/galaxy/scripts/mvc/ui/ui-tabs.js M client/galaxy/scripts/mvc/upload/default/default-view.js M client/galaxy/scripts/mvc/upload/upload-button.js M client/galaxy/scripts/mvc/upload/upload-view.js M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M client/galaxy/scripts/ui/hoverhighlight.js M client/galaxy/scripts/ui/loading-indicator.js M client/galaxy/scripts/ui/mode-button.js M client/galaxy/scripts/ui/pagination.js M client/galaxy/scripts/ui/peek-column-selector.js M client/galaxy/scripts/utils/localization.js M client/galaxy/scripts/utils/metrics-logger.js M client/galaxy/scripts/utils/utils.js M client/galaxy/scripts/viz/trackster/painters.js M client/galaxy/scripts/viz/trackster/tracks.js M client/galaxy/style/less/base.less M client/galaxy/style/less/frame.less M client/galaxy/style/less/library.less M client/galaxy/style/less/ui.less M client/grunt-tasks/install-libs.js M client/grunt-tasks/scripts.js M client/grunt-tasks/style.js M config/datatypes_conf.xml.sample M config/galaxy.ini.sample M config/job_conf.xml.sample_advanced M config/object_store_conf.xml.sample M config/plugins/interactive_environments/jupyter/config/jupyter.xml A config/plugins/interactive_environments/neo/config/allowed_images.yml.sample A config/plugins/interactive_environments/neo/config/neo.ini.sample A config/plugins/interactive_environments/neo/config/neo.xml A config/plugins/interactive_environments/neo/static/js/neo.js A config/plugins/interactive_environments/neo/templates/neo.mako M config/plugins/tours/core.galaxy_ui.yaml M config/plugins/tours/core.scratchbook.yaml M config/plugins/visualizations/charts/static/app.css M config/plugins/visualizations/charts/static/app.js M config/plugins/visualizations/charts/static/charts/forms/default.js M config/plugins/visualizations/charts/static/charts/jqplot/common/config.js M config/plugins/visualizations/charts/static/charts/nvd3/common/config.js M config/plugins/visualizations/charts/static/charts/nvd3/common/wrapper.js M config/plugins/visualizations/charts/static/charts/nvd3/pie/config.js M config/plugins/visualizations/charts/static/library/datasets.js M config/plugins/visualizations/charts/static/library/jobs.js M config/plugins/visualizations/charts/static/library/storage.js R 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doc/source/admin/chat-4.png A doc/source/admin/chat.rst A doc/source/admin/communication_server.png A doc/source/admin/communication_server_rooms.png A doc/source/admin/conda_faq.rst A doc/source/admin/grt.rst M doc/source/admin/index.rst M doc/source/admin/interactive_environments.rst M doc/source/dev/faq.rst M doc/source/dev/index.rst A doc/source/dev/interactive_environments.rst M doc/source/lib/galaxy.objectstore.rst A doc/source/releases/16.07.rst M doc/source/releases/16.07_announce.rst A doc/source/releases/16.10_announce.rst M lib/galaxy/app.py M lib/galaxy/auth/providers/ldap_ad.py M lib/galaxy/config.py M lib/galaxy/dataset_collections/structure.py M lib/galaxy/dataset_collections/subcollections.py M lib/galaxy/datatypes/assembly.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/converters/bed_to_gff_converter.py M lib/galaxy/datatypes/converters/fastq_to_fqtoc.py M lib/galaxy/datatypes/converters/fastqsolexa_to_fasta_converter.py M lib/galaxy/datatypes/converters/fastqsolexa_to_qual_converter.py M lib/galaxy/datatypes/converters/gff_to_bed_converter.py M lib/galaxy/datatypes/converters/interval_to_bed_converter.py M lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.py M lib/galaxy/datatypes/converters/interval_to_coverage.py M lib/galaxy/datatypes/converters/lped_to_fped_converter.py M lib/galaxy/datatypes/converters/lped_to_pbed_converter.py M lib/galaxy/datatypes/converters/maf_to_fasta_converter.py M lib/galaxy/datatypes/converters/maf_to_interval_converter.py M lib/galaxy/datatypes/converters/pbed_ldreduced_converter.py M lib/galaxy/datatypes/converters/pbed_to_lped_converter.py M lib/galaxy/datatypes/converters/picard_interval_list_to_bed6_converter.py A lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.py A lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.xml M lib/galaxy/datatypes/converters/wiggle_to_simple_converter.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/dataproviders/column.py M lib/galaxy/datatypes/dataproviders/line.py M lib/galaxy/datatypes/genetics.py M lib/galaxy/datatypes/images.py M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/molecules.py A lib/galaxy/datatypes/mothur.py M lib/galaxy/datatypes/msa.py A lib/galaxy/datatypes/neo4j.py M lib/galaxy/datatypes/ngsindex.py M lib/galaxy/datatypes/proteomics.py M lib/galaxy/datatypes/qualityscore.py M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/set_metadata_tool.xml M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/tabular.py A lib/galaxy/datatypes/test/NuBBE_1_obabel_3D.pdbqt A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.axes A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.filter A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.freq A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.lower.dist A 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tools/data_source/microbial_import.py M tools/data_source/microbial_import_code.py M tools/data_source/upload.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.xml M tools/filters/axt_to_fasta.xml M tools/filters/axt_to_lav.py M tools/filters/axt_to_lav.xml M tools/filters/bed2gff.xml M tools/filters/bed_to_bigbed.xml M tools/filters/bed_to_gff_converter.py M tools/filters/gff/extract_GFF_Features.py M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff2bed.xml M tools/filters/gff_to_bed_converter.py M tools/filters/gtf2bedgraph.xml M tools/filters/gtf_to_bedgraph_converter.py M tools/filters/join.py M tools/filters/joinWrapper.py M tools/filters/lav_to_bed.py M tools/filters/mergeCols.py M tools/filters/sff_extract.py M tools/filters/sorter.py M tools/filters/trimmer.xml M tools/filters/wiggle_to_simple.py M tools/genomespace/genomespace_exporter.py M tools/genomespace/genomespace_file_browser.py M tools/maf/interval_maf_to_merged_fasta.py M tools/maf/maf_split_by_species.py M tools/maf/maf_thread_for_species.py M tools/maf/maf_to_fasta_concat.py M tools/maf/maf_to_fasta_multiple_sets.py M tools/metag_tools/blat_wrapper.py M tools/metag_tools/shrimp_color_wrapper.py M tools/metag_tools/shrimp_wrapper.py M tools/next_gen_conversion/fastq_conversions.py M tools/next_gen_conversion/fastq_gen_conv.py M tools/next_gen_conversion/solid_to_fastq.py M tools/ngs_simulation/ngs_simulation.py M tools/phenotype_association/pagetag.py M tools/phenotype_association/senatag.py M tools/solid_tools/maq_cs_wrapper.py M tools/solid_tools/solid_qual_stats.py M tools/sr_assembly/velveth_wrapper.py M tools/sr_mapping/bfast_wrapper.py M tools/stats/aggregate_scores_in_intervals.py M tools/stats/filtering.py M tools/stats/filtering.xml M tools/stats/grouping.py M tools/stats/gsummary.py M tools/stats/gsummary.xml M tox.ini Log Message: ----------- Merge branch 'release_16.07' Commit: 9ff882944ee1fd78b6244dad5893ac7390eb76fa https://github.com/galaxyproject/galaxy/commit/9ff882944ee1fd78b6244dad5893… Author: anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-08-29 (Mon, 29 Aug 2016) Changed paths: M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/scripts/mvc/webhooks.js M config/plugins/webhooks/masthead_test/config/masthead_test.yml A config/plugins/webhooks/masthead_test/static/script.js M config/plugins/webhooks/phdcomics/helper/__init__.py M lib/galaxy/webapps/galaxy/api/webhooks.py M lib/galaxy/webhooks/__init__.py M static/maps/layout/menu.js.map M static/maps/mvc/tool/tool-form.js.map M static/maps/mvc/webhooks.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/menu.js M static/scripts/mvc/tool/tool-form.js M static/scripts/mvc/webhooks.js Log Message: ----------- - unify webhooks entry point - simlify webhooks code (on load) - improve code readability - clean up Commit: d2ec87548a22273a2e0d94bbe1b415fbf6352b36 https://github.com/galaxyproject/galaxy/commit/d2ec87548a22273a2e0d94bbe1b4… Author: anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-08-30 (Tue, 30 Aug 2016) Changed paths: M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/scripts/mvc/webhooks.js M config/plugins/webhooks/masthead_test/config/masthead_test.yml M config/plugins/webhooks/phdcomics/config/phdcomics.yaml M config/plugins/webhooks/xkcd/config/xkcd.yml M lib/galaxy/webapps/galaxy/api/webhooks.py M static/maps/mvc/tool/tool-form.js.map M static/maps/mvc/webhooks.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tool-form.js M static/scripts/mvc/webhooks.js M templates/webapps/galaxy/workflow/run_complete.mako Log Message: ----------- - add new entry point (Workflow) - temporarily hide masthead webhook (due to instability) Commit: e320b1aaa70aea38b7108ca6ae372b1d06fd30bc https://github.com/galaxyproject/galaxy/commit/e320b1aaa70aea38b7108ca6ae37… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-09-07 (Wed, 07 Sep 2016) Changed paths: M config/galaxy.ini.sample M doc/source/releases/16.07.rst M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/watcher.py Log Message: ----------- Merge branch 'release_16.07' Commit: b46d55e30fd3f8a2832130dd3f917082f442836f https://github.com/galaxyproject/galaxy/commit/b46d55e30fd3f8a2832130dd3f91… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-10-04 (Tue, 04 Oct 2016) Changed paths: M client/galaxy/scripts/apps/history-panel.js M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/mvc/webhooks.js A config/plugins/webhooks/history_test1/config/history_test1.yml A config/plugins/webhooks/history_test2/config/history_test2.yml M lib/galaxy/webapps/galaxy/api/webhooks.py M lib/galaxy/webapps/galaxy/buildapp.py M static/maps/mvc/history/options-menu.js.map M static/maps/mvc/webhooks.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/history/options-menu.js M static/scripts/mvc/webhooks.js Log Message: ----------- add new entry point for History Panel menu Commit: b98e49f2bc88e62b4835aa8d23f8d3386f81f66a https://github.com/galaxyproject/galaxy/commit/b98e49f2bc88e62b4835aa8d23f8… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-10-05 (Wed, 05 Oct 2016) Changed paths: M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/scripts/mvc/webhooks.js M config/plugins/webhooks/history_test1/config/history_test1.yml M config/plugins/webhooks/history_test2/config/history_test2.yml M config/plugins/webhooks/masthead_test/config/masthead_test.yml M config/plugins/webhooks/phdcomics/config/phdcomics.yaml M config/plugins/webhooks/xkcd/config/xkcd.yml M lib/galaxy/webhooks/__init__.py M static/maps/layout/menu.js.map M static/maps/mvc/history/options-menu.js.map M static/maps/mvc/tool/tool-form.js.map M static/maps/mvc/webhooks.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/menu.js M static/scripts/mvc/history/options-menu.js M static/scripts/mvc/tool/tool-form.js M static/scripts/mvc/webhooks.js Log Message: ----------- bug fixes and improvements Commit: 58e0d6e1a61b06c444b2086d7725e1100d49441a https://github.com/galaxyproject/galaxy/commit/58e0d6e1a61b06c444b2086d7725… Author: anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-10-05 (Wed, 05 Oct 2016) Changed paths: M config/galaxy.ini.sample A config/plugins/plugin1.xml A config/plugins/plugin2.xml A config/plugins/webhooks/plugin1/config/plugin1.yaml A config/plugins/webhooks/plugin2/config/plugin2.yml M lib/galaxy/app.py M lib/galaxy/config.py A lib/galaxy/webapps/galaxy/api/webhooks.py A lib/galaxy/webhooks/__init__.py Log Message: ----------- add Webhooks draft Commit: cbbcf3d625a1625e89bbe7c59997d3658d23ea55 https://github.com/galaxyproject/galaxy/commit/cbbcf3d625a1625e89bbe7c59997… Author: anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-10-05 (Wed, 05 Oct 2016) Changed paths: R config/plugins/plugin1.xml R config/plugins/plugin2.xml Log Message: ----------- remove extra files Commit: cf1fde577e9b918bacfe2d78d9f2b632a81ee20b https://github.com/galaxyproject/galaxy/commit/cf1fde577e9b918bacfe2d78d9f2… Author: anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-10-05 (Wed, 05 Oct 2016) Changed paths: A client/galaxy/scripts/mvc/tool/tool-webhooks.js A client/galaxy/scripts/mvc/webhooks.js M config/plugins/webhooks/plugin2/config/plugin2.yml A config/plugins/webhooks/plugin2/static/style.css M lib/galaxy/webapps/galaxy/api/webhooks.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webhooks/__init__.py A static/maps/mvc/tool/tool-webhooks.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map A static/scripts/mvc/tool/tool-webhooks.js Log Message: ----------- add very basic plugin system (for tools) Commit: ac5a0f5a6adea3493549d69627d1d2223b97c09e https://github.com/galaxyproject/galaxy/commit/ac5a0f5a6adea3493549d69627d1… Author: anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-10-05 (Wed, 05 Oct 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-webhooks.js R config/plugins/webhooks/plugin2/config/plugin2.yml R config/plugins/webhooks/plugin2/static/style.css A config/plugins/webhooks/xkcd/config/xkcd.yml A config/plugins/webhooks/xkcd/static/script.js A config/plugins/webhooks/xkcd/static/styles.css M lib/galaxy/webhooks/__init__.py M static/maps/mvc/tool/tool-webhooks.js.map M static/scripts/mvc/tool/tool-webhooks.js Log Message: ----------- add first webhook Commit: fecf493ecde3590e9da4629a063d5885dde99502 https://github.com/galaxyproject/galaxy/commit/fecf493ecde3590e9da4629a063d… Author: anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-10-05 (Wed, 05 Oct 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-webhooks.js A config/plugins/webhooks/phdcomics/config/phdcomics.yaml A config/plugins/webhooks/phdcomics/helper/__init__.py A config/plugins/webhooks/phdcomics/static/script.js A config/plugins/webhooks/phdcomics/static/styles.css R config/plugins/webhooks/plugin1/config/plugin1.yaml M config/plugins/webhooks/xkcd/static/script.js M config/plugins/webhooks/xkcd/static/styles.css M lib/galaxy/webapps/galaxy/api/webhooks.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webhooks/__init__.py M static/maps/mvc/tool/tool-webhooks.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tool-webhooks.js Log Message: ----------- add one more plugin Commit: 239731d45aa5019eecc4d65a771102bb38a79851 https://github.com/galaxyproject/galaxy/commit/239731d45aa5019eecc4d65a7711… Author: anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-10-05 (Wed, 05 Oct 2016) Changed paths: M client/galaxy/scripts/layout/masthead.js R client/galaxy/scripts/mvc/tool/tool-webhooks.js A config/plugins/webhooks/topbar_test/config/topbar_test.yml M lib/galaxy/webhooks/__init__.py A static/maps/mvc/webhooks.js.map A static/scripts/mvc/webhooks.js Log Message: ----------- topbar webhooks testing Commit: d35d99727b76ab71173ad7cccca1a4d66aa9ce70 https://github.com/galaxyproject/galaxy/commit/d35d99727b76ab71173ad7cccca1… Author: anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-10-05 (Wed, 05 Oct 2016) Changed paths: A config/plugins/plugin1.xml A config/plugins/plugin2.xml A config/plugins/webhooks/plugin1/config/plugin1.yaml A config/plugins/webhooks/plugin2/config/plugin2.yml Log Message: ----------- add Webhooks draft Commit: 1f7a4135318f0d6940e2a65a2b9f7ab29cdb0a41 https://github.com/galaxyproject/galaxy/commit/1f7a4135318f0d6940e2a65a2b9f… Author: anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-10-05 (Wed, 05 Oct 2016) Changed paths: R config/plugins/plugin1.xml R config/plugins/plugin2.xml Log Message: ----------- remove extra files Commit: adc92fd31740ebe4fe66bfec32fe14ef5b736c72 https://github.com/galaxyproject/galaxy/commit/adc92fd31740ebe4fe66bfec32fe… Author: anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-10-05 (Wed, 05 Oct 2016) Changed paths: A client/galaxy/scripts/mvc/tool/tool-webhooks.js M config/plugins/webhooks/plugin2/config/plugin2.yml A config/plugins/webhooks/plugin2/static/style.css Log Message: ----------- add very basic plugin system (for tools) Commit: d490415b0500dcbadca9a1f959cf0b996abe326e https://github.com/galaxyproject/galaxy/commit/d490415b0500dcbadca9a1f959cf… Author: anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-10-05 (Wed, 05 Oct 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-webhooks.js R config/plugins/webhooks/plugin2/config/plugin2.yml R config/plugins/webhooks/plugin2/static/style.css Log Message: ----------- add first webhook Commit: 86af65a7d6889086e1f16ef3ef4fcfa77ba3c88e https://github.com/galaxyproject/galaxy/commit/86af65a7d6889086e1f16ef3ef4f… Author: anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-10-05 (Wed, 05 Oct 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-webhooks.js R config/plugins/webhooks/plugin1/config/plugin1.yaml Log Message: ----------- add one more plugin Commit: 4635ff4575ea1a47fac8da2bbb50092cc3352c3f https://github.com/galaxyproject/galaxy/commit/4635ff4575ea1a47fac8da2bbb50… Author: anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-10-05 (Wed, 05 Oct 2016) Changed paths: R client/galaxy/scripts/mvc/tool/tool-webhooks.js Log Message: ----------- topbar webhooks testing Commit: 482e0b2bffe992c329f22e4f9b50a34cfd835518 https://github.com/galaxyproject/galaxy/commit/482e0b2bffe992c329f22e4f9b50… Author: anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-10-05 (Wed, 05 Oct 2016) Changed paths: A config/plugins/webhooks/masthead_test/config/masthead_test.yml M config/plugins/webhooks/phdcomics/config/phdcomics.yaml R config/plugins/webhooks/topbar_test/config/topbar_test.yml M config/plugins/webhooks/xkcd/config/xkcd.yml M lib/galaxy/webhooks/__init__.py M static/maps/mvc/webhooks.js.map M static/scripts/mvc/webhooks.js Log Message: ----------- renamings and fixes Commit: 6e534213e12820f69bb849b74aa8924787d9023e https://github.com/galaxyproject/galaxy/commit/6e534213e12820f69bb849b74aa8… Author: anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-10-05 (Wed, 05 Oct 2016) Changed paths: M config/plugins/webhooks/masthead_test/config/masthead_test.yml A config/plugins/webhooks/masthead_test/static/script.js M config/plugins/webhooks/phdcomics/helper/__init__.py M lib/galaxy/webapps/galaxy/api/webhooks.py M lib/galaxy/webhooks/__init__.py M static/maps/mvc/webhooks.js.map M static/scripts/mvc/webhooks.js Log Message: ----------- - unify webhooks entry point - simlify webhooks code (on load) - improve code readability - clean up Commit: fce44d257b9d05e68ca4323036e7e509d329e789 https://github.com/galaxyproject/galaxy/commit/fce44d257b9d05e68ca4323036e7… Author: anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-10-05 (Wed, 05 Oct 2016) Changed paths: M config/plugins/webhooks/masthead_test/config/masthead_test.yml M config/plugins/webhooks/phdcomics/config/phdcomics.yaml M config/plugins/webhooks/xkcd/config/xkcd.yml M lib/galaxy/webapps/galaxy/api/webhooks.py M static/maps/mvc/webhooks.js.map M static/scripts/mvc/webhooks.js M templates/webapps/galaxy/workflow/run_complete.mako Log Message: ----------- - add new entry point (Workflow) - temporarily hide masthead webhook (due to instability) Commit: 3c3819900fd293de1532a4c0a15685927a8fd2dd https://github.com/galaxyproject/galaxy/commit/3c3819900fd293de1532a4c0a156… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-10-05 (Wed, 05 Oct 2016) Changed paths: M client/galaxy/scripts/apps/history-panel.js M client/galaxy/scripts/mvc/history/options-menu.js A config/plugins/webhooks/history_test1/config/history_test1.yml A config/plugins/webhooks/history_test2/config/history_test2.yml M lib/galaxy/webapps/galaxy/api/webhooks.py M lib/galaxy/webapps/galaxy/buildapp.py M static/maps/mvc/history/options-menu.js.map M static/maps/mvc/webhooks.js.map M static/scripts/mvc/history/options-menu.js M static/scripts/mvc/webhooks.js Log Message: ----------- add new entry point for History Panel menu Commit: 6f109176d16a162b9f5a132927eef13e096bdce4 https://github.com/galaxyproject/galaxy/commit/6f109176d16a162b9f5a132927ee… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-10-05 (Wed, 05 Oct 2016) Changed paths: M client/galaxy/scripts/mvc/history/options-menu.js M config/plugins/webhooks/history_test1/config/history_test1.yml M config/plugins/webhooks/history_test2/config/history_test2.yml M config/plugins/webhooks/masthead_test/config/masthead_test.yml M config/plugins/webhooks/phdcomics/config/phdcomics.yaml M config/plugins/webhooks/xkcd/config/xkcd.yml M lib/galaxy/webhooks/__init__.py M static/maps/mvc/history/options-menu.js.map M static/maps/mvc/webhooks.js.map M static/scripts/mvc/history/options-menu.js M static/scripts/mvc/webhooks.js Log Message: ----------- bug fixes and improvements Commit: 31674ef5b789b9c9557bb78efaa5d13961744c1d https://github.com/galaxyproject/galaxy/commit/31674ef5b789b9c9557bb78efaa5… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-10-05 (Wed, 05 Oct 2016) Changed paths: M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/tool/tool-form.js M static/maps/layout/menu.js.map M static/maps/mvc/tool/tool-form.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/menu.js M static/scripts/mvc/tool/tool-form.js Log Message: ----------- Merge branch 'feature/plugin-system' of github.com:bgruening/galaxy into feature/plugin-system # Conflicts: # client/galaxy/scripts/layout/menu.js # client/galaxy/scripts/mvc/tool/tool-form.js # static/maps/layout/menu.js.map # static/maps/mvc/tool/tool-form.js.map # static/scripts/bundled/analysis.bundled.js # static/scripts/bundled/analysis.bundled.js.map # static/scripts/bundled/libs.bundled.js # static/scripts/bundled/libs.bundled.js.map # static/scripts/layout/menu.js # static/scripts/mvc/tool/tool-form.js Commit: 2bf0549a371a1a3f683d375233b9b3f5b1e37944 https://github.com/galaxyproject/galaxy/commit/2bf0549a371a1a3f683d375233b9… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-10-05 (Wed, 05 Oct 2016) Changed paths: M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/tool/tool-form.js M config/plugins/webhooks/xkcd/config/xkcd.yml M static/maps/layout/menu.js.map M static/maps/mvc/tool/tool-form.js.map M static/maps/mvc/webhooks.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/menu.js M static/scripts/mvc/tool/tool-form.js Log Message: ----------- fix bugs after previous commit Commit: d821c2745c014bc0e2e2cc31eac8d70bb576ea7e https://github.com/galaxyproject/galaxy/commit/d821c2745c014bc0e2e2cc31eac8… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-10-09 (Sun, 09 Oct 2016) Changed paths: M client/galaxy/scripts/mvc/webhooks.js M config/plugins/webhooks/masthead_test/config/masthead_test.yml R config/plugins/webhooks/masthead_test/static/script.js M config/plugins/webhooks/phdcomics/helper/__init__.py M lib/galaxy/webapps/galaxy/api/webhooks.py M static/maps/mvc/webhooks.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/webhooks.js Log Message: ----------- pass trans object into the helper function Commit: 1a80a0df7f371347976f0b9fb3ff1cb651d4170b https://github.com/galaxyproject/galaxy/commit/1a80a0df7f371347976f0b9fb3ff… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-10-09 (Sun, 09 Oct 2016) Changed paths: A doc/source/admin/webhooks.rst Log Message: ----------- Add initial docs Commit: 5361d7c03d23ed4fe4701b2e126f56114673cf7f https://github.com/galaxyproject/galaxy/commit/5361d7c03d23ed4fe4701b2e126f… Author: anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-10-09 (Sun, 09 Oct 2016) Changed paths: M config/galaxy.ini.sample A config/plugins/plugin1.xml A config/plugins/plugin2.xml A config/plugins/webhooks/plugin1/config/plugin1.yaml A config/plugins/webhooks/plugin2/config/plugin2.yml M lib/galaxy/app.py M lib/galaxy/config.py A lib/galaxy/webapps/galaxy/api/webhooks.py A lib/galaxy/webhooks/__init__.py Log Message: ----------- add Webhooks draft Commit: a34a1201fc72abff092ccb8c0366b07dfde31987 https://github.com/galaxyproject/galaxy/commit/a34a1201fc72abff092ccb8c0366… Author: anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-10-09 (Sun, 09 Oct 2016) Changed paths: R config/plugins/plugin1.xml R config/plugins/plugin2.xml Log Message: ----------- remove extra files Commit: 6e66fbeca8741748aa823e34432bd62527096491 https://github.com/galaxyproject/galaxy/commit/6e66fbeca8741748aa823e34432b… Author: anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-10-09 (Sun, 09 Oct 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form.js A client/galaxy/scripts/mvc/tool/tool-webhooks.js M config/plugins/webhooks/plugin2/config/plugin2.yml A config/plugins/webhooks/plugin2/static/style.css M lib/galaxy/webapps/galaxy/api/webhooks.