- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] e10660: Add a more correct zip file type.
by GitHub 09 Feb '16

09 Feb '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e106609c1c1eebca693e20bbe36e6597d5e6574a https://github.com/galaxyproject/galaxy/commit/e106609c1c1eebca693e20bbe36e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-03 (Wed, 03 Feb 2016) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py Log Message: ----------- Add a more correct zip file type. Commit: 87f3ee48b026628506afeb2b8f99b0b0e37c74a8 https://github.com/galaxyproject/galaxy/commit/87f3ee48b026628506afeb2b8f99… Author: Gildas Le Corguillé <lecorguille(a)MacBook.local> Date: 2016-02-03 (Wed, 03 Feb 2016) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- add a zip datatype which won't be extracted Commit: b81f3149bfb624b26e84c95b4efd519850045981 https://github.com/galaxyproject/galaxy/commit/b81f3149bfb624b26e84c95b4efd… Author: Gildas Le Corguillé <lecorguille(a)users.noreply.github.com> Date: 2016-02-04 (Thu, 04 Feb 2016) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py Log Message: ----------- Merge pull request #1 from jmchilton/zip_datatype I take :) Commit: eab2f1ff5c53a733bd4b0ecf5718f3a53274f413 https://github.com/galaxyproject/galaxy/commit/eab2f1ff5c53a733bd4b0ecf5718… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-08 (Mon, 08 Feb 2016) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py Log Message: ----------- Merge pull request #1665 from lecorguille/zip_datatype add a zip datatype which won't be extracted Compare: https://github.com/galaxyproject/galaxy/compare/7a60f669fa5f...eab2f1ff5c53

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[galaxyproject/galaxy] 20f187: added resolver dependency display to the tool view...
by GitHub 09 Feb '16

09 Feb '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 20f18793cd53c6c0c5c43838b7368eb14809188e https://github.com/galaxyproject/galaxy/commit/20f18793cd53c6c0c5c43838b736… Author: Zipho Mashologu <zipho(a)trustpay.biz> Date: 2016-02-01 (Mon, 01 Feb 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/tool_dependencies.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M templates/admin/tool_shed_repository/manage_repository.mako M templates/webapps/tool_shed/repository/common.mako Log Message: ----------- added resolver dependency display to the tool view page Commit: 95cb53a2fb28c214a9191ba2f8758914efe1d151 https://github.com/galaxyproject/galaxy/commit/95cb53a2fb28c214a9191ba2f875… Author: Zipho Mashologu <zipho(a)trustpay.biz> Date: 2016-02-02 (Tue, 02 Feb 2016) Changed paths: M .travis.yml M client/galaxy/scripts/mvc/form/form-select-content.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-libraryrow-view.js M client/galaxy/scripts/mvc/list/list-view.js M client/galaxy/scripts/mvc/tours.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/visualization/visualization-model.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/scripts/onload.js M client/galaxy/style/less/library.less M client/galaxy/style/less/tour.less M config/galaxy.ini.sample M config/plugins/visualizations/charts/Gruntfile.js M config/plugins/visualizations/charts/templates/charts.mako M config/plugins/visualizations/scatterplot/templates/scatterplot.mako A doc/source/admin/framework_dependencies.rst M doc/source/admin/index.rst M doc/source/project/issues.rst A doc/source/releases/16.01.rst M doc/source/releases/16.01_announce.rst A doc/source/releases/16.04_announce.rst M doc/source/releases/index.rst M lib/galaxy/app.py M lib/galaxy/config.py M lib/galaxy/datatypes/interval.py A lib/galaxy/dependencies/conda-environment.txt M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/actions/post.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/condor.py M lib/galaxy/jobs/runners/drmaa.py M lib/galaxy/managers/base.py M lib/galaxy/managers/containers.py M lib/galaxy/managers/histories.py A lib/galaxy/managers/history_contents.py M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/execute.py M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/linters/inputs.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/dynamic_options.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/tools/parameters/validation.py M lib/galaxy/tools/special_tools.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/util/heartbeat.py M lib/galaxy/webapps/galaxy/api/folder_contents.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/work/context.py M lib/galaxy/workflow/extract.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/scheduling_manager.py M lib/tool_shed/galaxy_install/install_manager.py M scripts/bootstrap_history.py M scripts/common_startup.sh R static/maps/libs/backbone/backbone.js.map M static/maps/mvc/form/form-select-content.js.map M static/maps/mvc/library/library-folderlist-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/maps/mvc/library/library-libraryrow-view.js.map M static/maps/mvc/list/list-view.js.map M static/maps/mvc/tours.js.map M static/maps/mvc/ui/ui-select-default.js.map M static/maps/mvc/upload/default/default-row.js.map M static/maps/mvc/visualization/visualization-model.js.map M static/maps/mvc/workflow/workflow-view.js.map M static/maps/onload.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map R static/scripts/libs/backbone/backbone.js M static/scripts/mvc/form/form-select-content.js M static/scripts/mvc/library/library-folderlist-view.js M static/scripts/mvc/library/library-folderrow-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/library/library-libraryrow-view.js M static/scripts/mvc/list/list-view.js M static/scripts/mvc/tours.js M static/scripts/mvc/ui/ui-select-default.js M static/scripts/mvc/upload/default/default-row.js M static/scripts/mvc/visualization/visualization-model.js M static/scripts/mvc/workflow/workflow-view.js M static/scripts/onload.js M static/style/blue/base.css M static/style/blue/library.css M templates/show_params.mako M templates/webapps/galaxy/workflow/editor_tool_form.mako M templates/webapps/galaxy/workflow/run.mako M test/api/test_workflows.py M test/api/workflows_format_2/converter.py M test/docker/base/run_test_wrapper.sh A test/functional/tools/for_workflows/1.bam A test/functional/tools/for_workflows/mapper.xml A test/functional/tools/for_workflows/pileup.xml M test/functional/tools/samples_tool_conf.xml A test/unit/managers/test_HistoryContentsManager.py M test/unit/managers/test_HistoryManager.py M test/unit/tools/test_data_parameters.py M test/unit/tools/test_evaluation.py M test/unit/tools/test_execution.py M test/unit/tools/test_select_parameters.py M test/unit/tools_support.py M tools/data_source/upload.xml Log Message: ----------- Merge branch 'dev' into resolver_dependencies Commit: 0a440f60ae3f9443599eb234f32fa3c149f05c61 https://github.com/galaxyproject/galaxy/commit/0a440f60ae3f9443599eb234f32f… Author: Zipho Mashologu <zipho(a)trustpay.biz> Date: 2016-02-02 (Tue, 02 Feb 2016) Changed paths: M templates/webapps/tool_shed/repository/common.mako Log Message: ----------- fixed variable names and making user feedback friendlier Commit: 7a60f669fa5fd9603ddbf30153cb8e17dbe8a1a8 https://github.com/galaxyproject/galaxy/commit/7a60f669fa5fd9603ddbf30153cb… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-08 (Mon, 08 Feb 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/tool_dependencies.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M templates/admin/tool_shed_repository/manage_repository.mako M templates/webapps/tool_shed/repository/common.mako Log Message: ----------- Merge pull request #1632 from zipho/resolver_dependencies added resolver dependency display to the tool view page Compare: https://github.com/galaxyproject/galaxy/compare/6a3452afff49...7a60f669fa5f