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webhooks/__init__.py A static/maps/mvc/tool/tool-webhooks.js.map A static/scripts/mvc/tool/tool-webhooks.js Log Message: ----------- add very basic plugin system (for tools) Commit: eb46e70206ba43a5e191153df74aa47dc441ed19 https://github.com/galaxyproject/galaxy/commit/eb46e70206ba43a5e191153df74a… Author: anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-10-09 (Sun, 09 Oct 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-webhooks.js R config/plugins/webhooks/plugin2/config/plugin2.yml R config/plugins/webhooks/plugin2/static/style.css A config/plugins/webhooks/xkcd/config/xkcd.yml A config/plugins/webhooks/xkcd/static/script.js A config/plugins/webhooks/xkcd/static/styles.css M lib/galaxy/webhooks/__init__.py M static/maps/mvc/tool/tool-webhooks.js.map M static/scripts/mvc/tool/tool-webhooks.js Log Message: ----------- add first webhook Commit: 40bcaaecf531920275d8f9f82d5e57bac60c43ae https://github.com/galaxyproject/galaxy/commit/40bcaaecf531920275d8f9f82d5e… Author: anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-10-09 (Sun, 09 Oct 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-webhooks.js A config/plugins/webhooks/phdcomics/config/phdcomics.yaml A config/plugins/webhooks/phdcomics/helper/__init__.py A config/plugins/webhooks/phdcomics/static/script.js A config/plugins/webhooks/phdcomics/static/styles.css R config/plugins/webhooks/plugin1/config/plugin1.yaml M config/plugins/webhooks/xkcd/static/script.js M config/plugins/webhooks/xkcd/static/styles.css M lib/galaxy/webapps/galaxy/api/webhooks.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webhooks/__init__.py M static/maps/mvc/tool/tool-webhooks.js.map M static/scripts/mvc/tool/tool-webhooks.js Log Message: ----------- add one more plugin Commit: bf4a1aa1a87050e030ead0e5ff8922bcb7338d98 https://github.com/galaxyproject/galaxy/commit/bf4a1aa1a87050e030ead0e5ff89… Author: anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-10-09 (Sun, 09 Oct 2016) Changed paths: M client/galaxy/scripts/layout/masthead.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/tool/tool-form.js R client/galaxy/scripts/mvc/tool/tool-webhooks.js A client/galaxy/scripts/mvc/webhooks.js A config/plugins/webhooks/topbar_test/config/topbar_test.yml M lib/galaxy/webhooks/__init__.py A static/maps/mvc/webhooks.js.map A static/scripts/mvc/webhooks.js Log Message: ----------- topbar webhooks testing Commit: 17440d7b11b5013e52033efe4668115a466115b0 https://github.com/galaxyproject/galaxy/commit/17440d7b11b5013e52033efe4668… Author: anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-10-09 (Sun, 09 Oct 2016) Changed paths: A config/plugins/plugin1.xml A config/plugins/plugin2.xml A config/plugins/webhooks/plugin1/config/plugin1.yaml A config/plugins/webhooks/plugin2/config/plugin2.yml M lib/galaxy/webapps/galaxy/api/webhooks.py M lib/galaxy/webhooks/__init__.py Log Message: ----------- add Webhooks draft Commit: 143a740dc38fec9f92211d26364cb0b40235a24e https://github.com/galaxyproject/galaxy/commit/143a740dc38fec9f92211d26364c… Author: anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-10-09 (Sun, 09 Oct 2016) Changed paths: R config/plugins/plugin1.xml R config/plugins/plugin2.xml Log Message: ----------- remove extra files Commit: 117c5263acdfb8853cc6771810ef87c755b006ce https://github.com/galaxyproject/galaxy/commit/117c5263acdfb8853cc6771810ef… Author: anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-10-09 (Sun, 09 Oct 2016) Changed paths: A client/galaxy/scripts/mvc/tool/tool-webhooks.js M config/plugins/webhooks/plugin2/config/plugin2.yml A config/plugins/webhooks/plugin2/static/style.css M lib/galaxy/webhooks/__init__.py Log Message: ----------- add very basic plugin system (for tools) Commit: ed2282d60b3f41c653e61be13d24ace6e83215ca https://github.com/galaxyproject/galaxy/commit/ed2282d60b3f41c653e61be13d24… Author: anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-10-09 (Sun, 09 Oct 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-webhooks.js R config/plugins/webhooks/plugin2/config/plugin2.yml R config/plugins/webhooks/plugin2/static/style.css M lib/galaxy/webhooks/__init__.py Log Message: ----------- add first webhook Commit: 29129463a0be1778c69fce6e783dd75da05d53c0 https://github.com/galaxyproject/galaxy/commit/29129463a0be1778c69fce6e783d… Author: anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-10-09 (Sun, 09 Oct 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-webhooks.js R config/plugins/webhooks/plugin1/config/plugin1.yaml Log Message: ----------- add one more plugin Commit: 411674521cf1d9d3c5479ae334fbead783d737fe https://github.com/galaxyproject/galaxy/commit/411674521cf1d9d3c5479ae334fb… Author: anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-10-09 (Sun, 09 Oct 2016) Changed paths: R client/galaxy/scripts/mvc/tool/tool-webhooks.js Log Message: ----------- topbar webhooks testing Commit: b215de947c007dfc84ae4325d1a6b0be846986b5 https://github.com/galaxyproject/galaxy/commit/b215de947c007dfc84ae4325d1a6… Author: anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-10-09 (Sun, 09 Oct 2016) Changed paths: M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/scripts/mvc/webhooks.js A config/plugins/webhooks/masthead_test/config/masthead_test.yml M config/plugins/webhooks/phdcomics/config/phdcomics.yaml R config/plugins/webhooks/topbar_test/config/topbar_test.yml M config/plugins/webhooks/xkcd/config/xkcd.yml M lib/galaxy/webhooks/__init__.py M static/maps/mvc/webhooks.js.map M static/scripts/mvc/webhooks.js Log Message: ----------- renamings and fixes Commit: bb9dc0560ade3f44037a4d03a24651b91af36dbd https://github.com/galaxyproject/galaxy/commit/bb9dc0560ade3f44037a4d03a246… Author: anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-10-09 (Sun, 09 Oct 2016) Changed paths: M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/scripts/mvc/webhooks.js M config/plugins/webhooks/masthead_test/config/masthead_test.yml A config/plugins/webhooks/masthead_test/static/script.js M config/plugins/webhooks/phdcomics/helper/__init__.py M lib/galaxy/webapps/galaxy/api/webhooks.py M static/maps/mvc/webhooks.js.map M static/scripts/mvc/webhooks.js Log Message: ----------- - unify webhooks entry point - simlify webhooks code (on load) - improve code readability - clean up Commit: e95392b4b62b5ff803390287d0eac4f385504ef1 https://github.com/galaxyproject/galaxy/commit/e95392b4b62b5ff803390287d0ea… Author: anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-10-09 (Sun, 09 Oct 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/scripts/mvc/webhooks.js M config/plugins/webhooks/masthead_test/config/masthead_test.yml M config/plugins/webhooks/phdcomics/config/phdcomics.yaml M config/plugins/webhooks/xkcd/config/xkcd.yml M lib/galaxy/webapps/galaxy/api/webhooks.py M static/maps/mvc/webhooks.js.map M static/scripts/mvc/webhooks.js Log Message: ----------- - add new entry point (Workflow) - temporarily hide masthead webhook (due to instability) Commit: f3b1232bdb46e9ccb4f27b3a1fc668d987d650cc https://github.com/galaxyproject/galaxy/commit/f3b1232bdb46e9ccb4f27b3a1fc6… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-10-09 (Sun, 09 Oct 2016) Changed paths: M client/galaxy/scripts/apps/history-panel.js M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/mvc/webhooks.js A config/plugins/webhooks/history_test1/config/history_test1.yml A config/plugins/webhooks/history_test2/config/history_test2.yml M lib/galaxy/webapps/galaxy/api/webhooks.py M lib/galaxy/webapps/galaxy/buildapp.py M static/maps/mvc/webhooks.js.map M static/scripts/mvc/webhooks.js Log Message: ----------- add new entry point for History Panel menu Commit: 578bdf679f0575e98922ddea004248de9b8b965c https://github.com/galaxyproject/galaxy/commit/578bdf679f0575e98922ddea0042… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-10-09 (Sun, 09 Oct 2016) Changed paths: M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/scripts/mvc/webhooks.js M config/plugins/webhooks/history_test1/config/history_test1.yml M config/plugins/webhooks/history_test2/config/history_test2.yml M config/plugins/webhooks/masthead_test/config/masthead_test.yml M config/plugins/webhooks/phdcomics/config/phdcomics.yaml M config/plugins/webhooks/xkcd/config/xkcd.yml M lib/galaxy/webhooks/__init__.py M static/maps/mvc/webhooks.js.map M static/scripts/mvc/webhooks.js Log Message: ----------- bug fixes and improvements Commit: 42adc9c7dfa1485162b78742f5ac3a7e8935902f https://github.com/galaxyproject/galaxy/commit/42adc9c7dfa1485162b78742f5ac… Author: anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-10-09 (Sun, 09 Oct 2016) Changed paths: A config/plugins/plugin1.xml A config/plugins/plugin2.xml A config/plugins/webhooks/plugin1/config/plugin1.yaml A config/plugins/webhooks/plugin2/config/plugin2.yml Log Message: ----------- add Webhooks draft Commit: 6bc57ec0209f22970c4303870ba48cfea528e0ff https://github.com/galaxyproject/galaxy/commit/6bc57ec0209f22970c4303870ba4… Author: anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-10-09 (Sun, 09 Oct 2016) Changed paths: R config/plugins/plugin1.xml R config/plugins/plugin2.xml Log Message: ----------- remove extra files Commit: ca769ab848209be8e4e48a6b28c13ecf52744e0f https://github.com/galaxyproject/galaxy/commit/ca769ab848209be8e4e48a6b28c1… Author: anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-10-09 (Sun, 09 Oct 2016) Changed paths: A client/galaxy/scripts/mvc/tool/tool-webhooks.js M config/plugins/webhooks/plugin2/config/plugin2.yml A config/plugins/webhooks/plugin2/static/style.css Log Message: ----------- add very basic plugin system (for tools) Commit: 1a8a82370bcfd157f1d82ee6f6634bfcbcfb62af https://github.com/galaxyproject/galaxy/commit/1a8a82370bcfd157f1d82ee6f663… Author: anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-10-09 (Sun, 09 Oct 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-webhooks.js R config/plugins/webhooks/plugin2/config/plugin2.yml R config/plugins/webhooks/plugin2/static/style.css M config/plugins/webhooks/xkcd/config/xkcd.yml Log Message: ----------- add first webhook Commit: 454a88b45174cfddae5ad79c31d92edffb07cabe https://github.com/galaxyproject/galaxy/commit/454a88b45174cfddae5ad79c31d9… Author: anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-10-09 (Sun, 09 Oct 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-webhooks.js R config/plugins/webhooks/plugin1/config/plugin1.yaml Log Message: ----------- add one more plugin Commit: 53f56c3426714b3531dd1c49ecca431f73b77de9 https://github.com/galaxyproject/galaxy/commit/53f56c3426714b3531dd1c49ecca… Author: anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-10-09 (Sun, 09 Oct 2016) Changed paths: R client/galaxy/scripts/mvc/tool/tool-webhooks.js A config/plugins/webhooks/topbar_test/config/topbar_test.yml M lib/galaxy/webhooks/__init__.py Log Message: ----------- topbar webhooks testing Commit: c7f35c41d72a6131bfd0a4a7b3525518ed29d78a https://github.com/galaxyproject/galaxy/commit/c7f35c41d72a6131bfd0a4a7b352… Author: anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-10-09 (Sun, 09 Oct 2016) Changed paths: A config/plugins/plugin1.xml A config/plugins/plugin2.xml A config/plugins/webhooks/plugin1/config/plugin1.yaml A config/plugins/webhooks/plugin2/config/plugin2.yml Log Message: ----------- add Webhooks draft Commit: a73d00fc04695b1f27a3cdf6091d352ee61f8f45 https://github.com/galaxyproject/galaxy/commit/a73d00fc04695b1f27a3cdf6091d… Author: anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-10-09 (Sun, 09 Oct 2016) Changed paths: R config/plugins/plugin1.xml R config/plugins/plugin2.xml Log Message: ----------- remove extra files Commit: 2b2be226ee9425742e0a629459e126b0c90e5e86 https://github.com/galaxyproject/galaxy/commit/2b2be226ee9425742e0a629459e1… Author: anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-10-09 (Sun, 09 Oct 2016) Changed paths: A client/galaxy/scripts/mvc/tool/tool-webhooks.js M config/plugins/webhooks/plugin2/config/plugin2.yml A config/plugins/webhooks/plugin2/static/style.css Log Message: ----------- add very basic plugin system (for tools) Commit: 211491fdf31a814590250edd4447916a5213120b https://github.com/galaxyproject/galaxy/commit/211491fdf31a814590250edd4447… Author: anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-10-09 (Sun, 09 Oct 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-webhooks.js R config/plugins/webhooks/plugin2/config/plugin2.yml R config/plugins/webhooks/plugin2/static/style.css Log Message: ----------- add first webhook Commit: 060df24ff5b329c37103f9c90caf65c4889c964d https://github.com/galaxyproject/galaxy/commit/060df24ff5b329c37103f9c90caf… Author: anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-10-09 (Sun, 09 Oct 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-webhooks.js R config/plugins/webhooks/plugin1/config/plugin1.yaml Log Message: ----------- add one more plugin Commit: 00cf0cb85ec2cca9091de22fcaa6579d611530f1 https://github.com/galaxyproject/galaxy/commit/00cf0cb85ec2cca9091de22fcaa6… Author: anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-10-09 (Sun, 09 Oct 2016) Changed paths: R client/galaxy/scripts/mvc/tool/tool-webhooks.js Log Message: ----------- topbar webhooks testing Commit: 27e0302ea3926e0a3ce6955317f6d1f38bc6f8b4 https://github.com/galaxyproject/galaxy/commit/27e0302ea3926e0a3ce6955317f6… Author: anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-10-09 (Sun, 09 Oct 2016) Changed paths: R config/plugins/webhooks/topbar_test/config/topbar_test.yml M config/plugins/webhooks/xkcd/config/xkcd.yml M lib/galaxy/webhooks/__init__.py Log Message: ----------- renamings and fixes Commit: 29a57ba0fdd9ab066e19110715bbb091014e3f7a https://github.com/galaxyproject/galaxy/commit/29a57ba0fdd9ab066e19110715bb… Author: anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-10-09 (Sun, 09 Oct 2016) Changed paths: M config/plugins/webhooks/xkcd/config/xkcd.yml Log Message: ----------- - add new entry point (Workflow) - temporarily hide masthead webhook (due to instability) Commit: e58fe7ca49f7b01244d1e6f4bfc92586459c799d https://github.com/galaxyproject/galaxy/commit/e58fe7ca49f7b01244d1e6f4bfc9… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-10-09 (Sun, 09 Oct 2016) Changed paths: M config/plugins/webhooks/xkcd/config/xkcd.yml Log Message: ----------- bug fixes and improvements Commit: 8b5716ddfda7d8d4bc604cf6d396d59fa45498c7 https://github.com/galaxyproject/galaxy/commit/8b5716ddfda7d8d4bc604cf6d396… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-10-09 (Sun, 09 Oct 2016) Changed paths: M config/plugins/webhooks/xkcd/config/xkcd.yml M static/maps/mvc/webhooks.js.map Log Message: ----------- fix bugs after previous commit Commit: ce346b6ad4482a1e6a0e8e9f92e79ea1d90a33b4 https://github.com/galaxyproject/galaxy/commit/ce346b6ad4482a1e6a0e8e9f92e7… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-10-09 (Sun, 09 Oct 2016) Changed paths: M client/galaxy/scripts/mvc/webhooks.js M config/plugins/webhooks/masthead_test/config/masthead_test.yml R config/plugins/webhooks/masthead_test/static/script.js M config/plugins/webhooks/phdcomics/helper/__init__.py M static/maps/mvc/webhooks.js.map M static/scripts/mvc/webhooks.js Log Message: ----------- pass trans object into the helper function Commit: 2cc133f32507cd2aec8784e247106cef540a1c17 https://github.com/galaxyproject/galaxy/commit/2cc133f32507cd2aec8784e24710… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-10-09 (Sun, 09 Oct 2016) Changed paths: A doc/source/admin/webhooks.rst Log Message: ----------- Add initial docs Commit: 69a9344c529e34cdb70fdd71634ba2944bf0a7e8 https://github.com/galaxyproject/galaxy/commit/69a9344c529e34cdb70fdd71634b… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-10-09 (Sun, 09 Oct 2016) Changed paths: M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/tool/tool-form.js A config/plugins/webhooks/trans_object/config/trans_object.yaml A config/plugins/webhooks/trans_object/helper/__init__.py M lib/galaxy/webapps/galaxy/api/webhooks.py M lib/galaxy/webhooks/__init__.py M static/maps/layout/menu.js.map M static/maps/mvc/history/options-menu.js.map M static/maps/mvc/tool/tool-form-composite.js.map M static/maps/mvc/tool/tool-form.js.map M static/maps/mvc/webhooks.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/layout/menu.js M static/scripts/mvc/history/options-menu.js M static/scripts/mvc/tool/tool-form-composite.js M static/scripts/mvc/tool/tool-form.js Log Message: ----------- - show Webhook on a workflow page - fix merge errors Commit: ef304a2223ca080c9181fad4117919c71d539211 https://github.com/galaxyproject/galaxy/commit/ef304a2223ca080c9181fad41179… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-10-09 (Sun, 09 Oct 2016) Changed paths: M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/mvc/tool/tool-form.js M lib/galaxy/webapps/galaxy/api/webhooks.py M static/maps/layout/menu.js.map M static/maps/mvc/history/options-menu.js.map M static/maps/mvc/tool/tool-form.js.map M static/maps/mvc/webhooks.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/layout/menu.js M static/scripts/mvc/history/options-menu.js M static/scripts/mvc/tool/tool-form.js A templates/webapps/galaxy/workflow/run_complete.mako Log Message: ----------- - merge Commit: a3627b98ab8f5940af529e1387c8da8a4595a9e0 https://github.com/galaxyproject/galaxy/commit/a3627b98ab8f5940af529e1387c8… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-10-09 (Sun, 09 Oct 2016) Changed paths: M static/maps/mvc/webhooks.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map Log Message: ----------- make client Commit: cc36793cd0d249fd2794c5de54af6ff10695b88e https://github.com/galaxyproject/galaxy/commit/cc36793cd0d249fd2794c5de54af… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-10-12 (Wed, 12 Oct 2016) Changed paths: M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/mvc/webhooks.js M lib/galaxy/webapps/galaxy/api/webhooks.py M static/maps/layout/menu.js.map M static/maps/mvc/history/options-menu.js.map M static/maps/mvc/webhooks.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/menu.js M static/scripts/mvc/history/options-menu.js M static/scripts/mvc/webhooks.js Log Message: ----------- - remove separate functions for adding masthead/history-menu plugins - choose a random tool/workflow plugin only among active ones Commit: 812aca5b34df584a09d3f82f9d938e89d396b2bd https://github.com/galaxyproject/galaxy/commit/812aca5b34df584a09d3f82f9d93… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-10-12 (Wed, 12 Oct 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/webhooks.py Log Message: ----------- bug fix Commit: 5f9154a6179f194a8186d0f91a375d449cb26ea2 https://github.com/galaxyproject/galaxy/commit/5f9154a6179f194a8186d0f91a37… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-10-12 (Wed, 12 Oct 2016) Changed paths: M doc/source/admin/webhooks.rst Log Message: ----------- tiny fixes Commit: cd92be8802e520a2f53eceb385f018ded4aea218 https://github.com/galaxyproject/galaxy/commit/cd92be8802e520a2f53eceb385f0… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-10-12 (Wed, 12 Oct 2016) Changed paths: M doc/source/admin/webhooks.rst Log Message: ----------- Include a section about plugin dependencies. Commit: 0ad7c99ea20ba49725fffe5a356ab39bf601111d https://github.com/galaxyproject/galaxy/commit/0ad7c99ea20ba49725fffe5a356a… Author: Joachim Wolff <wolffj(a)informatik.uni-freiburg.de> Date: 2016-10-12 (Wed, 12 Oct 2016) Changed paths: M doc/source/admin/webhooks.rst Log Message: ----------- Extended the documentation of webhooks and added an images directory. Commit: f29b003a8cd6a277ee67cb553653063fbc53dbfe https://github.com/galaxyproject/galaxy/commit/f29b003a8cd6a277ee67cb553653… Author: Joachim Wolff <wolffj(a)informatik.uni-freiburg.de> Date: 2016-10-12 (Wed, 12 Oct 2016) Changed paths: A doc/source/admin/images_webhooks/history-menu.png A doc/source/admin/images_webhooks/masthead.png A doc/source/admin/images_webhooks/masthead_trans_object.png A doc/source/admin/images_webhooks/tool.png A doc/source/admin/images_webhooks/workflow.png Log Message: ----------- Added images directory for webhooks documentation Commit: 95c1f186935a77ee71de59a3a616dc5d7f11c8c2 https://github.com/galaxyproject/galaxy/commit/95c1f186935a77ee71de59a3a616… Author: Joachim Wolff <wolffj(a)informatik.uni-freiburg.de> Date: 2016-10-12 (Wed, 12 Oct 2016) Changed paths: M doc/source/admin/webhooks.rst Log Message: ----------- Fixed formatting errors Commit: eb32ad229f5f22c8b2cb497344fd545f14f6eae3 https://github.com/galaxyproject/galaxy/commit/eb32ad229f5f22c8b2cb497344fd… Author: Joachim Wolff <wolffj(a)informatik.uni-freiburg.de> Date: 2016-10-12 (Wed, 12 Oct 2016) Changed paths: M doc/source/admin/webhooks.rst Log Message: ----------- Fixed formatting errors Commit: d1737110bf2d870346df43d5969b329cea1b16d8 https://github.com/galaxyproject/galaxy/commit/d1737110bf2d870346df43d5969b… Author: Joachim Wolff <wolffj(a)informatik.uni-freiburg.de> Date: 2016-10-12 (Wed, 12 Oct 2016) Changed paths: M doc/source/admin/webhooks.rst Log Message: ----------- Fixing errors Commit: 76b9e004d204b6569ef6d19b6e808b77db9984f2 https://github.com/galaxyproject/galaxy/commit/76b9e004d204b6569ef6d19b6e80… Author: Joachim Wolff <wolffj(a)informatik.uni-freiburg.de> Date: 2016-10-12 (Wed, 12 Oct 2016) Changed paths: M doc/source/admin/webhooks.rst Log Message: ----------- Fixing errors Commit: 8030d2025ddaa0ca5f5d58f12a24f85e860f9339 https://github.com/galaxyproject/galaxy/commit/8030d2025ddaa0ca5f5d58f12a24… Author: Joachim Wolff <wolffj(a)informatik.uni-freiburg.de> Date: 2016-10-12 (Wed, 12 Oct 2016) Changed paths: M doc/source/admin/webhooks.rst Log Message: ----------- Fixing errors Commit: acd99f76fc967445cc9b8cd1317793a6074997b7 https://github.com/galaxyproject/galaxy/commit/acd99f76fc967445cc9b8cd13177… Author: Joachim Wolff <wolffj(a)informatik.uni-freiburg.de> Date: 2016-10-12 (Wed, 12 Oct 2016) Changed paths: M doc/source/admin/webhooks.rst Log Message: ----------- Fixing errors Commit: 6684fd4e262f97c313d907bf44409d94172338c8 https://github.com/galaxyproject/galaxy/commit/6684fd4e262f97c313d907bf4440… Author: Joachim Wolff <wolffj(a)informatik.uni-freiburg.de> Date: 2016-10-12 (Wed, 12 Oct 2016) Changed paths: M doc/source/admin/webhooks.rst Log Message: ----------- Fixing errors Commit: fafeedc286035d78d1033220717b346e4c0d3c99 https://github.com/galaxyproject/galaxy/commit/fafeedc286035d78d1033220717b… Author: Joachim Wolff <wolffj(a)informatik.uni-freiburg.de> Date: 2016-10-12 (Wed, 12 Oct 2016) Changed paths: M doc/source/admin/webhooks.rst Log Message: ----------- Fixing errors Commit: af8a3f11048c86f91f17044344211a5cdba98b13 https://github.com/galaxyproject/galaxy/commit/af8a3f11048c86f91f1704434421… Author: Joachim Wolff <wolffj(a)informatik.uni-freiburg.de> Date: 2016-10-12 (Wed, 12 Oct 2016) Changed paths: M doc/source/admin/webhooks.rst Log Message: ----------- Fixing errors Commit: d5dc39ab0f034d79252a9fb0875824cbf8b02e04 https://github.com/galaxyproject/galaxy/commit/d5dc39ab0f034d79252a9fb08758… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-10-12 (Wed, 12 Oct 2016) Changed paths: A doc/source/admin/images_webhooks/history-menu.png A doc/source/admin/images_webhooks/masthead.png A doc/source/admin/images_webhooks/masthead_trans_object.png A doc/source/admin/images_webhooks/tool.png A doc/source/admin/images_webhooks/workflow.png M doc/source/admin/webhooks.rst Log Message: ----------- Merge pull request #21 from joachimwolff/feature/plugin-system Feature/plugin system Commit: 0a15289d31a189df71490bba5392726ac0f6db47 https://github.com/galaxyproject/galaxy/commit/0a15289d31a189df71490bba5392… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-10-12 (Wed, 12 Oct 2016) Changed paths: M config/plugins/webhooks/phdcomics/helper/__init__.py Log Message: ----------- added missing dependencies check Commit: bc51dc3ec72dc7a5bbcc42bcd4f1cc834c1a69b6 https://github.com/galaxyproject/galaxy/commit/bc51dc3ec72dc7a5bbcc42bcd4f1… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-10-12 (Wed, 12 Oct 2016) Changed paths: M doc/source/admin/webhooks.rst Log Message: ----------- Update webhooks.rst escape missing dependencies Commit: 95d6990cf3f6f1e4ade87b6ba6557c99471ff924 https://github.com/galaxyproject/galaxy/commit/95d6990cf3f6f1e4ade87b6ba655… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-10-12 (Wed, 12 Oct 2016) Changed paths: M doc/source/admin/webhooks.rst Log Message: ----------- Update webhooks.rst Commit: 4f89528c94d33f1e3eca8df9dd34c06965e7beec https://github.com/galaxyproject/galaxy/commit/4f89528c94d33f1e3eca8df9dd34… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-10-12 (Wed, 12 Oct 2016) Changed paths: M doc/source/admin/webhooks.rst Log Message: ----------- make activation procedure more clear Commit: 2d915a42f6329bd31dfdc76b5bfa56376a57c841 https://github.com/galaxyproject/galaxy/commit/2d915a42f6329bd31dfdc76b5bfa… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-10-13 (Thu, 13 Oct 2016) Changed paths: M doc/source/admin/webhooks.rst Log Message: ----------- tense changes Commit: b52d5be75b3f2bf9cae86d4a278689cb614095be https://github.com/galaxyproject/galaxy/commit/b52d5be75b3f2bf9cae86d4a2786… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-10-13 (Thu, 13 Oct 2016) Changed paths: M client/galaxy/scripts/layout/menu.js Log Message: ----------- Change according to Aysam's review Commit: 290c48b16c54fab54ec35601e04d6877071a78db https://github.com/galaxyproject/galaxy/commit/290c48b16c54fab54ec35601e04d… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-10-13 (Thu, 13 Oct 2016) Changed paths: M client/galaxy/scripts/layout/menu.js Log Message: ----------- Change according to Aysam's review Commit: a231e240ed1a8002318678dde5979c3febb11770 https://github.com/galaxyproject/galaxy/commit/a231e240ed1a8002318678dde597… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-10-13 (Thu, 13 Oct 2016) Changed paths: M client/galaxy/scripts/layout/menu.js Log Message: ----------- remove obsolete code Commit: 6a62dbc91a0f2ed282c2cc1e3c4227faed870ace https://github.com/galaxyproject/galaxy/commit/6a62dbc91a0f2ed282c2cc1e3c42… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2016-10-13 (Thu, 13 Oct 2016) Changed paths: M .ci/flake8_blacklist.txt M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M .travis.yml M client/galaxy/style/source_material/circle.py M config/galaxy.ini.sample M config/job_conf.xml.sample_advanced M doc/parse_gx_xsd.py M doc/source/admin/dependency_resolvers.rst M doc/source/admin/index.rst A doc/source/admin/mulled_containers.rst M lib/galaxy/config.py M lib/galaxy/datatypes/registry.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/tools/deps/__init__.py A lib/galaxy/tools/deps/conda_compat.py M lib/galaxy/tools/deps/conda_util.py A lib/galaxy/tools/deps/container_resolvers/__init__.py A lib/galaxy/tools/deps/container_resolvers/explicit.py A lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/containers.py A lib/galaxy/tools/deps/installable.py A lib/galaxy/tools/deps/mulled/__init__.py A lib/galaxy/tools/deps/mulled/_cli.py A lib/galaxy/tools/deps/mulled/invfile.lua A lib/galaxy/tools/deps/mulled/mulled_build.py A lib/galaxy/tools/deps/mulled/mulled_build_channel.py A lib/galaxy/tools/deps/mulled/mulled_build_files.py A lib/galaxy/tools/deps/mulled/mulled_build_tool.py A lib/galaxy/tools/deps/mulled/mulled_search.py A lib/galaxy/tools/deps/mulled/util.py M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/xsd/galaxy.xsd M test/api/helpers.py M test/api/test_api_batch.py M test/api/test_authenticate.py M test/api/test_dataset_collections.py M test/api/test_history_contents.py M test/api/test_page_revisions.py M test/api/test_pages.py M test/api/test_tool_data.py M test/api/test_tools.py M test/api/test_users.py M test/api/test_workflow_extraction.py M test/api/test_workflows.py M test/api/workflows_format_2/__init__.py M test/api/workflows_format_2/converter.py M test/base/api.py M test/base/driver_util.py M test/base/integration_util.py M test/base/interactor.py M test/base/test_logging.py M test/base/twilltestcase.py M test/functional/test_data_managers.py M test/functional/test_library_templates.py M test/functional/test_toolbox.py A test/functional/tools/mulled_example_multi_1.xml M test/functional/tools/samples_tool_conf.xml M test/functional/workflow.py M test/integration/test_resolvers.py M test/manual/workflows_scaling.py M test/shed_functional/base/test_db_util.py M test/shed_functional/functional/test_0300_reset_all_metadata.py M test/shed_functional/functional/test_1300_reset_all_metadata.py M test/shed_functional/functional_tests.py M test/unit/jobs/test_runner_local.py Log Message: ----------- Merge branch 'dev' into feature/plugin-system Commit: 8f5b54141dd2b46d3b532915b082c4bd5eeff44c https://github.com/galaxyproject/galaxy/commit/8f5b54141dd2b46d3b532915b082… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-10-13 (Thu, 13 Oct 2016) Changed paths: M client/galaxy/scripts/layout/menu.js Log Message: ----------- code optimization, thanks Sam Commit: 773d85453f965712cdd8bcc209b9a05897959994 https://github.com/galaxyproject/galaxy/commit/773d85453f965712cdd8bcc209b9… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2016-10-13 (Thu, 13 Oct 2016) Changed paths: A config/plugins/webhooks/demo/history_test1/config/history_test1.yml A config/plugins/webhooks/demo/history_test2/config/history_test2.yml A config/plugins/webhooks/demo/masthead_test/config/masthead_test.yml A config/plugins/webhooks/demo/phdcomics/config/phdcomics.yaml A config/plugins/webhooks/demo/phdcomics/helper/__init__.py A config/plugins/webhooks/demo/phdcomics/static/script.js A config/plugins/webhooks/demo/phdcomics/static/styles.css A config/plugins/webhooks/demo/trans_object/config/trans_object.yaml A config/plugins/webhooks/demo/trans_object/helper/__init__.py A config/plugins/webhooks/demo/xkcd/config/xkcd.yml A config/plugins/webhooks/demo/xkcd/static/script.js A config/plugins/webhooks/demo/xkcd/static/styles.css R config/plugins/webhooks/history_test1/config/history_test1.yml R config/plugins/webhooks/history_test2/config/history_test2.yml R config/plugins/webhooks/masthead_test/config/masthead_test.yml R config/plugins/webhooks/phdcomics/config/phdcomics.yaml R config/plugins/webhooks/phdcomics/helper/__init__.py R config/plugins/webhooks/phdcomics/static/script.js R config/plugins/webhooks/phdcomics/static/styles.css R config/plugins/webhooks/trans_object/config/trans_object.yaml R config/plugins/webhooks/trans_object/helper/__init__.py R config/plugins/webhooks/xkcd/config/xkcd.yml R config/plugins/webhooks/xkcd/static/script.js R config/plugins/webhooks/xkcd/static/styles.css Log Message: ----------- move all plugins into a demo folder Commit: a676d6e8234dd9db59376df7f54633a78e503f86 https://github.com/galaxyproject/galaxy/commit/a676d6e8234dd9db59376df7f546… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2016-10-13 (Thu, 13 Oct 2016) Changed paths: M lib/galaxy/app.py M lib/galaxy/config.py M lib/galaxy/webhooks/__init__.py Log Message: ----------- allow multiple webhook dirs Commit: 6894df3dcb0f308724331bceceff46dba23156a1 https://github.com/galaxyproject/galaxy/commit/6894df3dcb0f308724331bceceff… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-10-13 (Thu, 13 Oct 2016) Changed paths: M .ci/flake8_blacklist.txt M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M .travis.yml M client/galaxy/scripts/layout/menu.js M client/galaxy/style/source_material/circle.py M config/galaxy.ini.sample M config/job_conf.xml.sample_advanced A config/plugins/webhooks/demo/history_test1/config/history_test1.yml A config/plugins/webhooks/demo/history_test2/config/history_test2.yml A config/plugins/webhooks/demo/masthead_test/config/masthead_test.yml A config/plugins/webhooks/demo/phdcomics/config/phdcomics.yaml A config/plugins/webhooks/demo/phdcomics/helper/__init__.py A config/plugins/webhooks/demo/phdcomics/static/script.js A config/plugins/webhooks/demo/phdcomics/static/styles.css A config/plugins/webhooks/demo/trans_object/config/trans_object.yaml A config/plugins/webhooks/demo/trans_object/helper/__init__.py A config/plugins/webhooks/demo/xkcd/config/xkcd.yml A config/plugins/webhooks/demo/xkcd/static/script.js A config/plugins/webhooks/demo/xkcd/static/styles.css R config/plugins/webhooks/history_test1/config/history_test1.yml R config/plugins/webhooks/history_test2/config/history_test2.yml R config/plugins/webhooks/masthead_test/config/masthead_test.yml R config/plugins/webhooks/phdcomics/config/phdcomics.yaml R config/plugins/webhooks/phdcomics/helper/__init__.py R config/plugins/webhooks/phdcomics/static/script.js R config/plugins/webhooks/phdcomics/static/styles.css R config/plugins/webhooks/trans_object/config/trans_object.yaml R config/plugins/webhooks/trans_object/helper/__init__.py R config/plugins/webhooks/xkcd/config/xkcd.yml R config/plugins/webhooks/xkcd/static/script.js R config/plugins/webhooks/xkcd/static/styles.css M doc/parse_gx_xsd.py M doc/source/admin/dependency_resolvers.rst A doc/source/admin/images_webhooks/history-menu.png A doc/source/admin/images_webhooks/masthead.png A doc/source/admin/images_webhooks/masthead_trans_object.png A doc/source/admin/images_webhooks/tool.png A doc/source/admin/images_webhooks/workflow.png M doc/source/admin/index.rst A doc/source/admin/mulled_containers.rst M doc/source/admin/webhooks.rst M lib/galaxy/app.py M lib/galaxy/config.py M lib/galaxy/datatypes/registry.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/tools/deps/__init__.py A lib/galaxy/tools/deps/conda_compat.py M lib/galaxy/tools/deps/conda_util.py A lib/galaxy/tools/deps/container_resolvers/__init__.py A lib/galaxy/tools/deps/container_resolvers/explicit.py A lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/containers.py A lib/galaxy/tools/deps/installable.py A lib/galaxy/tools/deps/mulled/__init__.py A lib/galaxy/tools/deps/mulled/_cli.py A lib/galaxy/tools/deps/mulled/invfile.lua A lib/galaxy/tools/deps/mulled/mulled_build.py A lib/galaxy/tools/deps/mulled/mulled_build_channel.py A lib/galaxy/tools/deps/mulled/mulled_build_files.py A lib/galaxy/tools/deps/mulled/mulled_build_tool.py A lib/galaxy/tools/deps/mulled/mulled_search.py A lib/galaxy/tools/deps/mulled/util.py M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/webhooks/__init__.py M test/api/helpers.py M test/api/test_api_batch.py M test/api/test_authenticate.py M test/api/test_dataset_collections.py M test/api/test_history_contents.py M test/api/test_page_revisions.py M test/api/test_pages.py M test/api/test_tool_data.py M test/api/test_tools.py M test/api/test_users.py M test/api/test_workflow_extraction.py M test/api/test_workflows.py M test/api/workflows_format_2/__init__.py M test/api/workflows_format_2/converter.py M test/base/api.py M test/base/driver_util.py M test/base/integration_util.py M test/base/interactor.py M test/base/test_logging.py M test/base/twilltestcase.py M test/functional/test_data_managers.py M test/functional/test_library_templates.py M test/functional/test_toolbox.py A test/functional/tools/mulled_example_multi_1.xml M test/functional/tools/samples_tool_conf.xml M test/functional/workflow.py M test/integration/test_resolvers.py M test/manual/workflows_scaling.py M test/shed_functional/base/test_db_util.py M test/shed_functional/functional/test_0300_reset_all_metadata.py M test/shed_functional/functional/test_1300_reset_all_metadata.py M test/shed_functional/functional_tests.py M test/unit/jobs/test_runner_local.py Log Message: ----------- Merge branch 'feature/plugin-system' of github.com:bgruening/galaxy into feature/plugin-system Commit: 3f8d45b388e5788b23c39c2b544e4c98eae8018f https://github.com/galaxyproject/galaxy/commit/3f8d45b388e5788b23c39c2b544e… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-10-13 (Thu, 13 Oct 2016) Changed paths: M lib/galaxy/webhooks/__init__.py Log Message: ----------- PEP8 Commit: fb516d9387a2df9a1ccdd2c7a1a1ce162f7e52fc https://github.com/galaxyproject/galaxy/commit/fb516d9387a2df9a1ccdd2c7a1a1… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-10-13 (Thu, 13 Oct 2016) Changed paths: M lib/galaxy/webhooks/__init__.py Log Message: ----------- remove blank line Commit: e220ed097067124f5ab616d0ece35d0af4cb2539 https://github.com/galaxyproject/galaxy/commit/e220ed097067124f5ab616d0ece3… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2016-10-13 (Thu, 13 Oct 2016) Changed paths: M lib/galaxy/config.py M lib/galaxy/webhooks/__init__.py Log Message: ----------- use config_directories_from_setting Commit: b0b5157f36ec26090c9c11c0a133513083015735 https://github.com/galaxyproject/galaxy/commit/b0b5157f36ec26090c9c11c0a133… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2016-10-13 (Thu, 13 Oct 2016) Changed paths: M config/plugins/webhooks/demo/phdcomics/helper/__init__.py Log Message: ----------- merge Commit: f4dc38a54da3539f4d63f7e33708bcc2e33012fb https://github.com/galaxyproject/galaxy/commit/f4dc38a54da3539f4d63f7e33708… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2016-10-13 (Thu, 13 Oct 2016) Changed paths: M config/plugins/webhooks/demo/history_test1/config/history_test1.yml M config/plugins/webhooks/demo/history_test2/config/history_test2.yml M config/plugins/webhooks/demo/masthead_test/config/masthead_test.yml M config/plugins/webhooks/demo/phdcomics/config/phdcomics.yaml M config/plugins/webhooks/demo/trans_object/config/trans_object.yaml M config/plugins/webhooks/demo/xkcd/config/xkcd.yml Log Message: ----------- activate all plugins in the demo folder Commit: 2703ba1a0cc3a28314018299b8f1a686dfb6e995 https://github.com/galaxyproject/galaxy/commit/2703ba1a0cc3a28314018299b8f1… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-10-13 (Thu, 13 Oct 2016) Changed paths: M config/galaxy.ini.sample Log Message: ----------- activate all demo plugins in testing purposes Commit: 8694356ab7057c47164a92f8d4e47a800fca2f4d https://github.com/galaxyproject/galaxy/commit/8694356ab7057c47164a92f8d4e4… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-10-13 (Thu, 13 Oct 2016) Changed paths: M doc/source/admin/webhooks.rst Log Message: ----------- Adopt help to the latest changes Commit: 3aadd84b80bca7fc588ffccaa27f01c1d599b9d8 https://github.com/galaxyproject/galaxy/commit/3aadd84b80bca7fc588ffccaa27f… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2016-10-13 (Thu, 13 Oct 2016) Changed paths: M config/plugins/webhooks/demo/trans_object/helper/__init__.py Log Message: ----------- add case where no user is logged in Commit: 0dc2c95bd07e2a53dec27c8d0d4fc86747aa8878 https://github.com/galaxyproject/galaxy/commit/0dc2c95bd07e2a53dec27c8d0d4f… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2016-10-13 (Thu, 13 Oct 2016) Changed paths: M doc/source/admin/webhooks.rst Log Message: ----------- Merge branch 'feature/plugin-system' of https://github.com/bgruening/galaxy into feature/plugin-system Commit: 3cb8189e1fa48c58afaf609691a0801e784484b7 https://github.com/galaxyproject/galaxy/commit/3cb8189e1fa48c58afaf609691a0… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2016-10-13 (Thu, 13 Oct 2016) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M config/galaxy.ini.sample M lib/galaxy/managers/collections_util.py M lib/galaxy/model/item_attrs.py M lib/galaxy/model/metadata.py M lib/galaxy/model/orm/now.py M lib/galaxy/tools/cwl/__init__.py M lib/galaxy/tools/cwl/cwltool_deps.py M lib/galaxy/tools/cwl/parser.py M lib/galaxy/tools/cwl/runtime_actions.py M lib/galaxy/tools/deps/commands.py M lib/galaxy/tools/deps/conda_compat.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/docker_util.py M lib/galaxy/tools/deps/mulled/_cli.py M lib/galaxy/tools/deps/mulled/mulled_build.py M lib/galaxy/tools/deps/mulled/mulled_build_channel.py M lib/galaxy/tools/deps/mulled/mulled_build_files.py M lib/galaxy/tools/deps/mulled/mulled_build_tool.py M lib/galaxy/tools/deps/mulled/util.py M lib/galaxy/tools/deps/resolvers/brewed_tool_shed_packages.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/deps/resolvers/galaxy_packages.py M lib/galaxy/tools/deps/resolvers/homebrew.py M lib/galaxy/tools/deps/resolvers/modules.py M lib/galaxy/tools/deps/resolvers/tool_shed_packages.py M lib/galaxy/tools/deps/resolvers/unlinked_tool_shed_packages.py M lib/galaxy/tools/exception_handling.py M lib/galaxy/tools/execute.py M lib/galaxy/tools/loader.py M lib/galaxy/tools/loader_directory.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/dataset_matcher.py M lib/galaxy/tools/parameters/wrapped.py M lib/galaxy/tools/parameters/wrapped_json.py M lib/galaxy/tools/parser/__init__.py M lib/galaxy/tools/parser/factory.py M lib/galaxy/tools/toolbox/__init__.py M lib/galaxy/tools/toolbox/lineages/__init__.py M lib/galaxy/tools/toolbox/lineages/factory.py M lib/galaxy/tools/toolbox/lineages/tool_shed.py M lib/galaxy/tools/toolbox/parser.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/workflow/extract.py M lib/galaxy/workflow/run.py M lib/galaxy/workflow/schedulers/core.py M test/api/test_workflow_extraction.py M test/api/workflows_format_2/__init__.py M test/api/workflows_format_2/converter.py M test/api/workflows_format_2/main.py M test/base/driver_util.py A test/functional/tools/multi_data_optional.xml M test/functional/tools/samples_tool_conf.xml M test/unit/tools_support.py M test/unit/unittest_utils/utility.py M tools/filters/gff/gff_filter_by_attribute.py M tools/stats/filtering.py Log Message: ----------- Merge branch 'dev' into feature/plugin-system Commit: 37702392817107dfd12cbb54f0af1dcb18bd848e https://github.com/galaxyproject/galaxy/commit/37702392817107dfd12cbb54f0af… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-10-14 (Fri, 14 Oct 2016) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M config/galaxy.ini.sample M config/plugins/webhooks/demo/trans_object/helper/__init__.py M doc/source/admin/webhooks.rst M lib/galaxy/managers/collections_util.py M lib/galaxy/model/item_attrs.py M lib/galaxy/model/metadata.py M lib/galaxy/model/orm/now.py M lib/galaxy/tools/cwl/__init__.py M lib/galaxy/tools/cwl/cwltool_deps.py M lib/galaxy/tools/cwl/parser.py M lib/galaxy/tools/cwl/runtime_actions.py M lib/galaxy/tools/deps/commands.py M lib/galaxy/tools/deps/conda_compat.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/docker_util.py M lib/galaxy/tools/deps/mulled/_cli.py M lib/galaxy/tools/deps/mulled/mulled_build.py M lib/galaxy/tools/deps/mulled/mulled_build_channel.py M lib/galaxy/tools/deps/mulled/mulled_build_files.py M lib/galaxy/tools/deps/mulled/mulled_build_tool.py M lib/galaxy/tools/deps/mulled/util.py M lib/galaxy/tools/deps/resolvers/brewed_tool_shed_packages.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/deps/resolvers/galaxy_packages.py M lib/galaxy/tools/deps/resolvers/homebrew.py M lib/galaxy/tools/deps/resolvers/modules.py M lib/galaxy/tools/deps/resolvers/tool_shed_packages.py M lib/galaxy/tools/deps/resolvers/unlinked_tool_shed_packages.py M lib/galaxy/tools/exception_handling.py M lib/galaxy/tools/execute.py M lib/galaxy/tools/loader.py M lib/galaxy/tools/loader_directory.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/dataset_matcher.py M lib/galaxy/tools/parameters/wrapped.py M lib/galaxy/tools/parameters/wrapped_json.py M lib/galaxy/tools/parser/__init__.py M lib/galaxy/tools/parser/factory.py M lib/galaxy/tools/toolbox/__init__.py M lib/galaxy/tools/toolbox/lineages/__init__.py M lib/galaxy/tools/toolbox/lineages/factory.py M lib/galaxy/tools/toolbox/lineages/tool_shed.py M lib/galaxy/tools/toolbox/parser.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/workflow/extract.py M lib/galaxy/workflow/run.py M lib/galaxy/workflow/schedulers/core.py M test/api/test_workflow_extraction.py M test/api/workflows_format_2/__init__.py M test/api/workflows_format_2/converter.py M test/api/workflows_format_2/main.py M test/base/driver_util.py A test/functional/tools/multi_data_optional.xml M test/functional/tools/samples_tool_conf.xml M test/unit/tools_support.py M test/unit/unittest_utils/utility.py M tools/filters/gff/gff_filter_by_attribute.py M tools/stats/filtering.py Log Message: ----------- Merge branch 'feature/plugin-system' of github.com:bgruening/galaxy into feature/plugin-system Commit: bd20ab1aa57381b36e16dc08c20b6b176a7ed724 https://github.com/galaxyproject/galaxy/commit/bd20ab1aa57381b36e16dc08c20b… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-10-14 (Fri, 14 Oct 2016) Changed paths: M lib/galaxy/webhooks/__init__.py Log Message: ----------- pep8 Commit: 3d4f302c4734e9afc7e065645c915dfd8f37566e https://github.com/galaxyproject/galaxy/commit/3d4f302c4734e9afc7e065645c91… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2016-10-14 (Fri, 14 Oct 2016) Changed paths: M config/galaxy.ini.sample Log Message: ----------- change default settings in galaxy.ini.sample Commit: 4bbab51c0500922c9a191d022de295daa48f0dd5 https://github.com/galaxyproject/galaxy/commit/4bbab51c0500922c9a191d022de2… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-10-14 (Fri, 14 Oct 2016) Changed paths: M doc/source/admin/webhooks.rst Log Message: ----------- Add note about interface stability. Commit: ebaffa2e0d6a030dfc3c78a3b9515093b14f7103 https://github.com/galaxyproject/galaxy/commit/ebaffa2e0d6a030dfc3c78a3b951… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-10-14 (Fri, 14 Oct 2016) Changed paths: M config/plugins/webhooks/demo/phdcomics/helper/__init__.py M lib/galaxy/webapps/galaxy/api/webhooks.py Log Message: ----------- fix failing Travis tests #2 (TOX_ENV=py27-lint) and #6 (TOX_ENV=py27-lint-imports) Commit: a6d52cdbdc837c427c0971c6586eb5169a786752 https://github.com/galaxyproject/galaxy/commit/a6d52cdbdc837c427c0971c6586e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-10-23 (Sun, 23 Oct 2016) Changed paths: M client/galaxy/scripts/apps/history-panel.js M client/galaxy/scripts/layout/masthead.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/tool/tool-form.js A client/galaxy/scripts/mvc/webhooks.js M config/galaxy.ini.sample A config/plugins/webhooks/demo/history_test1/config/history_test1.yml A config/plugins/webhooks/demo/history_test2/config/history_test2.yml A config/plugins/webhooks/demo/masthead_test/config/masthead_test.yml A config/plugins/webhooks/demo/phdcomics/config/phdcomics.yaml A config/plugins/webhooks/demo/phdcomics/helper/__init__.py A config/plugins/webhooks/demo/phdcomics/static/script.js A config/plugins/webhooks/demo/phdcomics/static/styles.css A config/plugins/webhooks/demo/trans_object/config/trans_object.yaml A config/plugins/webhooks/demo/trans_object/helper/__init__.py A config/plugins/webhooks/demo/xkcd/config/xkcd.yml A config/plugins/webhooks/demo/xkcd/static/script.js A config/plugins/webhooks/demo/xkcd/static/styles.css A doc/source/admin/images_webhooks/history-menu.png A doc/source/admin/images_webhooks/masthead.png A doc/source/admin/images_webhooks/masthead_trans_object.png A doc/source/admin/images_webhooks/tool.png A doc/source/admin/images_webhooks/workflow.png A doc/source/admin/webhooks.rst M lib/galaxy/app.py M lib/galaxy/config.py A lib/galaxy/webapps/galaxy/api/webhooks.py M lib/galaxy/webapps/galaxy/buildapp.py A lib/galaxy/webhooks/__init__.py M static/maps/layout/menu.js.map M static/maps/mvc/history/options-menu.js.map M static/maps/mvc/tool/tool-form-composite.js.map M static/maps/mvc/tool/tool-form.js.map A static/maps/mvc/tool/tool-webhooks.js.map A static/maps/mvc/webhooks.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/layout/menu.js M static/scripts/mvc/history/options-menu.js M static/scripts/mvc/tool/tool-form-composite.js M static/scripts/mvc/tool/tool-form.js A static/scripts/mvc/tool/tool-webhooks.js A static/scripts/mvc/webhooks.js A templates/webapps/galaxy/workflow/run_complete.mako Log Message: ----------- Merge remote-tracking branch 'bgruening/feature/plugin-system' into dev Compare: https://github.com/galaxyproject/galaxy/compare/cfeb0135ac5f...a6d52cdbdc83