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[galaxyproject/galaxy] ebb412: added Phinch interactive environment
by GitHub 08 Feb '16

08 Feb '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ebb41225bef68042d7725bbff2f75721f23f0e66 https://github.com/galaxyproject/galaxy/commit/ebb41225bef68042d7725bbff2f7… Author: shiltemann <s.hiltemann(a)erasmusmc.nl> Date: 2016-02-02 (Tue, 02 Feb 2016) Changed paths: A config/plugins/interactive_environments/phinch/config/phinch.ini.sample A config/plugins/interactive_environments/phinch/config/phinch.xml A config/plugins/interactive_environments/phinch/static/js/phinch.js A config/plugins/interactive_environments/phinch/templates/phinch.mako Log Message: ----------- added Phinch interactive environment Commit: 87b5ba458fe574deb8c6200d8f12a8c329af98a1 https://github.com/galaxyproject/galaxy/commit/87b5ba458fe574deb8c6200d8f12… Author: shiltemann <s.hiltemann(a)erasmusmc.nl> Date: 2016-02-03 (Wed, 03 Feb 2016) Changed paths: M config/plugins/interactive_environments/phinch/config/phinch.ini.sample Log Message: ----------- changed docker tag to fit with Galaxy release Commit: 1b04ba3833597f2ebdc2e4f527044906ab7a4e7d https://github.com/galaxyproject/galaxy/commit/1b04ba3833597f2ebdc2e4f52704… Author: Saskia Hiltemann <zazkia(a)gmail.com> Date: 2016-02-04 (Thu, 04 Feb 2016) Changed paths: M config/plugins/interactive_environments/phinch/templates/phinch.mako Log Message: ----------- use bioblend for dataset import instead of mount Commit: 674bf530c65c05fea3e77a82404a77dc03f645ca https://github.com/galaxyproject/galaxy/commit/674bf530c65c05fea3e77a82404a… Author: Saskia Hiltemann <zazkia(a)gmail.com> Date: 2016-02-05 (Fri, 05 Feb 2016) Changed paths: M config/plugins/interactive_environments/phinch/static/js/phinch.js M config/plugins/interactive_environments/phinch/templates/phinch.mako Log Message: ----------- fix window height issue Commit: 6a3452afff49ec14fecc919e23a6012832ed3429 https://github.com/galaxyproject/galaxy/commit/6a3452afff49ec14fecc919e23a6… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-02-08 (Mon, 08 Feb 2016) Changed paths: A config/plugins/interactive_environments/phinch/config/phinch.ini.sample A config/plugins/interactive_environments/phinch/config/phinch.xml A config/plugins/interactive_environments/phinch/static/js/phinch.js A config/plugins/interactive_environments/phinch/templates/phinch.mako Log Message: ----------- Merge pull request #1647 from shiltemann/dev Phinch interactive environment Compare: https://github.com/galaxyproject/galaxy/compare/faeedd6f824f...6a3452afff49