1 0

[galaxyproject/galaxy] 91a190: Datasets: allow admin to serialize permissions
by GitHub 21 Oct '16

21 Oct '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/galaxy Commit: 91a190c6eb2f37e041575548bfae85d61b64ce7e https://github.com/galaxyproject/galaxy/commit/91a190c6eb2f37e041575548bfae… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-09-12 (Mon, 12 Sep 2016) Changed paths: M lib/galaxy/managers/datasets.py M test/unit/managers/test_DatasetManager.py Log Message: ----------- Datasets: allow admin to serialize permissions And updates tests. Commit: b88035955d7a81ff43858f092924b60bef1bca9c https://github.com/galaxyproject/galaxy/commit/b88035955d7a81ff43858f092924… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-09-12 (Mon, 12 Sep 2016) Changed paths: M test/unit/managers/test_DatasetManager.py Log Message: ----------- Datasets: confirm admin ability to set permissions The power was inside you all along. Commit: 8616c0e87c055ed8e41563625498818a76769b2f https://github.com/galaxyproject/galaxy/commit/8616c0e87c055ed8e41563625498… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-09-13 (Tue, 13 Sep 2016) Changed paths: M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/resolvers/__init__.py Log Message: ----------- Log the resolved dependency type Commit: fc3dcf3b875cbadf75a1eb34ce1395e29dbe0baf https://github.com/galaxyproject/galaxy/commit/fc3dcf3b875cbadf75a1eb34ce13… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-09-13 (Tue, 13 Sep 2016) Changed paths: M lib/galaxy/managers/datasets.py M lib/galaxy/managers/rbac_secured.py M test/unit/managers/test_DatasetManager.py Log Message: ----------- Permissions, datasets: allow admin in RBAC - Admin are considered permitted when calling ** dataset_manager.permssions.access and ** dataset_manager.permissions.manage - Update bad test - Add admin test to other permission checks Commit: 9636ea1b6cb1283ef9e5d8cb210a962eff45bbef https://github.com/galaxyproject/galaxy/commit/9636ea1b6cb1283ef9e5d8cb210a… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-09-13 (Tue, 13 Sep 2016) Changed paths: M test/unit/managers/test_DatasetManager.py Log Message: ----------- Datasets: test for anon access/manage Commit: e7cb0ac2a19f0141336285fdd8fcf9aeb32221f2 https://github.com/galaxyproject/galaxy/commit/e7cb0ac2a19f0141336285fdd8fc… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-09-13 (Tue, 13 Sep 2016) Changed paths: M test/unit/managers/test_DatasetManager.py Log Message: ----------- Datasets: test for anon deserialization Commit: b301fd42021245f5c3c7291207510659aa66b5ac https://github.com/galaxyproject/galaxy/commit/b301fd42021245f5c3c729120751… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-09-14 (Wed, 14 Sep 2016) Changed paths: M lib/galaxy/managers/rbac_secured.py Log Message: ----------- Dataset perms: correct comment Commit: 8bf7256ca8ec61a167bca1dcaafa0b83cf12fa5a https://github.com/galaxyproject/galaxy/commit/8bf7256ca8ec61a167bca1dcaafa… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-09-14 (Wed, 14 Sep 2016) Changed paths: M lib/galaxy/managers/rbac_secured.py M test/unit/managers/test_DatasetManager.py Log Message: ----------- Merge pull request #2912 from carlfeberhard/dataset.admin-permissions [16.01] Allow admin to serialize/deserialize dataset permissions Commit: b50d07d5bf128ee280eb823f9b2b5677e549b5e5 https://github.com/galaxyproject/galaxy/commit/b50d07d5bf128ee280eb823f9b2b… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-09-14 (Wed, 14 Sep 2016) Changed paths: M lib/galaxy/managers/rbac_secured.py M test/unit/managers/test_DatasetManager.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_16.01' into release_16.04 Commit: e5f4f2fab6ce44b4e98f1dc54bea138d1185aa85 https://github.com/galaxyproject/galaxy/commit/e5f4f2fab6ce44b4e98f1dc54bea… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-09-14 (Wed, 14 Sep 2016) Changed paths: M lib/galaxy/managers/rbac_secured.py M test/unit/managers/test_DatasetManager.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_16.04' into release_16.07 Commit: 646428d73f9cbcd312ed3ff5eff8e36ee12f213e https://github.com/galaxyproject/galaxy/commit/646428d73f9cbcd312ed3ff5eff8… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-09-14 (Wed, 14 Sep 2016) Changed paths: M templates/webapps/galaxy/workflow/run.mako Log Message: ----------- Remove change handler for data and collection multiinput selectors in old run workflow form Commit: b399c086254f35d8536c1afa9fd7a2e50ec339a9 https://github.com/galaxyproject/galaxy/commit/b399c086254f35d8536c1afa9fd7… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-09-14 (Wed, 14 Sep 2016) Changed paths: M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/resolvers/__init__.py Log Message: ----------- Merge pull request #2918 from martenson/pick-dep-log [16.07] cherry pick logging the resolved dependency type Commit: 67a3cf34ca0e639791ac88e849d120dce355d3ef https://github.com/galaxyproject/galaxy/commit/67a3cf34ca0e639791ac88e849d1… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M templates/webapps/galaxy/workflow/run.mako Log Message: ----------- Merge pull request #2920 from guerler/fix_collection_refresh [16.07] Prevent refresh for collection selector in old run workflow form Commit: dc5aff7e44e2b0f767b7578935d46db7d7707066 https://github.com/galaxyproject/galaxy/commit/dc5aff7e44e2b0f767b7578935d4… Author: Anthony Bretaudeau <abretaud(a)irisa.fr> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M lib/galaxy/dependencies/conditional-requirements.txt Log Message: ----------- Update python-ldap module Updating to the same version as galaxyproject/starforge#97 Commit: c497ea534897b4c1875186961e96da52129c4a3a https://github.com/galaxyproject/galaxy/commit/c497ea534897b4c1875186961e96… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-09-16 (Fri, 16 Sep 2016) Changed paths: M lib/galaxy/dependencies/conditional-requirements.txt Log Message: ----------- Merge pull request #2924 from nsoranzo/release_16.07_backport_2738 [16.07] Update python-ldap module Commit: 1f53c32ad68235537d8f6c843d1cd81eda5c11c3 https://github.com/galaxyproject/galaxy/commit/1f53c32ad68235537d8f6c843d1c… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-09-19 (Mon, 19 Sep 2016) Changed paths: A lib/galaxy/datatypes/converters/tabular_to_dbnsfp.py Log Message: ----------- Add missing tabular_to_dbnsfp.py for dbnsfp.tabular to snpsiftdbnsfp conversion This should have been added in https://bitbucket.org/galaxy/galaxy-central/pull-requests/640/ Actual source code comes from https://github.com/galaxyproject/tools-iuc/blob/master/datatypes/snpsift_db… Commit: b748250193a26ddce4010759b9a22d012d281b81 https://github.com/galaxyproject/galaxy/commit/b748250193a26ddce4010759b9a2… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-09-20 (Tue, 20 Sep 2016) Changed paths: A lib/galaxy/datatypes/converters/tabular_to_dbnsfp.py Log Message: ----------- Merge pull request #2938 from nsoranzo/release_16.04_tabular_to_dbnsfp [16.04] Add missing tabular_to_dbnsfp.py for dbnsfp.tabular to snpsiftdbnsfp conversion Commit: 7627abb3856a4e757b5ed5c55ec05a4f97bd4cac https://github.com/galaxyproject/galaxy/commit/7627abb3856a4e757b5ed5c55ec0… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-09-20 (Tue, 20 Sep 2016) Changed paths: A lib/galaxy/datatypes/converters/tabular_to_dbnsfp.py Log Message: ----------- Merge branch 'release_16.04' into release_16.07 Commit: 8b3356b869beba70820235c2d0894cee9e590ffe https://github.com/galaxyproject/galaxy/commit/8b3356b869beba70820235c2d089… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-09-21 (Wed, 21 Sep 2016) Changed paths: M lib/galaxy/jobs/runners/slurm.py Log Message: ----------- Strip stderr message from sacct Commit: 34d60e2b27ab08a3ebc5201d1c3282d346d40af0 https://github.com/galaxyproject/galaxy/commit/34d60e2b27ab08a3ebc5201d1c32… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-09-21 (Wed, 21 Sep 2016) Changed paths: M lib/galaxy/jobs/runners/slurm.py Log Message: ----------- Merge pull request #2945 from nsoranzo/release_16.07_strip_stderr [16.07] Strip stderr message from sacct Commit: b83f0a10247119ef18bf72688d4e0bb8cfee8e36 https://github.com/galaxyproject/galaxy/commit/b83f0a10247119ef18bf72688d4e… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-09-21 (Wed, 21 Sep 2016) Changed paths: M scripts/tool_shed/build_ts_whoosh_index.py Log Message: ----------- Fix whoosh indexing. Commit: d7ab1c5cfbfcdff3ce3e201f6fb0684fdb914096 https://github.com/galaxyproject/galaxy/commit/d7ab1c5cfbfcdff3ce3e201f6fb0… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-09-22 (Thu, 22 Sep 2016) Changed paths: M client/galaxy/scripts/mvc/ui/ui-modal.js M static/maps/mvc/ui/ui-modal.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/ui/ui-modal.js Log Message: ----------- UI, Modal: re-build dom on render Moves templating to render (and updates dom node attributes after) to reset modal and prevent inline styling and other modifications to the singleton from persisting between calls to show. Commit: c0e8a7608351679b8ebdb71207339384161d6616 https://github.com/galaxyproject/galaxy/commit/c0e8a7608351679b8ebdb7120733… Author: Dave B <dave(a)bx.psu.edu> Date: 2016-09-22 (Thu, 22 Sep 2016) Changed paths: M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/webapps/tool_shed/model/__init__.py M lib/tool_shed/util/metadata_util.py Log Message: ----------- [16.07] Fix tool dependencies handling in Tool Shed model (#2950) * Fix the cause of toolshed test 1400 failing. * Fix handling of repositories without tool dependencies. * Fix tool dependency retrieval. In some cases, a process might attempt to fetch tool dependencies for revision 1:7334f6d0ac17, but the repository has been updated, and tool dependency metadata has been reassigned to e.g. 7:ce22ceec214a. This commit resolves that issue. * Correct the logic that returns an empty string for an empty dict. * Fix getting latest revision with tool dependencies. * Use self.app instead of trans.app Commit: 9b3c061addb4f3e61d72465cf492396b9e07464e https://github.com/galaxyproject/galaxy/commit/9b3c061addb4f3e61d72465cf492… Author: Dave B <dave(a)bx.psu.edu> Date: 2016-09-22 (Thu, 22 Sep 2016) Changed paths: M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/webapps/tool_shed/model/__init__.py M lib/tool_shed/util/metadata_util.py Log Message: ----------- [16.07] Fix tool dependencies handling in Tool Shed model (#2950) * Fix the cause of toolshed test 1400 failing. * Fix handling of repositories without tool dependencies. * Fix tool dependency retrieval. In some cases, a process might attempt to fetch tool dependencies for revision 1:7334f6d0ac17, but the repository has been updated, and tool dependency metadata has been reassigned to e.g. 7:ce22ceec214a. This commit resolves that issue. * Correct the logic that returns an empty string for an empty dict. * Fix getting latest revision with tool dependencies. * Use self.app instead of trans.app Conflicts: lib/galaxy/webapps/tool_shed/controllers/repository.py Commit: a78b8bcd2aa02abf787f0974fe567ab4f70f41a1 https://github.com/galaxyproject/galaxy/commit/a78b8bcd2aa02abf787f0974fe56… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-09-22 (Thu, 22 Sep 2016) Changed paths: A lib/galaxy/datatypes/converters/tabular_to_dbnsfp.py M lib/galaxy/managers/rbac_secured.py M test/unit/managers/test_DatasetManager.py Log Message: ----------- Merge branch 'release_16.04' of https://github.com/galaxyproject/galaxy into release_16.04 Commit: e18d4ed33b8b453229f969f2d05c997b2fa7fe96 https://github.com/galaxyproject/galaxy/commit/e18d4ed33b8b453229f969f2d05c… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-09-22 (Thu, 22 Sep 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/dataset.py Log Message: ----------- UI, datasets: fix optional column form values Updates metadata column checkbox flag from 'true' to '__NOTHING__' to reflect newer form_builder values. Fixes #2175 Commit: aa2e7834f697f02ebf11545b53882baee8b87f4e https://github.com/galaxyproject/galaxy/commit/aa2e7834f697f02ebf11545b5388… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-09-22 (Thu, 22 Sep 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/library_common.py Log Message: ----------- Fix optional flag for library datasets in legacy library ui Commit: c06f8c29968971c6c1e0dfc6847b3baf755f3a96 https://github.com/galaxyproject/galaxy/commit/c06f8c29968971c6c1e0dfc6847b… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-09-22 (Thu, 22 Sep 2016) Changed paths: M lib/galaxy/webapps/tool_shed/model/__init__.py Log Message: ----------- correct the method call Commit: 5e7ee28e0d6937fa53f39b350e04357b554ce9ae https://github.com/galaxyproject/galaxy/commit/5e7ee28e0d6937fa53f39b350e04… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-09-22 (Thu, 22 Sep 2016) Changed paths: M test/shed_functional/functional/test_1400_review_migration_stages.py Log Message: ----------- bump freebayes in test (since it was updated) Commit: 45e6949eeae88c0d3c4c3f6341ddc5695d329bb2 https://github.com/galaxyproject/galaxy/commit/45e6949eeae88c0d3c4c3f6341dd… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-09-23 (Fri, 23 Sep 2016) Changed paths: M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/webapps/tool_shed/model/__init__.py M lib/tool_shed/util/metadata_util.py M test/shed_functional/functional/test_1400_review_migration_stages.py Log Message: ----------- Merge pull request #2959 from martenson/release_16.04 [16.04] backport of model tool dependencies fix Commit: 2c8a5d9d58c49c662aed4193f71caaf3fafe5651 https://github.com/galaxyproject/galaxy/commit/2c8a5d9d58c49c662aed4193f71c… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-09-23 (Fri, 23 Sep 2016) Changed paths: M scripts/tool_shed/build_ts_whoosh_index.py Log Message: ----------- Correct import order. Commit: 3b3e2e3358aa73a5374345686581310d37349ff9 https://github.com/galaxyproject/galaxy/commit/3b3e2e3358aa73a5374345686581… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-09-23 (Fri, 23 Sep 2016) Changed paths: M test/shed_functional/functional/test_1400_review_migration_stages.py Log Message: ----------- Merge branch 'release_16.04' into release_16.07 Conflicts: lib/galaxy/webapps/tool_shed/controllers/repository.py lib/galaxy/webapps/tool_shed/model/__init__.py Commit: 092a7307c21afa8d66129dca23567b49a540d66a https://github.com/galaxyproject/galaxy/commit/092a7307c21afa8d66129dca2356… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-09-23 (Fri, 23 Sep 2016) Changed paths: M scripts/tool_shed/build_ts_whoosh_index.py Log Message: ----------- Merge pull request #2949 from davebx/backport_whoosh [16.07] Fix missing import in whoosh indexing script Commit: 26d381c9a5d77ecfa6bf3e96b2cb77df3d3f846d https://github.com/galaxyproject/galaxy/commit/26d381c9a5d77ecfa6bf3e96b2cb… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-09-24 (Sat, 24 Sep 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/library_common.py Log Message: ----------- Merge pull request #2962 from guerler/fix_library_optional_flag [16.07] Fix optional flag for library datasets in legacy library ui Commit: e667f9f360388839d723421b884836acb6974e6c https://github.com/galaxyproject/galaxy/commit/e667f9f360388839d723421b8848… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-09-25 (Sun, 25 Sep 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/dataset.py Log Message: ----------- Merge pull request #2960 from carlfeberhard/fix.bed-columns [16.07] UI, datasets: fix optional column form values Commit: 04d62e242412d0eb6e739f3577256d99b1aaa5bf https://github.com/galaxyproject/galaxy/commit/04d62e242412d0eb6e739f357725… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-09-26 (Mon, 26 Sep 2016) Changed paths: M client/galaxy/scripts/mvc/ui/ui-modal.js M static/maps/mvc/ui/ui-modal.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/ui/ui-modal.js Log Message: ----------- Merge pull request #2955 from carlfeberhard/fix.modal-resetting [16.07] UI, Modal: re-build dom on render Commit: 375ed8cc81590a18a52b61e32307562488fd551e https://github.com/galaxyproject/galaxy/commit/375ed8cc81590a18a52b61e32307… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-10-03 (Mon, 03 Oct 2016) Changed paths: M doc/source/admin/conda_faq.rst Log Message: ----------- polish resolvers section in conda faq docs Commit: ba274e37f2f0e8c9973b19c46fe99c5565c5118c https://github.com/galaxyproject/galaxy/commit/ba274e37f2f0e8c9973b19c46fe9… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-10-03 (Mon, 03 Oct 2016) Changed paths: M doc/source/admin/conda_faq.rst Log Message: ----------- describe the conda installation behavior a bit better Commit: 2899372791fdbba4f8db7c414a5447cf049987f3 https://github.com/galaxyproject/galaxy/commit/2899372791fdbba4f8db7c414a54… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-10-03 (Mon, 03 Oct 2016) Changed paths: M doc/source/admin/conda_faq.rst Log Message: ----------- Update conda_faq.rst Commit: fdfe9d8c20a63e6e6e6951d5fe5cbd7d74446d0a https://github.com/galaxyproject/galaxy/commit/fdfe9d8c20a63e6e6e6951d5fe5c… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-10-03 (Mon, 03 Oct 2016) Changed paths: M doc/source/admin/conda_faq.rst Log Message: ----------- Merge pull request #19 from martenson/nsoranzo-patch-1-1 Small fixes to conda_faq.rst changes Commit: d9fab3345856770a16a98f18cf9e6185a4eae91a https://github.com/galaxyproject/galaxy/commit/d9fab3345856770a16a98f18cf9e… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-10-03 (Mon, 03 Oct 2016) Changed paths: M doc/source/admin/conda_faq.rst Log Message: ----------- Merge pull request #2998 from martenson/conda-faq-polish [16.07] Conda FAQ polish Commit: 1e8337df5a4acf9e899adc07883f967973cbcac7 https://github.com/galaxyproject/galaxy/commit/1e8337df5a4acf9e899adc07883f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-10-05 (Wed, 05 Oct 2016) Changed paths: M lib/galaxy/tools/deps/__init__.py Log Message: ----------- Fix setting conda_copy_dependencies in galaxy.ini. (cherry picked from commit 9246b8629c3831ab623983c9003c4e92cbde97d5) Commit: 6d27a3c4b6184b393e535afd32f87e55e7a07b70 https://github.com/galaxyproject/galaxy/commit/6d27a3c4b6184b393e535afd32f8… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-10-05 (Wed, 05 Oct 2016) Changed paths: M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- Fix initial conda version at 4.0.5 This should prevent missing `activate` in <conda_prefix>/bin when downgrading to 3.19.3. This is what the conda people use in their CI environment ( [see](https://github.com/conda/conda/blob/master/utils/travis-run-install.sh… and perhaps why that bug made it into the release in the first place). Commit: f7c3e25e5db1a1d99c81380f552719bee07c1790 https://github.com/galaxyproject/galaxy/commit/f7c3e25e5db1a1d99c81380f5527… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-10-05 (Wed, 05 Oct 2016) Changed paths: M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- Merge pull request #3009 from mvdbeek/conda_downgrade [16.01] Backport #2869 Fix initial conda version at 4.0.5 Commit: 224c2126c73617ec906abc1e08d5f5a7548633b1 https://github.com/galaxyproject/galaxy/commit/224c2126c73617ec906abc1e08d5… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-10-05 (Wed, 05 Oct 2016) Changed paths: M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- Merge branch 'release_16.01' into release_16.04 Commit: d6845c249466d013b58ab021540fc5176096aaa0 https://github.com/galaxyproject/galaxy/commit/d6845c249466d013b58ab021540f… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-10-05 (Wed, 05 Oct 2016) Changed paths: M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- Merge branch 'release_16.04' into release_16.07 Commit: f32b6446a7a4fd5a0bca2fa8e93d4407e0ce3938 https://github.com/galaxyproject/galaxy/commit/f32b6446a7a4fd5a0bca2fa8e93d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-10-05 (Wed, 05 Oct 2016) Changed paths: M lib/galaxy/tools/deps/__init__.py Log Message: ----------- Merge pull request #3008 from natefoo/conda-copy-dependencies [16.07] Fix setting conda_copy_dependencies in galaxy.ini. Commit: 89278b0ec70b7a8f1cf42bda87335cf4f98f175b https://github.com/galaxyproject/galaxy/commit/89278b0ec70b7a8f1cf42bda8733… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-10-07 (Fri, 07 Oct 2016) Changed paths: M config/galaxy.ini.sample M doc/source/admin/dependency_resolvers.rst M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Fix for bioconda recipes depending on conda-forge. Some bioconda recipes now depend on conda forge, this fix is needed for them to work properly. Commit: ddacf38a11a9f752b3cfe13a8b63182ff1d02d06 https://github.com/galaxyproject/galaxy/commit/ddacf38a11a9f752b3cfe13a8b63… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-10-10 (Mon, 10 Oct 2016) Changed paths: M config/galaxy.ini.sample M doc/source/admin/dependency_resolvers.rst M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Merge pull request #3023 from jmchilton/fix_abyss [16.07] Fix for bioconda recipes depending on conda-forge. Commit: 39fb030f13c45991d4a2ca811b66e7872fb0a4e7 https://github.com/galaxyproject/galaxy/commit/39fb030f13c45991d4a2ca811b66… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-10-11 (Tue, 11 Oct 2016) Changed paths: M .travis.yml Log Message: ----------- Remove travis-ci python installation, since python2.7 is preinstalled on OSX images now Commit: 2adb98e58cc0f1d0d25aecc260d7108902d4b02c https://github.com/galaxyproject/galaxy/commit/2adb98e58cc0f1d0d25aecc260d7… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-10-11 (Tue, 11 Oct 2016) Changed paths: M .travis.yml Log Message: ----------- Merge pull request #3034 from mvdbeek/skip_python_install_travis [16.04] Remove travis-ci python installation, since python2.7 is preinstalled… Commit: 3300a73c9db6b99cbec6ae952e3e59f8a72e651b https://github.com/galaxyproject/galaxy/commit/3300a73c9db6b99cbec6ae952e3e… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-10-11 (Tue, 11 Oct 2016) Changed paths: M .travis.yml Log Message: ----------- Merge branch 'release_16.04' into release_16.07 Commit: 600112256970c1024b3ba4e6fa57cd61f9fe199d https://github.com/galaxyproject/galaxy/commit/600112256970c1024b3ba4e6fa57… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-10-13 (Thu, 13 Oct 2016) Changed paths: M templates/user/index.mako Log Message: ----------- remove the communication server check from non-galaxy calls Commit: cf0e4e84ce4137334ee6e8c20e56a52070179c4d https://github.com/galaxyproject/galaxy/commit/cf0e4e84ce4137334ee6e8c20e56… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-10-14 (Fri, 14 Oct 2016) Changed paths: M templates/user/index.mako Log Message: ----------- Merge pull request #3053 from martenson/fix-userindex-for-ts [16.07] remove the communication server check Commit: d10758a4f22daa24bdf55863f360493a4a3902f7 https://github.com/galaxyproject/galaxy/commit/d10758a4f22daa24bdf55863f360… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-10-21 (Fri, 21 Oct 2016) Changed paths: M .travis.yml M client/galaxy/scripts/mvc/ui/ui-modal.js M config/galaxy.ini.sample M doc/source/admin/conda_faq.rst M doc/source/admin/dependency_resolvers.rst A lib/galaxy/datatypes/converters/tabular_to_dbnsfp.py M lib/galaxy/dependencies/conditional-requirements.txt M lib/galaxy/jobs/runners/slurm.py M lib/galaxy/managers/rbac_secured.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/webapps/tool_shed/model/__init__.py M lib/tool_shed/util/metadata_util.py M scripts/tool_shed/build_ts_whoosh_index.py M static/maps/mvc/ui/ui-modal.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/ui/ui-modal.js M templates/user/index.mako M templates/webapps/galaxy/workflow/run.mako M test/shed_functional/functional/test_1400_review_migration_stages.py M test/unit/managers/test_DatasetManager.py Log Message: ----------- Merge pull request #3077 from galaxyproject/release_16.07 [master] bring master on par with release_16.07 Compare: https://github.com/galaxyproject/galaxy/compare/e320b1aaa70a...d10758a4f22d

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[galaxyproject/usegalaxy-playbook] c6b399: Update Main
by GitHub 20 Oct '16

20 Oct '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: c6b3998b3b084aa60958153f4e08a823fa1555b1 https://github.com/galaxyproject/usegalaxy-playbook/commit/c6b3998b3b084aa6… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-10-20 (Thu, 20 Oct 2016) Changed paths: M production/galaxy_version.yml Log Message: ----------- Update Main

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[galaxyproject/galaxy] 3a99bb: Add deprecated, legacy attribute default_value to ...
by GitHub 19 Oct '16

19 Oct '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 3a99bbae0716c98aa8e8d290a666909ac88c0817 https://github.com/galaxyproject/galaxy/commit/3a99bbae0716c98aa8e8d290a666… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-10-19 (Wed, 19 Oct 2016) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Add deprecated, legacy attribute default_value to XSD. Cleanup use of ``gxdocs:deprecated``. Commit: 05f792edcd4bf779d0e9c91f5f4c92396979f17b https://github.com/galaxyproject/galaxy/commit/05f792edcd4bf779d0e9c91f5f4c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-10-19 (Wed, 19 Oct 2016) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Specify actual parameter to use in lieu of default_value in XSD. As suggested by @nsoranzo. Commit: cfeb0135ac5fc3334d5a3afcfdfd1e586ce5d32f https://github.com/galaxyproject/galaxy/commit/cfeb0135ac5fc3334d5a3afcfdfd… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-10-19 (Wed, 19 Oct 2016) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Merge pull request #3072 from jmchilton/default_value_legacy_xsd Add deprecated, legacy attribute default_value to XSD. Compare: https://github.com/galaxyproject/galaxy/compare/2a7e4f79c0c0...cfeb0135ac5f

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[galaxyproject/galaxy] bdc882: Dataset metadata should not be cached when buildin...
by GitHub 18 Oct '16

18 Oct '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: bdc8829dd2363c759b362a275757448173afcd22 https://github.com/galaxyproject/galaxy/commit/bdc8829dd2363c759b362a275757… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-10-17 (Mon, 17 Oct 2016) Changed paths: M config/plugins/visualizations/charts/static/client/app.js Log Message: ----------- Dataset metadata should not be cached when building chart visualizations Commit: 2a7e4f79c0c04158fe37dbd6c1b95cc251537173 https://github.com/galaxyproject/galaxy/commit/2a7e4f79c0c04158fe37dbd6c1b9… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-10-18 (Tue, 18 Oct 2016) Changed paths: M config/plugins/visualizations/charts/static/client/app.js Log Message: ----------- Merge pull request #3062 from guerler/fix_dataset_caching Dataset metadata should not be cached when building chart visualizations Compare: https://github.com/galaxyproject/galaxy/compare/569723a4e548...2a7e4f79c0c0

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[galaxyproject/galaxy] 3e737c: Add Galaxy Architecture slides in .md
by GitHub 18 Oct '16

18 Oct '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 3e737c99ea21dcb7ea3a326d36aee9c715c8d70b https://github.com/galaxyproject/galaxy/commit/3e737c99ea21dcb7ea3a326d36ae… Author: Remi Marenco <remi.marenco(a)gmail.com> Date: 2016-10-17 (Mon, 17 Oct 2016) Changed paths: M .gitignore M Makefile M doc/source/conf.py A doc/source/slideshow/architecture/galaxy_architecture.md A doc/source/slideshow/architecture/images/backbone-model-view.svg A doc/source/slideshow/architecture/images/cluster_support.svg A doc/source/slideshow/architecture/images/data_managers.svg A doc/source/slideshow/architecture/images/docker-chart.png A doc/source/slideshow/architecture/images/family/team.png A doc/source/slideshow/architecture/images/galaxy_schema.png A doc/source/slideshow/architecture/images/hda.svg A doc/source/slideshow/architecture/images/hda_dataset.plantuml.svg A doc/source/slideshow/architecture/images/hda_dataset.plantuml.txt A doc/source/slideshow/architecture/images/hda_hdca.plantuml.svg A doc/source/slideshow/architecture/images/hda_hdca.plantuml.txt A doc/source/slideshow/architecture/images/jsload.png A doc/source/slideshow/architecture/images/libraries.svg A doc/source/slideshow/architecture/images/library_permissions.svg A doc/source/slideshow/architecture/images/objectstore.plantuml.svg A doc/source/slideshow/architecture/images/objectstore.plantuml.txt A doc/source/slideshow/architecture/images/objectstore_diagram.svg A doc/source/slideshow/architecture/images/plantuml_options.txt A doc/source/slideshow/architecture/images/sequence.json A doc/source/slideshow/architecture/images/server_client.plantuml.svg A doc/source/slideshow/architecture/images/server_client.plantuml.txt A doc/source/slideshow/architecture/images/server_client_old.plantuml.svg A doc/source/slideshow/architecture/images/server_client_old.plantuml.txt A doc/source/slideshow/architecture/images/sqla_arch_small.png A doc/source/slideshow/architecture/images/usegalaxy_webservers.svg A doc/source/slideshow/architecture/images/usegalaxyorg.svg A doc/source/slideshow/architecture/images/webapp.plantuml.svg A doc/source/slideshow/architecture/images/webapp.plantuml.txt A doc/source/slideshow/architecture/images/what-is-webpack.svg A doc/source/slideshow/architecture/images/workflow_definition.svg A doc/source/slideshow/architecture/images/workflow_run.svg A doc/source/slideshow/architecture/images/wsgi_app.svg A doc/source/slideshow/architecture/images/wsgi_request.svg A doc/source/slideshow/architecture/remark-latest.min.js A doc/source/slideshow/architecture/style.css M lib/galaxy/model/migrate/check.py A scripts/slideshow/__init__.py A scripts/slideshow/build_slideshow.py A scripts/slideshow/example.md A scripts/slideshow/slideshow_template.html A scripts/slideshow/style.sample.css Log Message: ----------- Add Galaxy Architecture slides in .md + the plumbing for slides creation Init of #2244, second part: Python converter md to html + wip on GCC 2015 talk conversion Add the 2. Galaxy app architecture. Need images Add the 3. Galaxy components and object model Add more content in md Fix linting error by adding newline at the end of build_slideshow.py Moved the galaxyArchitecture.md into a folder dedicated to it Add 7th and 17th image + add style.css to have a better management of layout + added first slide as the first in GCC2015 slide Set properly the CSS used in the whole presentation + add special to p and first slide Add special orange for regular text and green emphasis (emphasis_2_galaxy) Changed the font to PT Sans Add 3. with images + few modifications Removed the images integrated using background-image by now Markdown imaging (still need work, image's size seems not good by default Add Makefile target to build architecture slides... 2016 Updates to 2015 architecture talk. More intro slides for Galaxy architecture. Update author line. Progress on architecture slides... - Improved styling (use Oxygen - closer to Galaxy font) - Add ability to generate SVG diagrams to slide infrastructure - Add newer client-server sequence diagram based on that. Improved logging when there are problems with SQL migrations. More misc work on architecture talk. More images, slides, slide formatting, and initial work on an IPython notebook. Improved styling for architecture slides... Updates to architecture talk... - Infrastructure for building class diagrams with plantuml - Bring in move SVGs from last year's google docs. - Fill out section on client architecture. More work on slides for architecture talk. Add startup_output. Replace mermaid diagrams with plantuml diagrams. Fill out these diagrams more and style them for a black background in Galaxy oranges. Commit: 564aeeccd7379a5717de2180f5eb3208e479ea98 https://github.com/galaxyproject/galaxy/commit/564aeeccd7379a5717de2180f5eb… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-10-17 (Mon, 17 Oct 2016) Changed paths: M Makefile Log Message: ----------- remove the duplicated variable Commit: 569723a4e5487c4eab25dfe619cda5b044b6115b https://github.com/galaxyproject/galaxy/commit/569723a4e5487c4eab25dfe619cd… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-10-18 (Tue, 18 Oct 2016) Changed paths: M .gitignore M Makefile M doc/source/conf.py A doc/source/slideshow/architecture/galaxy_architecture.md A doc/source/slideshow/architecture/images/backbone-model-view.svg A doc/source/slideshow/architecture/images/cluster_support.svg A doc/source/slideshow/architecture/images/data_managers.svg A doc/source/slideshow/architecture/images/docker-chart.png A doc/source/slideshow/architecture/images/family/team.png A doc/source/slideshow/architecture/images/galaxy_schema.png A doc/source/slideshow/architecture/images/hda.svg A doc/source/slideshow/architecture/images/hda_dataset.plantuml.svg A doc/source/slideshow/architecture/images/hda_dataset.plantuml.txt A doc/source/slideshow/architecture/images/hda_hdca.plantuml.svg A doc/source/slideshow/architecture/images/hda_hdca.plantuml.txt A doc/source/slideshow/architecture/images/jsload.png A doc/source/slideshow/architecture/images/libraries.svg A doc/source/slideshow/architecture/images/library_permissions.svg A doc/source/slideshow/architecture/images/objectstore.plantuml.svg A doc/source/slideshow/architecture/images/objectstore.plantuml.txt A doc/source/slideshow/architecture/images/objectstore_diagram.svg A doc/source/slideshow/architecture/images/plantuml_options.txt A doc/source/slideshow/architecture/images/sequence.json A doc/source/slideshow/architecture/images/server_client.plantuml.svg A doc/source/slideshow/architecture/images/server_client.plantuml.txt A doc/source/slideshow/architecture/images/server_client_old.plantuml.svg A doc/source/slideshow/architecture/images/server_client_old.plantuml.txt A doc/source/slideshow/architecture/images/sqla_arch_small.png A doc/source/slideshow/architecture/images/usegalaxy_webservers.svg A doc/source/slideshow/architecture/images/usegalaxyorg.svg A doc/source/slideshow/architecture/images/webapp.plantuml.svg A doc/source/slideshow/architecture/images/webapp.plantuml.txt A doc/source/slideshow/architecture/images/what-is-webpack.svg A doc/source/slideshow/architecture/images/workflow_definition.svg A doc/source/slideshow/architecture/images/workflow_run.svg A doc/source/slideshow/architecture/images/wsgi_app.svg A doc/source/slideshow/architecture/images/wsgi_request.svg A doc/source/slideshow/architecture/remark-latest.min.js A doc/source/slideshow/architecture/style.css M lib/galaxy/model/migrate/check.py A scripts/slideshow/__init__.py A scripts/slideshow/build_slideshow.py A scripts/slideshow/example.md A scripts/slideshow/slideshow_template.html A scripts/slideshow/style.sample.css Log Message: ----------- Merge pull request #3060 from martenson/remimarenco-gcc2015_talk Add Galaxy Architecture slides in .md Compare: https://github.com/galaxyproject/galaxy/compare/1dc2d6a4ead3...569723a4e548

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[galaxyproject/galaxy] 8e0eaf: Add biojs multiple sequence viewer
by GitHub 17 Oct '16