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[galaxyproject/galaxy] 5e77af: Update help text rST note/warning/error box stylin...
by GitHub 08 Feb '16

08 Feb '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: 5e77af198a9b81646dbe59a02b991d496b334967 https://github.com/galaxyproject/galaxy/commit/5e77af198a9b81646dbe59a02b99… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-08 (Mon, 08 Feb 2016) Changed paths: M client/galaxy/style/less/base.less 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/style/blue/base.css Log Message: ----------- Update help text rST note/warning/error box styling for change in div class from toolHelpBody to ui-form-help. Commit: 054c04f490fe5e641c1dec8c4f8af53cf02daffd https://github.com/galaxyproject/galaxy/commit/054c04f490fe5e641c1dec8c4f8a… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-02-08 (Mon, 08 Feb 2016) Changed paths: M client/galaxy/style/less/base.less 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/style/blue/base.css Log Message: ----------- Merge pull request #1695 from natefoo/help-message-css [16.01] Update help text rST note/warning/error box styling for change in div class from toolHelpBody to ui-form-help. Compare: https://github.com/galaxyproject/galaxy/compare/ef6bd90f2039...054c04f490fe

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[galaxyproject/galaxy] 47b9eb: Add tox startup test and build matrix for travis-c...
by GitHub 08 Feb '16

08 Feb '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 47b9eb47ddd64d770791556f18fedceaf3a705ec https://github.com/galaxyproject/galaxy/commit/47b9eb47ddd64d770791556f18fe… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-02-02 (Tue, 02 Feb 2016) Changed paths: A .ci/first_startup.sh M .travis.yml M tox.ini Log Message: ----------- Add tox startup test and build matrix for travis-ci. Commit: 4176bc9115b94eba30c6ad9c7a1bf08823a3791b https://github.com/galaxyproject/galaxy/commit/4176bc9115b94eba30c6ad9c7a1b… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-02-02 (Tue, 02 Feb 2016) Changed paths: M .travis.yml Log Message: ----------- Move first_startup to last position Commit: 3d4ddc438eb8e7e8822a2b0b05820098140ad6f3 https://github.com/galaxyproject/galaxy/commit/3d4ddc438eb8e7e8822a2b0b0582… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-02-02 (Tue, 02 Feb 2016) Changed paths: M .travis.yml Log Message: ----------- Add py27-unit tests on osx Commit: 84b783027d68beb4d2f83ca21311d1ee3ea64042 https://github.com/galaxyproject/galaxy/commit/84b783027d68beb4d2f83ca21311… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-02-02 (Tue, 02 Feb 2016) Changed paths: M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/style/less/base.less M lib/galaxy/config.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/dependencies/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/objectstore/__init__.py M lib/galaxy/util/__init__.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py M scripts/common_startup.sh M static/maps/mvc/form/form-section.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-section.js M static/style/blue/base.css M templates/user/info.mako M templates/user/username.mako Log Message: ----------- Merge remote-tracking branch 'galaxy/dev' into HEAD Commit: faeedd6f824f5d5def7839d2e72248f6e38e4aef https://github.com/galaxyproject/galaxy/commit/faeedd6f824f5d5def7839d2e722… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-08 (Mon, 08 Feb 2016) Changed paths: A .ci/first_startup.sh M .travis.yml M tox.ini Log Message: ----------- Merge pull request #1649 from mvdbeek/add_startup_test Add tox startup (run.sh) test and test on OS X and linux Compare: https://github.com/galaxyproject/galaxy/compare/75f1b58ecb8a...faeedd6f824f

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[galaxyproject/galaxy] ada39d: handle correctly application/json pased in POST
by GitHub 08 Feb '16

08 Feb '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: ada39dea6ab68be543f53feb7a30e97167d96013 https://github.com/galaxyproject/galaxy/commit/ada39dea6ab68be543f53feb7a30… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-02-04 (Thu, 04 Feb 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/lda_datasets.py Log Message: ----------- handle correctly application/json pased in POST Commit: 530501c682be85b595bd8115bc2fc0ebc53f57a0 https://github.com/galaxyproject/galaxy/commit/530501c682be85b595bd8115bc2f… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-02-04 (Thu, 04 Feb 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/libraries.py Log Message: ----------- fix setting library permissions to accept JSON correctly Commit: 5dd839960e1ca5170b528c4c88ad8965eebde08b https://github.com/galaxyproject/galaxy/commit/5dd839960e1ca5170b528c4c88ad… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-02-04 (Thu, 04 Feb 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/libraries.py Log Message: ----------- unify api for library creation; support POST with url params Commit: edd8b222acac34cd2e35e768ab1cbd888b2fc824 https://github.com/galaxyproject/galaxy/commit/edd8b222acac34cd2e35e768ab1c… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-02-04 (Thu, 04 Feb 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/libraries.py Log Message: ----------- catch value errors from id decoding Commit: 0398aafb1cf0aa0863d0867d20dd79a09bc2fb85 https://github.com/galaxyproject/galaxy/commit/0398aafb1cf0aa0863d0867d20dd… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-02-04 (Thu, 04 Feb 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/libraries.py Log Message: ----------- fix updating library API to not require payload and to properly handle optional params Commit: 4b51be57d114d840112970baccb979ec1876663b https://github.com/galaxyproject/galaxy/commit/4b51be57d114d840112970baccb9… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-02-04 (Thu, 04 Feb 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/libraries.py Log Message: ----------- allow specifying DELETE params in JSON Commit: c288b43627d3da925c5fe4b2fd0ebd5a7bc752b2 https://github.com/galaxyproject/galaxy/commit/c288b43627d3da925c5fe4b2fd0e… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-02-04 (Thu, 04 Feb 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/folders.py Log Message: ----------- allow creating folders with JSON payload Commit: 7867f3e0835a2cbd99658ad25debd9be278300f2 https://github.com/galaxyproject/galaxy/commit/7867f3e0835a2cbd99658ad25deb… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-02-04 (Thu, 04 Feb 2016) Changed paths: M client/galaxy/scripts/mvc/library/library-folder-view.js M lib/galaxy/webapps/galaxy/api/folders.py M static/maps/mvc/library/library-folder-view.js.map M static/scripts/mvc/library/library-folder-view.js Log Message: ----------- accept json as input for setting permissions; fix inconsistency by leveraging role_manager Commit: a4c2098da010d79a70a9425e8ccb6c1e69807442 https://github.com/galaxyproject/galaxy/commit/a4c2098da010d79a70a9425e8ccb… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-02-04 (Thu, 04 Feb 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/folders.py Log Message: ----------- allow PATCHing with payload in urlparams Commit: b46636a53f579fc6ffa63fbca888196bb0ff99f6 https://github.com/galaxyproject/galaxy/commit/b46636a53f579fc6ffa63fbca888… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-02-04 (Thu, 04 Feb 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/libraries.py Log Message: ----------- remove deletion of the payload dict item it is not necessary and the key does not have to exist Commit: 170c83e6c283e97b1e399bc122ee94ddb8cb34b4 https://github.com/galaxyproject/galaxy/commit/170c83e6c283e97b1e399bc122ee… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-02-04 (Thu, 04 Feb 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/folders.py M lib/galaxy/webapps/galaxy/api/libraries.py Log Message: ----------- fix unused imports and unused vars Commit: 134d792c1fcfba5d09e2937074c3263792bea991 https://github.com/galaxyproject/galaxy/commit/134d792c1fcfba5d09e2937074c3… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-02-05 (Fri, 05 Feb 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/libraries.py Log Message: ----------- delete the 'payload' if it is in kwd so it is not supplied twice Commit: e7b6b4b13bd93a8520942c94d0ed28d110af261b https://github.com/galaxyproject/galaxy/commit/e7b6b4b13bd93a8520942c94d0ed… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-02-05 (Fri, 05 Feb 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/libraries.py Log Message: ----------- Revert "delete the 'payload' if it is in kwd so it is not supplied twice" This reverts commit 134d792c1fcfba5d09e2937074c3263792bea991. Commit: 5301269fbb54753e75969ecd446b8cb74c6093b6 https://github.com/galaxyproject/galaxy/commit/5301269fbb54753e75969ecd446b… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-02-05 (Fri, 05 Feb 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/folder_contents.py M lib/galaxy/webapps/galaxy/api/folders.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py M lib/galaxy/webapps/galaxy/api/libraries.py Log Message: ----------- update docs of the data libraries API Commit: ef6bd90f20394f6fb74b1bdedbd0f94ecb752018 https://github.com/galaxyproject/galaxy/commit/ef6bd90f20394f6fb74b1bdedbd0… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-08 (Mon, 08 Feb 2016) Changed paths: M client/galaxy/scripts/mvc/library/library-folder-view.js M lib/galaxy/webapps/galaxy/api/folder_contents.py M lib/galaxy/webapps/galaxy/api/folders.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py M lib/galaxy/webapps/galaxy/api/libraries.py M static/maps/mvc/library/library-folder-view.js.map M static/scripts/mvc/library/library-folder-view.js Log Message: ----------- Merge pull request #1641 from martenson/libraries-load-handle-payload [16.01] libraries: handle correctly application/json pased in POST Compare: https://github.com/galaxyproject/galaxy/compare/c693b69b3444...ef6bd90f2039