17 Oct '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 8e0eaf2427a99f093a35d686532214534c1bb043 https://github.com/galaxyproject/galaxy/commit/8e0eaf2427a99f093a35d6865322… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-24 (Wed, 24 Aug 2016) Changed paths: M config/plugins/visualizations/charts/config/charts.xml A config/plugins/visualizations/charts/static/charts/biojs/msa/config.js A config/plugins/visualizations/charts/static/charts/biojs/msa/logo.png A config/plugins/visualizations/charts/static/charts/biojs/msa/wrapper.js M config/plugins/visualizations/charts/static/charts/overview.js M config/plugins/visualizations/charts/static/charts/types.js A config/plugins/visualizations/charts/static/plugins/biojs/biojs.msa.js M config/plugins/visualizations/charts/static/views/editor.js M config/plugins/visualizations/charts/static/views/groups.js M config/plugins/visualizations/charts/static/views/settings.js M config/plugins/visualizations/charts/static/views/viewport.js M config/plugins/visualizations/charts/templates/charts.mako Log Message: ----------- Add biojs multiple sequence viewer Commit: 97519231e536ab689d5285ce328c46e19fa2566b https://github.com/galaxyproject/galaxy/commit/97519231e536ab689d5285ce328c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-24 (Wed, 24 Aug 2016) Changed paths: M config/plugins/visualizations/charts/static/app.css Log Message: ----------- Fix style Commit: 6a450b9a06a81a58875297af7832f1d5a2cab8a5 https://github.com/galaxyproject/galaxy/commit/6a450b9a06a81a58875297af7832… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-24 (Wed, 24 Aug 2016) Changed paths: M config/plugins/visualizations/charts/static/charts/biojs/msa/config.js M config/plugins/visualizations/charts/static/charts/biojs/msa/wrapper.js Log Message: ----------- Add basic options to configure msa viewer Commit: 72ea2b030242cf448829f82d02e77a10ef7ce75d https://github.com/galaxyproject/galaxy/commit/72ea2b030242cf448829f82d02e7… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-25 (Thu, 25 Aug 2016) Changed paths: M config/plugins/visualizations/charts/static/app.js M config/plugins/visualizations/charts/static/charts/biojs/msa/wrapper.js M config/plugins/visualizations/charts/static/charts/jqplot/bar/wrapper.js M config/plugins/visualizations/charts/static/charts/jqplot/boxplot/wrapper.js M config/plugins/visualizations/charts/static/charts/jqplot/common/wrapper.js M config/plugins/visualizations/charts/static/charts/jqplot/histogram_discrete/wrapper.js M config/plugins/visualizations/charts/static/charts/jqplot/line/wrapper.js M config/plugins/visualizations/charts/static/charts/jqplot/scatter/wrapper.js M config/plugins/visualizations/charts/static/charts/nvd3/bar/wrapper.js M config/plugins/visualizations/charts/static/charts/nvd3/bar_horizontal/wrapper.js M config/plugins/visualizations/charts/static/charts/nvd3/bar_horizontal_stacked/wrapper.js M config/plugins/visualizations/charts/static/charts/nvd3/bar_stacked/wrapper.js M config/plugins/visualizations/charts/static/charts/nvd3/common/wrapper.js M config/plugins/visualizations/charts/static/charts/nvd3/histogram/wrapper.js M config/plugins/visualizations/charts/static/charts/nvd3/histogram_discrete/wrapper.js M config/plugins/visualizations/charts/static/charts/nvd3/line/wrapper.js M config/plugins/visualizations/charts/static/charts/nvd3/line_focus/wrapper.js M config/plugins/visualizations/charts/static/charts/nvd3/pie/wrapper.js M config/plugins/visualizations/charts/static/charts/nvd3/scatter/wrapper.js M config/plugins/visualizations/charts/static/charts/nvd3/stackedarea/wrapper.js M config/plugins/visualizations/charts/static/charts/nvd3/stackedarea_full/wrapper.js M config/plugins/visualizations/charts/static/charts/nvd3/stackedarea_stream/wrapper.js M config/plugins/visualizations/charts/static/charts/others/heatmap/heatmap-plugin.js M config/plugins/visualizations/charts/static/charts/others/heatmap/wrapper.js M config/plugins/visualizations/charts/static/charts/others/heatmap_cluster/wrapper.js M config/plugins/visualizations/charts/static/components/jobs.js M config/plugins/visualizations/charts/static/components/model.js M config/plugins/visualizations/charts/static/views/types.js M config/plugins/visualizations/charts/static/views/viewport.js Log Message: ----------- Avoid parsing app to chart wrappers Commit: e02eb60296eac4339aa2265313a38d4dc36aa415 https://github.com/galaxyproject/galaxy/commit/e02eb60296eac4339aa2265313a3… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-25 (Thu, 25 Aug 2016) Changed paths: M config/plugins/visualizations/charts/static/app.js M config/plugins/visualizations/charts/static/components/storage.js Log Message: ----------- Decouple storage, parse parameters explicitly Commit: 37c1e316a74348ad1023bd071f19e4396758540a https://github.com/galaxyproject/galaxy/commit/37c1e316a74348ad1023bd071f19… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-25 (Thu, 25 Aug 2016) Changed paths: M config/plugins/visualizations/charts/static/app.js M config/plugins/visualizations/charts/static/components/storage.js Log Message: ----------- Move chart listener into storage Commit: 48ff0790bf9b2115d891ca4c1a375f7f266b3399 https://github.com/galaxyproject/galaxy/commit/48ff0790bf9b2115d891ca4c1a37… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-25 (Thu, 25 Aug 2016) Changed paths: M config/plugins/visualizations/charts/static/components/storage.js Log Message: ----------- Fix save failed message Commit: 3048b56006cc1ee0877e24767e2535ccbe5164b7 https://github.com/galaxyproject/galaxy/commit/3048b56006cc1ee0877e24767e25… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-25 (Thu, 25 Aug 2016) Changed paths: M config/plugins/visualizations/charts/static/charts/biojs/msa/wrapper.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/others/example/wrapper.js M config/plugins/visualizations/charts/static/charts/utilities/tabular-utilities.js M config/plugins/visualizations/charts/static/views/viewport.js Log Message: ----------- Remove unused container list Commit: a63b07795c23a7412592d8aa7e395ff6394625ae https://github.com/galaxyproject/galaxy/commit/a63b07795c23a7412592d8aa7e39… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-25 (Thu, 25 Aug 2016) Changed paths: M config/plugins/visualizations/charts/static/app.css M config/plugins/visualizations/charts/static/views/viewport.js Log Message: ----------- Fix scrolling behavior Commit: f2c1e23409f407b773913629714c697a04fb0740 https://github.com/galaxyproject/galaxy/commit/f2c1e23409f407b773913629714c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-25 (Thu, 25 Aug 2016) Changed paths: M config/plugins/visualizations/charts/static/charts/overview.js M config/plugins/visualizations/charts/static/views/viewer.js Log Message: ----------- Add description for biojs Commit: 7107705b9c821c20a07ae3275c50eac517b44a37 https://github.com/galaxyproject/galaxy/commit/7107705b9c821c20a07ae3275c50… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-25 (Thu, 25 Aug 2016) Changed paths: M config/plugins/visualizations/charts/static/views/viewport.js Log Message: ----------- Remove unused menu div Commit: 5f642113156435b34d3ff6de01144069d2e370c1 https://github.com/galaxyproject/galaxy/commit/5f642113156435b34d3ff6de0114… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-25 (Thu, 25 Aug 2016) Changed paths: M config/plugins/visualizations/charts/static/views/viewport.js Log Message: ----------- Use shorter dom query command Commit: ebd0dab936b4fbb82dbb21218851ca7579197bf7 https://github.com/galaxyproject/galaxy/commit/ebd0dab936b4fbb82dbb21218851… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-25 (Thu, 25 Aug 2016) Changed paths: M config/plugins/visualizations/charts/static/views/editor.js Log Message: ----------- Change draw label to indicate that the chart will be saved too Commit: 30bd72310e4d51f49e9fe020b119c02642ffe854 https://github.com/galaxyproject/galaxy/commit/30bd72310e4d51f49e9fe020b119… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-25 (Thu, 25 Aug 2016) Changed paths: M config/plugins/visualizations/charts/static/views/editor.js Log Message: ----------- Fix tooltip Commit: 9481939154269253e59a2d9ffafe506947287dc1 https://github.com/galaxyproject/galaxy/commit/9481939154269253e59a2d9ffafe… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-25 (Thu, 25 Aug 2016) Changed paths: M config/plugins/visualizations/charts/static/charts/utilities/tabular-form.js R config/plugins/visualizations/charts/static/charts/utilities/tabular-inputs.js M config/plugins/visualizations/charts/static/views/settings.js Log Message: ----------- Remove separated tabular input element Commit: 70e68c204b3f250e76032761d796f62552f63d70 https://github.com/galaxyproject/galaxy/commit/70e68c204b3f250e76032761d796… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-25 (Thu, 25 Aug 2016) Changed paths: M config/plugins/visualizations/charts/static/views/settings.js Log Message: ----------- Fix spacing Commit: 77dddc3fa42e28eef9ad14c30d8047b2b2865c09 https://github.com/galaxyproject/galaxy/commit/77dddc3fa42e28eef9ad14c30d80… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-25 (Thu, 25 Aug 2016) Changed paths: M config/plugins/visualizations/charts/static/views/settings.js Log Message: ----------- Generalize internal use panels parameter option Commit: d6f174e487b77862c005b65843af79c53bd560c7 https://github.com/galaxyproject/galaxy/commit/d6f174e487b77862c005b65843af… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-25 (Thu, 25 Aug 2016) Changed paths: M client/galaxy/scripts/mvc/ui/ui-buttons.js M config/plugins/visualizations/charts/static/app.js M config/plugins/visualizations/charts/static/charts/jqplot/common/config.js M config/plugins/visualizations/charts/static/charts/nvd3/common/config.js M config/plugins/visualizations/charts/static/views/viewer.js M static/maps/mvc/ui/ui-buttons.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/ui/ui-buttons.js Log Message: ----------- Filter exportable datatypes by chart type Commit: 6d28721158e9e385c5d734de280eb4c9d3386672 https://github.com/galaxyproject/galaxy/commit/6d28721158e9e385c5d734de280e… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-25 (Thu, 25 Aug 2016) Changed paths: M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Repack Commit: 6c0df63e255c198380ca1e168ebed87a8467924f https://github.com/galaxyproject/galaxy/commit/6c0df63e255c198380ca1e168ebe… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-25 (Thu, 25 Aug 2016) Changed paths: M config/plugins/visualizations/charts/static/views/viewer.js Log Message: ----------- Fix tooltip Commit: 004fbd6e551a8fbd3bc9f9317ca34b4f55e10ea4 https://github.com/galaxyproject/galaxy/commit/004fbd6e551a8fbd3bc9f9317ca3… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-25 (Thu, 25 Aug 2016) Changed paths: M config/plugins/visualizations/charts/static/charts/others/example/config.js Log Message: ----------- Fix developer examples config Commit: 9e2e0dc7394814066c98b65e990e5a3750b9756e https://github.com/galaxyproject/galaxy/commit/9e2e0dc7394814066c98b65e990e… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-25 (Thu, 25 Aug 2016) Changed paths: M config/plugins/visualizations/charts/static/charts/others/example/wrapper.js Log Message: ----------- Fix developer example Commit: e8eb48a9c42de08edd6e9a4ea529bcac0d698df9 https://github.com/galaxyproject/galaxy/commit/e8eb48a9c42de08edd6e9a4ea529… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-25 (Thu, 25 Aug 2016) Changed paths: M config/plugins/visualizations/charts/templates/charts.mako Log Message: ----------- Remove unused app variable Commit: f98ade125f0fbe5d90ca0f005a84f8f7d91fb3d5 https://github.com/galaxyproject/galaxy/commit/f98ade125f0fbe5d90ca0f005a84… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-25 (Thu, 25 Aug 2016) Changed paths: M config/plugins/visualizations/charts/static/charts/biojs/msa/config.js Log Message: ----------- Add basic description for msa viewer Commit: c4e9ecfe4c9dec4f9c58597fc755a4c4ab944a83 https://github.com/galaxyproject/galaxy/commit/c4e9ecfe4c9dec4f9c58597fc755… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-25 (Thu, 25 Aug 2016) Changed paths: M config/plugins/visualizations/charts/static/charts/biojs/msa/config.js M config/plugins/visualizations/charts/static/charts/nvd3/pie/config.js M config/plugins/visualizations/charts/static/charts/others/example/config.js M config/plugins/visualizations/charts/static/charts/utilities/tabular-form.js M config/plugins/visualizations/charts/static/views/types.js Log Message: ----------- Allow multiple datatype matching Commit: edfdef2853e2df3f5058d97e1578c4129fb292de https://github.com/galaxyproject/galaxy/commit/edfdef2853e2df3f5058d97e1578… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-25 (Thu, 25 Aug 2016) Changed paths: M client/galaxy/scripts/mvc/ui/ui-buttons.js M static/maps/mvc/ui/ui-buttons.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/ui/ui-buttons.js Log Message: ----------- Enhance ui menu button view Commit: 72f89a4c262de328d398ebbb4c6ccfefc483b75d https://github.com/galaxyproject/galaxy/commit/72f89a4c262de328d398ebbb4c6c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-26 (Fri, 26 Aug 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M static/maps/mvc/tool/tool-form-base.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tool-form-base.js Log Message: ----------- Fix requirements message Commit: 59852d0e0f4897b09a964091d5792458de48deb0 https://github.com/galaxyproject/galaxy/commit/59852d0e0f4897b09a964091d579… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-30 (Tue, 30 Aug 2016) Changed paths: M config/plugins/visualizations/charts/static/app.js R 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config/plugins/visualizations/charts/static/charts/overview.js R config/plugins/visualizations/charts/static/charts/types.js R config/plugins/visualizations/charts/static/charts/utilities/tabular-datasets.js R config/plugins/visualizations/charts/static/charts/utilities/tabular-form.js R config/plugins/visualizations/charts/static/charts/utilities/tabular-utilities.js R config/plugins/visualizations/charts/static/components/jobs.js R config/plugins/visualizations/charts/static/plugins/biojs/biojs.msa.js R config/plugins/visualizations/charts/static/plugins/canvg/canvg.js R config/plugins/visualizations/charts/static/plugins/canvg/rgbcolor.js R config/plugins/visualizations/charts/static/plugins/crossfilter/crossfilter.js R config/plugins/visualizations/charts/static/plugins/jqplot/jquery.jqplot.css R config/plugins/visualizations/charts/static/plugins/jqplot/jquery.jqplot.js R config/plugins/visualizations/charts/static/plugins/jqplot/jquery.jqplot.plugins.js R 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R config/plugins/visualizations/charts/static/plugins/jqplot/plugins/jqplot.highlighter.min.js R config/plugins/visualizations/charts/static/plugins/jqplot/plugins/jqplot.ohlcRenderer.min.js R config/plugins/visualizations/charts/static/plugins/nvd3/nv.d3.css R config/plugins/visualizations/charts/static/plugins/nvd3/nv.d3.js M config/plugins/visualizations/charts/static/views/description.js M config/plugins/visualizations/charts/static/views/types.js M config/plugins/visualizations/charts/static/views/viewport.js M config/plugins/visualizations/charts/templates/charts.mako Log Message: ----------- Use remote repo for chart plugins Commit: af45adb7e6e57d4180b49581c5f48274df54117f https://github.com/galaxyproject/galaxy/commit/af45adb7e6e57d4180b49581c5f4… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-30 (Tue, 30 Aug 2016) Changed paths: M config/plugins/visualizations/charts/static/app.js M config/plugins/visualizations/charts/static/views/types.js M config/plugins/visualizations/charts/static/views/viewport.js M config/plugins/visualizations/charts/templates/charts.mako Log Message: ----------- Add error message if charts fails to retrieve plugin resources from its repository Commit: 3e7302fc3c6d8f0713d8698f6536662fc46f42b0 https://github.com/galaxyproject/galaxy/commit/3e7302fc3c6d8f0713d8698f6536… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-30 (Tue, 30 Aug 2016) Changed paths: M config/plugins/visualizations/charts/static/views/viewport.js Log Message: ----------- Fix remote url Commit: 42854e31ea50eae1e26ce2112696cd86ccb247be https://github.com/galaxyproject/galaxy/commit/42854e31ea50eae1e26ce2112696… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-30 (Tue, 30 Aug 2016) Changed paths: M config/plugins/visualizations/charts/static/views/types.js Log Message: ----------- Bundle thumbnail view Commit: d4d403d678a9c6d5a5dbf1df5c23b8425f1a1311 https://github.com/galaxyproject/galaxy/commit/d4d403d678a9c6d5a5dbf1df5c23… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-30 (Tue, 30 Aug 2016) Changed paths: M config/plugins/visualizations/charts/static/app.css M config/plugins/visualizations/charts/static/views/types.js Log Message: ----------- Show list instead Commit: 6f444e5cdbc69ba0fdca4a04c1dce7d7493420be https://github.com/galaxyproject/galaxy/commit/6f444e5cdbc69ba0fdca4a04c1dc… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-30 (Tue, 30 Aug 2016) Changed paths: M config/plugins/visualizations/charts/static/app.css M config/plugins/visualizations/charts/static/app.js M config/plugins/visualizations/charts/static/views/types.js Log Message: ----------- Restore regular selection view Commit: ccd265ed0705d3166f792d7d1473f229c8b5accb https://github.com/galaxyproject/galaxy/commit/ccd265ed0705d3166f792d7d1473… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-30 (Tue, 30 Aug 2016) Changed paths: M config/plugins/visualizations/charts/static/views/types.js Log Message: ----------- Fix tab creation behavior Commit: d65bf1e4f773c6c6d27b83e7a850b51bfd3d3faa https://github.com/galaxyproject/galaxy/commit/d65bf1e4f773c6c6d27b83e7a850… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-30 (Tue, 30 Aug 2016) Changed paths: M config/plugins/visualizations/charts/static/views/types.js Log Message: ----------- Fix sorting Commit: bee75fb77909ddc938290c134eb689a7f5729254 https://github.com/galaxyproject/galaxy/commit/bee75fb77909ddc938290c134eb6… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-30 (Tue, 30 Aug 2016) Changed paths: M config/plugins/visualizations/charts/static/views/types.js Log Message: ----------- Fix order Commit: 9601a0f607b71e8725dafff90288ee8486dbfcf1 https://github.com/galaxyproject/galaxy/commit/9601a0f607b71e8725dafff90288… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-30 (Tue, 30 Aug 2016) Changed paths: M config/plugins/visualizations/charts/static/app.css M config/plugins/visualizations/charts/static/views/types.js Log Message: ----------- Revise thumbnail view Commit: ec038cb0904b24c6df8cb5f7b16e671997004aa7 https://github.com/galaxyproject/galaxy/commit/ec038cb0904b24c6df8cb5f7b16e… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-30 (Tue, 30 Aug 2016) Changed paths: M config/plugins/visualizations/charts/static/views/types.js Log Message: ----------- Use original order Commit: 5cae6f7735436800c586065be690a43c1a1683e5 https://github.com/galaxyproject/galaxy/commit/5cae6f7735436800c586065be690… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-30 (Tue, 30 Aug 2016) Changed paths: M config/plugins/visualizations/charts/static/views/types.js Log Message: ----------- Fix spacing Commit: 71fe20ab040df9393c8ac0c083a31006a65ab848 https://github.com/galaxyproject/galaxy/commit/71fe20ab040df9393c8ac0c083a3… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-30 (Tue, 30 Aug 2016) Changed paths: M client/galaxy/scripts/utils/utils.js M config/plugins/visualizations/charts/static/views/description.js M static/maps/utils/utils.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/utils/utils.js Log Message: ----------- Identify links in visualizations plugins descriptions Commit: e0617bb29b280f5f7f756ccbfdd6678ed3e185ef https://github.com/galaxyproject/galaxy/commit/e0617bb29b280f5f7f756ccbfdd6… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-30 (Tue, 30 Aug 2016) Changed paths: M config/plugins/visualizations/charts/static/views/types.js Log Message: ----------- Add tooltip to thumbnail view? Commit: f03a06488feb0e1c471c92d11cff14c6bf5c0cf1 https://github.com/galaxyproject/galaxy/commit/f03a06488feb0e1c471c92d11cff… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-30 (Tue, 30 Aug 2016) Changed paths: M config/plugins/visualizations/charts/static/views/types.js Log Message: ----------- Limit title length for thumbnails Commit: f2b26a61cb14ff468ecc2971d6394e6cea64f889 https://github.com/galaxyproject/galaxy/commit/f2b26a61cb14ff468ecc2971d639… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-30 (Tue, 30 Aug 2016) Changed paths: M config/plugins/visualizations/charts/static/app.js M config/plugins/visualizations/charts/static/views/types.js M config/plugins/visualizations/charts/static/views/viewport.js Log Message: ----------- Filter suitable visualization types on initialization Commit: 84942582b57499a753cf9e8039486c3bc9efa4f3 https://github.com/galaxyproject/galaxy/commit/84942582b57499a753cf9e803948… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-30 (Tue, 30 Aug 2016) Changed paths: M config/plugins/visualizations/charts/static/app.js Log Message: ----------- Modify error message Commit: 3e79da902163b131aff677a7b1bad9fa87e61d89 https://github.com/galaxyproject/galaxy/commit/3e79da902163b131aff677a7b1ba… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-30 (Tue, 30 Aug 2016) Changed paths: M config/plugins/visualizations/charts/static/components/screenshot.js M config/plugins/visualizations/charts/static/views/description.js M config/plugins/visualizations/charts/templates/charts.mako Log Message: ----------- Fix error messages Commit: 5d780d68d1a2ec5d1928a0156637a1d522f5b743 https://github.com/galaxyproject/galaxy/commit/5d780d68d1a2ec5d1928a0156637… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-31 (Wed, 31 Aug 2016) Changed paths: M config/plugins/visualizations/charts/static/components/screenshot.js Log Message: ----------- Revise exporting functions, increase png quality, remove unused libraries Commit: 78bd9e8f867eb5747218644e2a5a1f5417079b73 https://github.com/galaxyproject/galaxy/commit/78bd9e8f867eb5747218644e2a5a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-31 (Wed, 31 Aug 2016) Changed paths: M Makefile M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/scratchbook.js R database/info.txt A doc/source/admin/chat-0.png A doc/source/admin/chat-1.png A doc/source/admin/chat-2.png A doc/source/admin/chat-3.png A doc/source/admin/chat-4.png A doc/source/admin/chat.rst A doc/source/admin/communication_server.png A doc/source/admin/communication_server_rooms.png A doc/source/admin/conda_faq.rst M doc/source/admin/index.rst A doc/source/releases/16.07.rst M doc/source/releases/16.07_announce.rst A doc/source/releases/16.10_announce.rst M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/watcher.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M scripts/bootstrap_history.py M static/maps/layout/menu.js.map M static/maps/layout/scratchbook.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/menu.js M static/scripts/layout/scratchbook.js R templates/admin/tool_shed_repository/browse_categories.mako A templates/admin/tool_shed_repository/browse_toolsheds.mako R templates/admin/tool_shed_repository/preview_repository.mako M templates/webapps/galaxy/workflow/display.mako M templates/webapps/tool_shed/index.mako Log Message: ----------- Merge branch 'dev' into remote_chart_plugins Commit: a97b4bae546a5621dc37b6beaaba747d51c8ed9e 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M config/plugins/visualizations/charts/static/components/model.js R config/plugins/visualizations/charts/static/components/storage.js M config/plugins/visualizations/charts/static/views/editor.js Log Message: ----------- Simplify storage handling Commit: 7d20e9055e1be434c7914fc540ceb64a8e4d1051 https://github.com/galaxyproject/galaxy/commit/7d20e9055e1be434c7914fc540ce… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-09-01 (Thu, 01 Sep 2016) Changed paths: M config/plugins/visualizations/charts/static/components/model.js Log Message: ----------- Remove unused options variable Commit: 30d4e338b473797816e8b8a5da93dcd5420e24fc https://github.com/galaxyproject/galaxy/commit/30d4e338b473797816e8b8a5da93… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-09-01 (Thu, 01 Sep 2016) Changed paths: M config/plugins/visualizations/charts/static/app.js M config/plugins/visualizations/charts/static/components/model.js M config/plugins/visualizations/charts/templates/charts.mako Log Message: ----------- Revise visualization config handling Commit: 57b41b201964b57daf9a95c06120cbe1bba14e1b https://github.com/galaxyproject/galaxy/commit/57b41b201964b57daf9a95c06120… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-09-01 (Thu, 01 Sep 2016) Changed paths: M config/plugins/visualizations/charts/static/components/model.js Log Message: ----------- Fix chart saving Commit: 22e79f7aa943edb9ca6a80d1b035931ab8c9232f https://github.com/galaxyproject/galaxy/commit/22e79f7aa943edb9ca6a80d1b035… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-09-01 (Thu, 01 Sep 2016) Changed paths: M config/plugins/visualizations/charts/static/components/model.js M config/plugins/visualizations/charts/static/components/screenshot.js M config/plugins/visualizations/charts/static/views/editor.js M config/plugins/visualizations/charts/static/views/types.js Log Message: ----------- Improve handling for cases with missing plugins Commit: 76c9948742d659b2dd73452cc2d3c49f44f00cd7 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M tools/maf/maf_to_fasta_multiple_sets.py M tools/maf/vcf_to_maf_customtrack.py M tools/metag_tools/shrimp_color_wrapper.py M tools/metag_tools/shrimp_wrapper.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/phenotype_association/pagetag.py M tools/phenotype_association/senatag.py M tools/solid_tools/maq_cs_wrapper.py M tools/solid_tools/solid_qual_stats.py M tools/sr_assembly/velvetg_wrapper.py M tools/sr_mapping/bfast_wrapper.py M tools/stats/filtering.py M tools/stats/grouping.py M tools/stats/gsummary.py M tools/visualization/LAJ_code.py M tox.ini Log Message: ----------- Merge branch 'dev' into remote_chart_plugins Commit: b7a25fc653fa30a78d97b2aa23e9a5ad43814694 https://github.com/galaxyproject/galaxy/commit/b7a25fc653fa30a78d97b2aa23e9… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-10-08 (Sat, 08 Oct 2016) Changed paths: M config/plugins/visualizations/charts/templates/charts.mako Log Message: ----------- Update repository revision to new drawrnajs logo Commit: bf5cc30b843838f30a4b40faa9834cbc28a01991 https://github.com/galaxyproject/galaxy/commit/bf5cc30b843838f30a4b40faa983… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-10-11 (Tue, 11 Oct 2016) Changed paths: R config/plugins/visualizations/charts/sample.txt M config/plugins/visualizations/charts/static/views/groups.js M config/plugins/visualizations/charts/static/views/viewport.js Log Message: ----------- Remove tabular file from repo, fix comments Commit: 1805ac8b5948ded11e154c887a2da99481ac70c6 https://github.com/galaxyproject/galaxy/commit/1805ac8b5948ded11e154c887a2d… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-10-11 (Tue, 11 Oct 2016) Changed paths: R config/plugins/visualizations/charts/Gruntfile.js M config/plugins/visualizations/charts/package.json R config/plugins/visualizations/charts/static/app.css R 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config/plugins/visualizations/charts/static/views/settings.js R config/plugins/visualizations/charts/static/views/types.js R config/plugins/visualizations/charts/static/views/viewer.js R config/plugins/visualizations/charts/static/views/viewport.js M config/plugins/visualizations/charts/templates/charts.mako A config/plugins/visualizations/charts/webpack.config.js Log Message: ----------- Add chart plugins back to plugins directory of visualization framework Commit: f467384fdd97dba43ee0f9b7c3592498de738ee8 https://github.com/galaxyproject/galaxy/commit/f467384fdd97dba43ee0f9b7c359… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-10-11 (Tue, 11 Oct 2016) Changed paths: M config/plugins/visualizations/charts/templates/charts.mako Log Message: ----------- Use fixed repository path Commit: fe73009db5248a04844db86584064b48a86f2cb2 https://github.com/galaxyproject/galaxy/commit/fe73009db5248a04844db8658406… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-10-11 (Tue, 11 Oct 2016) Changed paths: M config/plugins/visualizations/charts/static/client/components/model.js Log Message: ----------- Fix default options for storing request Commit: f053f9bb3d2820c09aab1a0bc3b29e27eed56d09 https://github.com/galaxyproject/galaxy/commit/f053f9bb3d2820c09aab1a0bc3b2… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-10-14 (Fri, 14 Oct 2016) Changed paths: M .ci/flake8_blacklist.txt M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M .travis.yml M client/galaxy/scripts/mvc/tool/tools.js M client/galaxy/style/source_material/circle.py M config/galaxy.ini.sample M config/job_conf.xml.sample_advanced M doc/parse_gx_xsd.py M doc/source/admin/dependency_resolvers.rst M doc/source/admin/index.rst A doc/source/admin/mulled_containers.rst M lib/galaxy/config.py M lib/galaxy/datatypes/images.py M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/sequence.py R lib/galaxy/datatypes/util/image_util.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/managers/collections_util.py M lib/galaxy/model/item_attrs.py M lib/galaxy/model/metadata.py M lib/galaxy/model/orm/now.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/cwl/__init__.py M lib/galaxy/tools/cwl/cwltool_deps.py M lib/galaxy/tools/cwl/parser.py M lib/galaxy/tools/cwl/runtime_actions.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/commands.py A lib/galaxy/tools/deps/conda_compat.py M lib/galaxy/tools/deps/conda_util.py A lib/galaxy/tools/deps/container_resolvers/__init__.py A lib/galaxy/tools/deps/container_resolvers/explicit.py A lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/deps/docker_util.py A lib/galaxy/tools/deps/installable.py A lib/galaxy/tools/deps/mulled/__init__.py A lib/galaxy/tools/deps/mulled/_cli.py A lib/galaxy/tools/deps/mulled/invfile.lua A lib/galaxy/tools/deps/mulled/mulled_build.py A 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lib/galaxy/tools/parameters/wrapped_json.py M lib/galaxy/tools/parser/__init__.py M lib/galaxy/tools/parser/factory.py M lib/galaxy/tools/toolbox/__init__.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/lineages/__init__.py M lib/galaxy/tools/toolbox/lineages/factory.py M lib/galaxy/tools/toolbox/lineages/tool_shed.py M lib/galaxy/tools/toolbox/parser.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/util/checkers.py A lib/galaxy/util/image_util.py M lib/galaxy/workflow/extract.py M lib/galaxy/workflow/run.py M lib/galaxy/workflow/schedulers/core.py M static/maps/mvc/tool/tools.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tools.js M test/api/helpers.py M test/api/test_api_batch.py M test/api/test_authenticate.py M test/api/test_dataset_collections.py M test/api/test_history_contents.py M test/api/test_page_revisions.py M test/api/test_pages.py M test/api/test_tool_data.py M test/api/test_tools.py M test/api/test_users.py M test/api/test_workflow_extraction.py M test/api/test_workflows.py M test/api/workflows_format_2/__init__.py M test/api/workflows_format_2/converter.py M test/api/workflows_format_2/main.py M test/base/api.py M test/base/driver_util.py M test/base/integration_util.py M test/base/interactor.py M test/base/test_logging.py M test/base/twilltestcase.py M test/functional/test_data_managers.py M test/functional/test_library_templates.py M test/functional/test_toolbox.py A test/functional/tools/mulled_example_multi_1.xml A test/functional/tools/multi_data_optional.xml M test/functional/tools/samples_tool_conf.xml M test/functional/workflow.py M test/integration/test_resolvers.py M test/manual/workflows_scaling.py M test/shed_functional/base/test_db_util.py M test/shed_functional/functional/test_0300_reset_all_metadata.py M test/shed_functional/functional/test_1300_reset_all_metadata.py M test/shed_functional/functional_tests.py M test/unit/jobs/test_runner_local.py M test/unit/tools_support.py M test/unit/unittest_utils/utility.py M tools/data_source/upload.py M tools/filters/gff/gff_filter_by_attribute.py M tools/stats/filtering.py Log Message: ----------- Merge branch 'dev' into remote_chart_plugins Commit: 1dc2d6a4ead34b9d8bdaecf85f146ca17b5e803c https://github.com/galaxyproject/galaxy/commit/1dc2d6a4ead34b9d8bdaecf85f14… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-10-17 (Mon, 17 Oct 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/ui/ui-buttons.js M client/galaxy/scripts/utils/utils.js R config/plugins/visualizations/charts/Gruntfile.js M config/plugins/visualizations/charts/config/charts.xml M config/plugins/visualizations/charts/package.json R config/plugins/visualizations/charts/sample.txt R config/plugins/visualizations/charts/static/app.css R config/plugins/visualizations/charts/static/app.js R 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config/plugins/visualizations/charts/static/repository/visualizations/nvd3/stackedarea_stream/wrapper.js A config/plugins/visualizations/charts/static/repository/visualizations/others/example/config.js A config/plugins/visualizations/charts/static/repository/visualizations/others/example/logo.png A config/plugins/visualizations/charts/static/repository/visualizations/others/example/wrapper.js A config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap/config.js A config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap/heatmap-parameters.js A config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap/heatmap-plugin.js A config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap/logo.png A config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap/wrapper.js A config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap_cluster/config.js A config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap_cluster/logo.png A config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap_cluster/wrapper.js A config/plugins/visualizations/charts/static/repository/visualizations/pv/viewer/config.js A config/plugins/visualizations/charts/static/repository/visualizations/pv/viewer/logo.png A config/plugins/visualizations/charts/static/repository/visualizations/pv/viewer/wrapper.js A config/plugins/visualizations/charts/static/repository/visualizations/utilities/tabular-datasets.js A config/plugins/visualizations/charts/static/repository/visualizations/utilities/tabular-form.js A config/plugins/visualizations/charts/static/repository/visualizations/utilities/tabular-utilities.js R config/plugins/visualizations/charts/static/views/description.js R config/plugins/visualizations/charts/static/views/editor.js R config/plugins/visualizations/charts/static/views/groups.js R config/plugins/visualizations/charts/static/views/settings.js R config/plugins/visualizations/charts/static/views/types.js R config/plugins/visualizations/charts/static/views/viewer.js R config/plugins/visualizations/charts/static/views/viewport.js M config/plugins/visualizations/charts/templates/charts.mako A config/plugins/visualizations/charts/webpack.config.js M static/maps/mvc/tool/tool-form-base.js.map M static/maps/mvc/ui/ui-buttons.js.map M static/maps/utils/utils.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/ui/ui-buttons.js M static/scripts/utils/utils.js Log Message: ----------- Merge pull request #2875 from guerler/remote_chart_plugins Link charts to external repo, adjust interface Compare: https://github.com/galaxyproject/galaxy/compare/7eb413f4e8ee...1dc2d6a4ead3

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[galaxyproject/galaxy] 5549a9: Fix link in galaxy.xsd.
by GitHub 17 Oct '16

17 Oct '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 5549a9ee2bd01940254c49e58ab143d4aa95049a https://github.com/galaxyproject/galaxy/commit/5549a9ee2bd01940254c49e58ab1… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-09-23 (Fri, 23 Sep 2016) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Fix link in galaxy.xsd. Commit: e8f35310ba581e8f88d719053979c4c3603c930a https://github.com/galaxyproject/galaxy/commit/e8f35310ba581e8f88d719053979… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-09-23 (Fri, 23 Sep 2016) Changed paths: M doc/schema_template.md M lib/galaxy/jobs/__init__.py M lib/galaxy/tools/xsd/galaxy.xsd M test/functional/tools/samples_tool_conf.xml A test/functional/tools/version_command.py A test/functional/tools/version_command_interpreter.xml A test/functional/tools/version_command_plain.xml A test/functional/tools/version_command_tool_dir.xml M test/unit/jobs/test_job_wrapper.py Log Message: ----------- Revise and improve ``version_command`` tag. - Include deprecated ``interpreter`` tag in XSD. (Closes galaxyproject/planemo#574) - Allow the use of ``$__tool_directory__`` in interpreter command (so we can actually call ``interpreter`` deprecated). - Include sample tools of both of these styles. - General improvements to the version command documentation. Commit: 7eb413f4e8ee97d68a6fa466d9c5189b324dde52 https://github.com/galaxyproject/galaxy/commit/7eb413f4e8ee97d68a6fa466d9c5… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-10-17 (Mon, 17 Oct 2016) Changed paths: M doc/schema_template.md M lib/galaxy/jobs/__init__.py M lib/galaxy/tools/xsd/galaxy.xsd M test/functional/tools/samples_tool_conf.xml A test/functional/tools/version_command.py A test/functional/tools/version_command_interpreter.xml A test/functional/tools/version_command_plain.xml A test/functional/tools/version_command_tool_dir.xml M test/unit/jobs/test_job_wrapper.py Log Message: ----------- Merge pull request #2961 from jmchilton/xsd_fixes_1 Improve ``version_command`` tag. Compare: https://github.com/galaxyproject/galaxy/compare/22839eeee0b0...7eb413f4e8ee

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[galaxyproject/galaxy] 868658: Always display text, with test cases
by GitHub 17 Oct '16

17 Oct '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 868658c7e72e3d0f37e36c51316a72a56a270376 https://github.com/galaxyproject/galaxy/commit/868658c7e72e3d0f37e36c51316a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-10-14 (Fri, 14 Oct 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Always display text, with test cases Commit: 22839eeee0b0909bc2726e60ffb26a213ddfc553 https://github.com/galaxyproject/galaxy/commit/22839eeee0b0909bc2726e60ffb2… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-10-17 (Mon, 17 Oct 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Merge pull request #3052 from guerler/always_display_text Always display text Compare: https://github.com/galaxyproject/galaxy/compare/7207c1509038...22839eeee0b0

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[galaxyproject/galaxy] d93ced: Increase min number of columns for pileup sniffing...
by GitHub 17 Oct '16

17 Oct '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d93cedef8a3e727bc0a089ad6eda4c5734cd55c7 https://github.com/galaxyproject/galaxy/commit/d93cedef8a3e727bc0a089ad6eda… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-10-11 (Tue, 11 Oct 2016) Changed paths: M lib/galaxy/datatypes/tabular.py Log Message: ----------- Increase min number of columns for pileup sniffing to 5 Fix #3001. Commit: 3be66005dc4cbd2a7d45e2a482f297dcaf493c02 https://github.com/galaxyproject/galaxy/commit/3be66005dc4cbd2a7d45e2a482f2… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-10-11 (Tue, 11 Oct 2016) Changed paths: M lib/galaxy/datatypes/tabular.py Log Message: ----------- Check that chromosome number is >=0 Commit: 7207c15090385a397493da0503b06dbea1004d68 https://github.com/galaxyproject/galaxy/commit/7207c15090385a397493da0503b0… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-10-17 (Mon, 17 Oct 2016) Changed paths: M lib/galaxy/datatypes/tabular.py Log Message: ----------- Merge pull request #3033 from nsoranzo/fix_for_3001 Increase min number of columns for pileup sniffing to 5 Compare: https://github.com/galaxyproject/galaxy/compare/4bf1994fc3fd...7207c1509038

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[galaxyproject/galaxy] 762337: Fix import orders for updates to flake8_import_ord...
by GitHub 17 Oct '16

17 Oct '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 762337e110d7a8d4058d7fcc7fd41147b0d89020 https://github.com/galaxyproject/galaxy/commit/762337e110d7a8d4058d7fcc7fd4… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-10-17 (Mon, 17 Oct 2016) Changed paths: M lib/galaxy/jobs/metrics/instrumenters/collectl.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/util/object_wrapper.py M lib/galaxy/web/framework/middleware/static.py M lib/galaxy/webapps/galaxy/api/tours.py M lib/galaxy/webapps/galaxy/controllers/userskeys.py M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/util/workflow_util.py M test/api/test_histories.py M test/api/test_libraries.py M test/unit/tools/test_tool_dependency_description.py Log Message: ----------- Fix import orders for updates to flake8_import_order. Commit: 4bf1994fc3fd09b874c9ea29a8871269d44ad193 https://github.com/galaxyproject/galaxy/commit/4bf1994fc3fd09b874c9ea29a887… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-10-17 (Mon, 17 Oct 2016) Changed paths: M lib/galaxy/jobs/metrics/instrumenters/collectl.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/util/object_wrapper.py M lib/galaxy/web/framework/middleware/static.py M lib/galaxy/webapps/galaxy/api/tours.py M lib/galaxy/webapps/galaxy/controllers/userskeys.py M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/util/workflow_util.py M test/api/test_histories.py M test/api/test_libraries.py M test/unit/tools/test_tool_dependency_description.py Log Message: ----------- Merge pull request #3059 from jmchilton/import_update Fix import orders for updates to flake8_import_order. Compare: https://github.com/galaxyproject/galaxy/compare/31cb477e1a53...4bf1994fc3fd

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[galaxyproject/galaxy] a2e0e6: Initial commit for new 'Merge Collection' tool. To...
by GitHub 17 Oct '16

17 Oct '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a2e0e6ba6c404aa899a91817ccf091b9a8fcecfa https://github.com/galaxyproject/galaxy/commit/a2e0e6ba6c404aa899a91817ccf0… Author: takadonet <philipmabon(a)gmail.com> Date: 2016-08-10 (Wed, 10 Aug 2016) Changed paths: M config/tool_conf.xml.sample M lib/galaxy/tools/__init__.py A lib/galaxy/tools/merge_collection.xml Log Message: ----------- Initial commit for new 'Merge Collection' tool. Tool takes two input list collection and combined them together into a single unified list. Tool provides options on how to deal when element_identifier are found in both list Commit: a76960b9a6523376e8d9ca6b2420d0e4883d1de0 https://github.com/galaxyproject/galaxy/commit/a76960b9a6523376e8d9ca6b2420… Author: takadonet <philipmabon(a)gmail.com> Date: 2016-08-10 (Wed, 10 Aug 2016) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- changed return statement to what it was before I forked. Commit: d5ea4ee380c5b8ed9a536e421c7365eeb379e3a2 https://github.com/galaxyproject/galaxy/commit/d5ea4ee380c5b8ed9a536e421c73… Author: takadonet <philipmabon(a)gmail.com> Date: 2016-08-10 (Wed, 10 Aug 2016) Changed paths: M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/ui/ui-portlet.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/style/less/ui.less M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/dataset_matcher.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py M static/maps/mvc/form/form-input.js.map M static/maps/mvc/form/form-parameters.js.map M static/maps/mvc/form/form-section.js.map M static/maps/mvc/form/form-view.js.map M static/maps/mvc/tool/tool-form-composite.js.map M static/maps/mvc/ui/ui-portlet.js.map M static/maps/mvc/ui/ui-select-default.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/form/form-input.js M static/scripts/mvc/form/form-parameters.js M static/scripts/mvc/form/form-section.js M static/scripts/mvc/form/form-view.js M static/scripts/mvc/tool/tool-form-composite.js M static/scripts/mvc/ui/ui-portlet.js M static/scripts/mvc/ui/ui-select-default.js M static/style/blue/base.css M test/qunit/test-data/fakeserver.js M test/qunit/tests/form_tests.js Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into dev Commit: a9b4d9518d1a7a7660d95a8dd312adae6ce48257 https://github.com/galaxyproject/galaxy/commit/a9b4d9518d1a7a7660d95a8dd312… Author: takadonet <philipmabon(a)gmail.com> Date: 2016-08-10 (Wed, 10 Aug 2016) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- re-worked logic to be more clear that there are three different modes when handling name conflicts Commit: 607d10275169f54f54c6e4a9357a4bf5d05b946e https://github.com/galaxyproject/galaxy/commit/607d10275169f54f54c6e4a9357a… Author: takadonet <philipmabon(a)gmail.com> Date: 2016-08-12 (Fri, 12 Aug 2016) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- changes based on flake8 erros Commit: d64d278ca9c3cc766620d1f3b0659dc8a6614e9a https://github.com/galaxyproject/galaxy/commit/d64d278ca9c3cc766620d1f3b065… Author: takadonet <philipmabon(a)gmail.com> Date: 2016-08-22 (Mon, 22 Aug 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/merge_collection.xml Log Message: ----------- Add the ability to change the suffix template to 3 different preset values. Same as Flatten collection tool. Added a test to ensure that its working. Commit: 424acd5fcf0937b09a7be8c58e674d143d0402a8 https://github.com/galaxyproject/galaxy/commit/424acd5fcf0937b09a7be8c58e67… Author: takadonet <philipmabon(a)gmail.com> Date: 2016-08-24 (Wed, 24 Aug 2016) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- fixed flake formatting errors Commit: c29f481dceeaaa790be1d8fdadfd58f1cb2d68c6 https://github.com/galaxyproject/galaxy/commit/c29f481dceeaaa790be1d8fdadfd… Author: takadonet <philipmabon(a)gmail.com> Date: 2016-08-26 (Fri, 26 Aug 2016) Changed paths: M config/tool_conf.xml.sample M lib/galaxy/tools/__init__.py A lib/galaxy/tools/append_collection.xml Log Message: ----------- initial version of append collection tool. Allow's user to add one or more datasets to an existing collection. Provides options when we have name conflicts Commit: b97ddd7ea52da1215c8251029f632cc972c6dba3 https://github.com/galaxyproject/galaxy/commit/b97ddd7ea52da1215c8251029f63… Author: takadonet <philipmabon(a)gmail.com> Date: 2016-08-26 (Fri, 26 Aug 2016) Changed paths: M .ci/first_startup.sh M .ci/flake8_lint_include_list.txt M Makefile M client/galaxy/scripts/mvc/dataset/data.js M client/galaxy/scripts/mvc/form/form-data.js M client/galaxy/scripts/mvc/form/form-repeat.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/ui/ui-color-picker.js M client/galaxy/scripts/mvc/ui/ui-tabs.js M client/galaxy/scripts/utils/utils.js M client/galaxy/style/less/library.less M config/datatypes_conf.xml.sample M config/galaxy.ini.sample M config/plugins/visualizations/charts/static/app.css M config/plugins/visualizations/charts/static/app.js R config/plugins/visualizations/charts/static/charts/forms/default.js M config/plugins/visualizations/charts/static/charts/jqplot/bar/config.js M config/plugins/visualizations/charts/static/charts/jqplot/bar/wrapper.js M config/plugins/visualizations/charts/static/charts/jqplot/boxplot/config.js M config/plugins/visualizations/charts/static/charts/jqplot/boxplot/wrapper.js M config/plugins/visualizations/charts/static/charts/jqplot/common/config.js M config/plugins/visualizations/charts/static/charts/jqplot/common/plot-config.js M config/plugins/visualizations/charts/static/charts/jqplot/common/wrapper.js M config/plugins/visualizations/charts/static/charts/jqplot/histogram_discrete/config.js M config/plugins/visualizations/charts/static/charts/jqplot/histogram_discrete/wrapper.js M config/plugins/visualizations/charts/static/charts/jqplot/line/config.js M config/plugins/visualizations/charts/static/charts/jqplot/line/wrapper.js M 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lib/galaxy/webapps/galaxy/api/lda_datasets.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/reports/buildapp.py M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/app.py M lib/galaxy/webapps/tool_shed/buildapp.py M lib/galaxy/webapps/tool_shed/config.py M lib/galaxy/webapps/tool_shed/controllers/hg.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/workflow/modules.py M lib/galaxy_ext/metadata/set_metadata.py M lib/tool_shed/galaxy_install/update_repository_manager.py M run.sh M scripts/bootstrap_history.py M scripts/common_startup.sh M static/maps/mvc/dataset/data.js.map M static/maps/mvc/form/form-data.js.map M static/maps/mvc/form/form-repeat.js.map M static/maps/mvc/form/form-section.js.map M 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test/functional/tools/samples_tool_conf.xml A test/functional/tools/tool_provided_metadata_1.xml A test/functional/tools/tool_provided_metadata_2.xml A test/functional/tools/tool_provided_metadata_3.xml M test/qunit/test-data/fakeserver.js M test/qunit/tests/form_tests.js M tools/genomespace/genomespace_file_browser.py M tools/genomespace/genomespace_importer.py Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into collection_tools Commit: 5159f878cfbdaa2627be76db1d69741b3579b68f https://github.com/galaxyproject/galaxy/commit/5159f878cfbdaa2627be76db1d69… Author: takadonet <philipmabon(a)gmail.com> Date: 2016-08-26 (Fri, 26 Aug 2016) Changed paths: M lib/galaxy/tools/append_collection.xml Log Message: ----------- change tool description Commit: f88e8a19fa270615bdfe482ca4f2d1175f56d10b https://github.com/galaxyproject/galaxy/commit/f88e8a19fa270615bdfe482ca4f2… Author: takadonet <philipmabon(a)gmail.com> Date: 2016-08-29 (Mon, 29 Aug 2016) Changed paths: M lib/galaxy/tools/append_collection.xml Log Message: ----------- changed tool name and description Commit: f54bf1bb3b0afc28d948a511001895abcaf8b15f https://github.com/galaxyproject/galaxy/commit/f54bf1bb3b0afc28d948a5110018… Author: takadonet <philipmabon(a)gmail.com> Date: 2016-08-29 (Mon, 29 Aug 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/filter_failed_collection.xml Log Message: ----------- Now allow filter_failed_collection to accept and filter out list:paired collection Commit: 97ba98037992a577a9a1a6b844893f63a7339034 https://github.com/galaxyproject/galaxy/commit/97ba98037992a577a9a1a6b84489… Author: takadonet <philipmabon(a)gmail.com> Date: 2016-08-29 (Mon, 29 Aug 2016) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- now change to see if the element has dataset_instance before attempting to call it. Commit: 4729565dfdc32482b177e3e2740f8abcbc23ab0f https://github.com/galaxyproject/galaxy/commit/4729565dfdc32482b177e3e2740f… Author: takadonet <philipmabon(a)gmail.com> Date: 2016-08-29 (Mon, 29 Aug 2016) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- added AppendCollectionTool to list of tool_classes Commit: 19a09e18a84a860d60e66517b3b68b58628843c7 https://github.com/galaxyproject/galaxy/commit/19a09e18a84a860d60e66517b3b6… Author: takadonet <philipmabon(a)gmail.com> Date: 2016-08-30 (Tue, 30 Aug 2016) Changed paths: M config/tool_conf.xml.sample M lib/galaxy/tools/__init__.py R lib/galaxy/tools/append_collection.xml Log Message: ----------- removed append_collection tool due to John request. MergeCollection should cover all cases that append would have anyway. Commit: ecc415369ff50dce02f5db73bdaf6fe8e60b6020 https://github.com/galaxyproject/galaxy/commit/ecc415369ff50dce02f5db73bdaf… Author: takadonet <philipmabon(a)gmail.com> Date: 2016-08-30 (Tue, 30 Aug 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/merge_collection.xml Log Message: ----------- added support to merge two list:paired collection together. Added single test to reflect new changes. Commit: 15ad14e6620706d6dbb39176783e274e01eebb3b https://github.com/galaxyproject/galaxy/commit/15ad14e6620706d6dbb39176783e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-10-16 (Sun, 16 Oct 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/merge_collection.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Enhance merge collection work from @Takadonet with more merge conflict actions. And allow it to work over any number of input collections. Commit: 448a27a4a1ebe2b25b40eca11b7aa319f7345c61 https://github.com/galaxyproject/galaxy/commit/448a27a4a1ebe2b25b40eca11b7a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-10-16 (Sun, 16 Oct 2016) Changed paths: M .ci/flake8_blacklist.txt A .ci/flake8_docstrings_include_list.txt M .ci/flake8_lint_include_list.txt M .ci/flake8_wrapper.sh A .ci/flake8_wrapper_docstrings.sh M .ci/py3_sources.txt A .ci/validate_test_tools.sh M .gitignore M .travis.yml M CONTRIBUTORS.md M LICENSE.txt M Makefile M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/scratchbook.js A client/galaxy/scripts/libs/bbi/bigwig.js A client/galaxy/scripts/libs/bbi/jquery-ajax-native.js A client/galaxy/scripts/libs/bbi/jszlib.js A client/galaxy/scripts/libs/bbi/spans.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/tool/tool-form-workflow.js M client/galaxy/scripts/mvc/tool/tool-form.js M 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M tools/maf/maf_to_fasta_multiple_sets.py M tools/maf/vcf_to_maf_customtrack.py M tools/metag_tools/shrimp_color_wrapper.py M tools/metag_tools/shrimp_wrapper.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/phenotype_association/pagetag.py M tools/phenotype_association/senatag.py M tools/solid_tools/maq_cs_wrapper.py M tools/solid_tools/solid_qual_stats.py M tools/sr_assembly/velvetg_wrapper.py M tools/sr_mapping/bfast_wrapper.py M tools/stats/filtering.py M tools/stats/grouping.py M tools/stats/gsummary.py M tools/visualization/LAJ_code.py M tox.ini Log Message: ----------- Merge remote-tracking branch 'jmchilton/dev' into collection_tools Commit: 49eac93882226e6f29624c676d593ae78719d7e5 https://github.com/galaxyproject/galaxy/commit/49eac93882226e6f29624c676d59… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-10-16 (Sun, 16 Oct 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/merge_collection.xml Log Message: ----------- Cleanup merge collection and get test cases working again. 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static/scripts/mvc/tool/tool-form-workflow.js M static/scripts/mvc/tool/tool-form.js M static/scripts/mvc/tool/tools.js M static/scripts/mvc/ui/ui-modal.js M static/scripts/mvc/ui/ui-portlet.js M static/scripts/mvc/ui/ui-select-content.js M static/scripts/utils/utils.js A static/scripts/viz/bbi-data-manager.js M static/scripts/viz/trackster/painters.js M static/scripts/viz/trackster/tracks.js M static/style/blue/base.css R templates/admin/tool_shed_repository/browse_categories.mako A templates/admin/tool_shed_repository/browse_toolsheds.mako M templates/admin/tool_shed_repository/common.mako R templates/admin/tool_shed_repository/preview_repository.mako M templates/show_params.mako M templates/user/info.mako M templates/user/register.mako M templates/user/username.mako M templates/webapps/galaxy/dataset/copy_view.mako M templates/webapps/galaxy/library/common/common.mako M templates/webapps/galaxy/workflow/build_from_current_history.mako M templates/webapps/galaxy/workflow/display.mako M templates/webapps/galaxy/workflow/run.mako R templates/webapps/galaxy/workflow/run_complete.mako M templates/webapps/tool_shed/repository/tool_form.mako M test/api/helpers.py M test/api/test_api_batch.py M test/api/test_authenticate.py M test/api/test_dataset_collections.py M test/api/test_history_contents.py M test/api/test_page_revisions.py M test/api/test_pages.py M test/api/test_tool_data.py M test/api/test_tools.py M test/api/test_users.py A test/api/test_workflow_batch.ga M test/api/test_workflow_extraction.py M test/api/test_workflows.py M test/api/workflows_format_2/__init__.py M test/api/workflows_format_2/converter.py M test/api/workflows_format_2/main.py M test/base/api.py M test/base/driver_util.py M test/base/integration_util.py M test/base/interactor.py M test/base/test_logging.py M test/base/twilltestcase.py M test/functional/test_data_managers.py M test/functional/test_library_templates.py M test/functional/test_toolbox.py A test/functional/tools/color_param.xml M test/functional/tools/column_multi_param.xml M test/functional/tools/column_param.xml M test/functional/tools/identifier_collection.xml M test/functional/tools/identifier_multiple.xml M test/functional/tools/identifier_single.xml M test/functional/tools/inputs_as_json.xml A test/functional/tools/metadata_column_names.xml A test/functional/tools/mulled_example_multi_1.xml A test/functional/tools/multi_data_optional.xml M test/functional/tools/multi_output.xml M test/functional/tools/multi_output_assign_primary.xml M test/functional/tools/multi_output_configured.xml R test/functional/tools/multi_page.xml M test/functional/tools/samples_tool_conf.xml M test/functional/tools/tool_directory.xml M test/functional/tools/validation_repeat.xml M test/functional/workflow.py M test/integration/test_resolvers.py M test/manual/workflows_scaling.py M test/qunit/tests/form_tests.js M test/shed_functional/base/test_db_util.py M test/shed_functional/functional/test_0300_reset_all_metadata.py M test/shed_functional/functional/test_1040_install_repository_basic_circular_dependencies.py M test/shed_functional/functional/test_1080_advanced_circular_dependency_installation.py M test/shed_functional/functional/test_1300_reset_all_metadata.py M test/shed_functional/functional/test_1400_review_migration_stages.py M test/shed_functional/functional_tests.py M test/unit/jobs/test_job_wrapper.py M test/unit/jobs/test_runner_local.py M test/unit/managers/test_DatasetManager.py M test/unit/managers/test_UserManager.py M test/unit/shed_unit/test_tool_panel_manager.py M test/unit/test_galaxy_mapping.py M test/unit/test_objectstore.py M test/unit/tools/test_data_parameters.py M test/unit/tools/test_parameter_parsing.py M test/unit/tools/test_parsing.py M test/unit/tools/test_tool_deps.py M test/unit/tools/test_tool_loader.py M test/unit/tools/test_toolbox.py M test/unit/tools/test_toolbox_filters.py M test/unit/tools/test_watcher.py M test/unit/tools/test_wrappers.py M test/unit/tools_support.py M test/unit/unittest_utils/galaxy_mock.py M test/unit/unittest_utils/utility.py M test/unit/workflows/test_run_parameters.py M tools/data_source/data_source.py M tools/data_source/hbvar_filter.py M tools/data_source/microbial_import_code.py M tools/data_source/upload.py M tools/data_source/upload.xml M tools/evolution/add_scores.py M tools/evolution/codingSnps_filter.py M tools/extract/extract_genomic_dna.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/axt_to_lav_code.py M tools/filters/bed_to_gff_converter.py M tools/filters/convert_characters.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/gtf_filter_by_attribute_values_list.py M tools/filters/gff_to_bed_converter.py M tools/filters/grep.py M tools/filters/gtf_to_bedgraph_converter.py M tools/filters/join.py M tools/filters/lav_to_bed.py M tools/filters/lav_to_bed_code.py M tools/filters/mergeCols.py M tools/filters/random_lines_two_pass.py M tools/filters/secure_hash_message_digest.py M tools/filters/sff_extract.py M tools/filters/trimmer.py M tools/filters/ucsc_gene_bed_to_exon_bed.py M tools/filters/ucsc_gene_bed_to_intron_bed.py M tools/filters/ucsc_gene_table_to_intervals.py M tools/filters/uniq.py M tools/filters/wiggle_to_simple.py M tools/genomespace/genomespace_exporter.py M tools/genomespace/genomespace_file_browser.py M tools/genomespace/genomespace_importer.py M tools/maf/interval2maf.py 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/vcf_to_maf_customtrack.py M tools/metag_tools/shrimp_color_wrapper.py M tools/metag_tools/shrimp_wrapper.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/phenotype_association/pagetag.py M tools/phenotype_association/senatag.py M tools/solid_tools/maq_cs_wrapper.py M tools/solid_tools/solid_qual_stats.py M tools/sr_assembly/velvetg_wrapper.py M tools/sr_mapping/bfast_wrapper.py M tools/stats/filtering.py M tools/stats/grouping.py M tools/stats/gsummary.py M tools/visualization/LAJ_code.py M tox.ini Log Message: ----------- Merge pull request #1 from jmchilton/collection_tools Enhance the Merge Collections Tool Commit: 31cb477e1a538c74360f039dda23907d0856adb6 https://github.com/galaxyproject/galaxy/commit/31cb477e1a538c74360f039dda23… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-10-17 (Mon, 17 Oct 2016) Changed paths: M config/tool_conf.xml.sample M lib/galaxy/tools/__init__.py M lib/galaxy/tools/filter_failed_collection.xml A lib/galaxy/tools/merge_collection.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #2771 from Takadonet/dev Collection Operator tools Compare: https://github.com/galaxyproject/galaxy/compare/a895c823daaf...31cb477e1a53

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[galaxyproject/usegalaxy-playbook] ef5103: update MTS
by GitHub 14 Oct '16

14 Oct '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: ef5103c91cffeb3acd129ece6205b7ed43a4383e https://github.com/galaxyproject/usegalaxy-playbook/commit/ef5103c91cffeb3a… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-10-14 (Fri, 14 Oct 2016) Changed paths: M common_roles M production/group_vars/toolshedservers.yml Log Message: ----------- update MTS

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[galaxyproject/galaxy] 600112: remove the communication server check
by GitHub 14 Oct '16

14 Oct '16

Branch: refs/heads/master-toolshed Home: https://github.com/galaxyproject/galaxy Commit: 600112256970c1024b3ba4e6fa57cd61f9fe199d https://github.com/galaxyproject/galaxy/commit/600112256970c1024b3ba4e6fa57… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-10-13 (Thu, 13 Oct 2016) Changed paths: M templates/user/index.mako Log Message: ----------- remove the communication server check from non-galaxy calls Commit: cf0e4e84ce4137334ee6e8c20e56a52070179c4d https://github.com/galaxyproject/galaxy/commit/cf0e4e84ce4137334ee6e8c20e56… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-10-14 (Fri, 14 Oct 2016) Changed paths: M templates/user/index.mako Log Message: ----------- Merge pull request #3053 from martenson/fix-userindex-for-ts [16.07] remove the communication server check Commit: 14dcf65132331170bf86c279b23241b7496d16d3 https://github.com/galaxyproject/galaxy/commit/14dcf65132331170bf86c279b232… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-10-14 (Fri, 14 Oct 2016) Changed paths: M templates/user/index.mako Log Message: ----------- Merge pull request #3056 from galaxyproject/release_16.07 [master-toolshed]merge in release_16.07 Compare: https://github.com/galaxyproject/galaxy/compare/735c682ead5f...14dcf6513233

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[galaxyproject/galaxy] 600112: remove the communication server check
by GitHub 14 Oct '16

14 Oct '16

Branch: refs/heads/release_16.07 Home: https://github.com/galaxyproject/galaxy Commit: 600112256970c1024b3ba4e6fa57cd61f9fe199d https://github.com/galaxyproject/galaxy/commit/600112256970c1024b3ba4e6fa57… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-10-13 (Thu, 13 Oct 2016) Changed paths: M templates/user/index.mako Log Message: ----------- remove the communication server check from non-galaxy calls Commit: cf0e4e84ce4137334ee6e8c20e56a52070179c4d https://github.com/galaxyproject/galaxy/commit/cf0e4e84ce4137334ee6e8c20e56… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-10-14 (Fri, 14 Oct 2016) Changed paths: M templates/user/index.mako Log Message: ----------- Merge pull request #3053 from martenson/fix-userindex-for-ts [16.07] remove the communication server check Compare: https://github.com/galaxyproject/galaxy/compare/3300a73c9db6...cf0e4e84ce41

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[galaxyproject/usegalaxy-playbook] b3aa09: Set Java memory on reserved destinations as well
by GitHub 14 Oct '16

14 Oct '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: b3aa0904fc2c468e6c109ed19817d35bdd1277a4 https://github.com/galaxyproject/usegalaxy-playbook/commit/b3aa0904fc2c468e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-10-14 (Fri, 14 Oct 2016) Changed paths: M templates/galaxy/usegalaxy.org/config/job_conf.xml.j2 Log Message: ----------- Set Java memory on reserved destinations as well

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[galaxyproject/usegalaxy-playbook] 505e87: Correctly set JVM memory size for Java tools
by GitHub 14 Oct '16

14 Oct '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 505e87545af74c1cfd7e276b1d35a53d74ada938 https://github.com/galaxyproject/usegalaxy-playbook/commit/505e87545af74c1c… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-10-14 (Fri, 14 Oct 2016) Changed paths: M templates/galaxy/usegalaxy.org/config/job_conf.xml.j2 Log Message: ----------- Correctly set JVM memory size for Java tools

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[galaxyproject/galaxy] 604dfb: Fix for reruning tool with workflow resume that is...
by GitHub 14 Oct '16

14 Oct '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 604dfb27ce0acba176c059f08642aae7a390ddf0 https://github.com/galaxyproject/galaxy/commit/604dfb27ce0acba176c059f08642… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-10-07 (Fri, 07 Oct 2016) Changed paths: M lib/galaxy/tools/parameters/__init__.py Log Message: ----------- Fix for reruning tool with workflow resume that is part of a collection. The special casing of "__identifier__" that occurs here and elsewhere in the code is less than ideal. Commit: a895c823daaf01c2b1b883dc256452411de9a728 https://github.com/galaxyproject/galaxy/commit/a895c823daaf01c2b1b883dc2564… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-10-14 (Fri, 14 Oct 2016) Changed paths: M lib/galaxy/tools/parameters/__init__.py Log Message: ----------- Merge pull request #3019 from blankenberg/collection-wf-resume-error Fix for rerunning tool with workflow resume that is part of a collection. Compare: https://github.com/galaxyproject/galaxy/compare/28bb83f0ab5e...a895c823daaf

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[galaxyproject/galaxy] 36134b: Added code to adjust top setting of tool search if...
by GitHub 14 Oct '16

14 Oct '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 36134bca694c9dc6b2584fb661dfbce4ddb793e6 https://github.com/galaxyproject/galaxy/commit/36134bca694c9dc6b2584fb661df… Author: Scott Szakonyi <sszakony(a)nd.edu> Date: 2016-10-14 (Fri, 14 Oct 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tools.js Log Message: ----------- Added code to adjust top setting of tool search if messagebox is visible, issue 2907 Commit: 6312d8052b9668a03b3bb25ea02b9d42ac32de6d https://github.com/galaxyproject/galaxy/commit/6312d8052b9668a03b3bb25ea02b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-10-14 (Fri, 14 Oct 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tools.js M static/maps/mvc/tool/tools.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tools.js Log Message: ----------- Rebuild cilent. Commit: 28bb83f0ab5e93b5f961f12dac555bf96a9073ea https://github.com/galaxyproject/galaxy/commit/28bb83f0ab5e93b5f961f12dac55… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-10-14 (Fri, 14 Oct 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tools.js M static/maps/mvc/tool/tools.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tools.js Log Message: ----------- Merge pull request #3055 from dannon/cherrypick_masthead_fix Cherrypick masthead fix Compare: https://github.com/galaxyproject/galaxy/compare/e5913a49e260...28bb83f0ab5e

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[galaxyproject/galaxy] f6d5f3: Fix downloading tool tarball with boolean test inp...
by GitHub 14 Oct '16

14 Oct '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f6d5f3c4a2e51bd6b75a99dc015360e4ca9a6461 https://github.com/galaxyproject/galaxy/commit/f6d5f3c4a2e51bd6b75a99dc0153… Author: Dave B <dave(a)bx.psu.edu> Date: 2016-10-13 (Thu, 13 Oct 2016) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Fix downloading tool tarball with boolean test input values. Commit: e5913a49e260be47ff4f32ae21780264731d98d5 https://github.com/galaxyproject/galaxy/commit/e5913a49e260be47ff4f32ae2178… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-10-14 (Fri, 14 Oct 2016) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge pull request #3047 from galaxyproject/tool_tarball_fix Fix downloading tool tarball with boolean test input values. Compare: https://github.com/galaxyproject/galaxy/compare/d26f46423e5d...e5913a49e260

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[galaxyproject/galaxy] bb4428: Failthrough to using imghdr when PIL does not dete...
by GitHub 14 Oct '16

14 Oct '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: bb4428896839898fb5d0c9b88ae18fc9b705a27b https://github.com/galaxyproject/galaxy/commit/bb4428896839898fb5d0c9b88ae1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-10-13 (Thu, 13 Oct 2016) Changed paths: M lib/galaxy/datatypes/images.py M lib/galaxy/datatypes/util/image_util.py M lib/galaxy/util/checkers.py M tools/data_source/upload.py Log Message: ----------- Failthrough to using imghdr when PIL does not detect an image correctly. Some misc cleanup, avoiding use of system functions as variable names, etc. Commit: cb6e25278c4a59d4ea2edd9ce5e9c757b1ebf7f8 https://github.com/galaxyproject/galaxy/commit/cb6e25278c4a59d4ea2edd9ce5e9… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-10-13 (Thu, 13 Oct 2016) Changed paths: M lib/galaxy/datatypes/images.py M lib/galaxy/datatypes/sequence.py R lib/galaxy/datatypes/util/image_util.py M lib/galaxy/util/checkers.py A lib/galaxy/util/image_util.py M tools/data_source/upload.py Log Message: ----------- Refactoring, because it was bugging me. Commit: ed263bf8a52b37199cc7822126598a75a9984335 https://github.com/galaxyproject/galaxy/commit/ed263bf8a52b37199cc782212659… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-10-13 (Thu, 13 Oct 2016) Changed paths: M lib/galaxy/util/image_util.py Log Message: ----------- import order. Commit: 4bc429776853239961c45c9656c69b3be0ae01bc https://github.com/galaxyproject/galaxy/commit/4bc429776853239961c45c9656c6… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-10-13 (Thu, 13 Oct 2016) Changed paths: M lib/galaxy/util/image_util.py Log Message: ----------- Simplify, strip out passing of image. Commit: d26f46423e5d79dd8d0519d90350389838fece3c https://github.com/galaxyproject/galaxy/commit/d26f46423e5d79dd8d0519d90350… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-10-14 (Fri, 14 Oct 2016) Changed paths: M lib/galaxy/datatypes/images.py M lib/galaxy/datatypes/sequence.py R lib/galaxy/datatypes/util/image_util.py M lib/galaxy/util/checkers.py A lib/galaxy/util/image_util.py M tools/data_source/upload.py Log Message: ----------- Merge pull request #3042 from dannon/image_detection_fixes Image detection fixes Compare: https://github.com/galaxyproject/galaxy/compare/4446ccc98c97...d26f46423e5d

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[galaxyproject/galaxy] b6d447: Fix for displaying parameters to the user, that ha...
by GitHub 13 Oct '16

13 Oct '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b6d4473aa0975f88b2d2cf8aa1372aecfc92919b https://github.com/galaxyproject/galaxy/commit/b6d4473aa0975f88b2d2cf8aa137… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-10-13 (Thu, 13 Oct 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Fix for displaying parameters to the user, that have a False value. Previously, e.g. an integer with a value of 0 would display "Not available.". Commit: 4446ccc98c970f5077080f563585c90b1f84dc3a https://github.com/galaxyproject/galaxy/commit/4446ccc98c970f5077080f563585… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-10-13 (Thu, 13 Oct 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Merge pull request #3045 from blankenberg/value_to_display_text-fix Fix for displaying parameters to the user, that have a False value. Compare: https://github.com/galaxyproject/galaxy/compare/0062eacfdf86...4446ccc98c97

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