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[galaxyproject/galaxy] 1e79c8: Optionally pass dataset lists as a single file wit...
by GitHub 05 Feb '16

05 Feb '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1e79c8c77e29f0aa5e6377d77ffa68d808ca4c89 https://github.com/galaxyproject/galaxy/commit/1e79c8c77e29f0aa5e6377d77ffa… Author: Mark Einon <mark.einon(a)gmail.com> Date: 2016-02-04 (Thu, 04 Feb 2016) Changed paths: M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/wrappers.py Log Message: ----------- Optionally pass dataset lists as a single file within tool wrappers This change introduces an extra boolean XML attribute 'pass_as_file', that when used with an input parameter already having the 'multiple=True' attribute, passes the dataset list of files to the wrapped program as a single file containing a list of the dataset files. Commit: 27618a319d9c3bac01484bad80494f4423c04673 https://github.com/galaxyproject/galaxy/commit/27618a319d9c3bac01484bad8049… Author: Mark Einon <mark.einon(a)gmail.com> Date: 2016-02-04 (Thu, 04 Feb 2016) Changed paths: M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/wrappers.py Log Message: ----------- [Trivial] Whitespace fixes to please pylint Commit: 66350fb87100a8986a95c28f9b532564c98f0034 https://github.com/galaxyproject/galaxy/commit/66350fb87100a8986a95c28f9b53… Author: Mark Einon <mark.einon(a)gmail.com> Date: 2016-02-04 (Thu, 04 Feb 2016) Changed paths: M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/wrapped.py M lib/galaxy/tools/wrappers.py A test/functional/tools/paths_as_file.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Modify pass_as_file to apply to all Multiple parameters and add test case Change the pass_as_file XML attribute to a cheetah method call, and apply to all paramter types that can have Multiple=True set - those given in DatasetListWrappers and DatasetCollectionWrappers. Test case and modification suggestion provided by John Chilton <jmchilton(a)gmail.com> Commit: 75f1b58ecb8a4e60fd9f3bbcbc6b9501005b903d https://github.com/galaxyproject/galaxy/commit/75f1b58ecb8a4e60fd9f3bbcbc6b… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-02-05 (Fri, 05 Feb 2016) Changed paths: M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/wrapped.py M lib/galaxy/tools/wrappers.py A test/functional/tools/paths_as_file.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #1658 from einon/pass_lists_as_file Optionally pass dataset lists as a single file within tool wrappers Compare: https://github.com/galaxyproject/galaxy/compare/dfceb5c144de...75f1b58ecb8a

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[galaxyproject/galaxy] 4b24d9: Improve documentation about binary-compatibility.c...
by GitHub 05 Feb '16

05 Feb '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: 4b24d95f6f95124f357b72434a29113fa9bacf73 https://github.com/galaxyproject/galaxy/commit/4b24d95f6f95124f357b72434a29… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-04 (Thu, 04 Feb 2016) Changed paths: M doc/source/admin/framework_dependencies.rst Log Message: ----------- Improve documentation about binary-compatibility.cfg. Resolves #1672. Commit: 9c7c75b7661989b5fe6f2e4819b04ae6e7b901a1 https://github.com/galaxyproject/galaxy/commit/9c7c75b7661989b5fe6f2e4819b0… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-05 (Fri, 05 Feb 2016) Changed paths: M doc/source/admin/framework_dependencies.rst Log Message: ----------- Typo Commit: c693b69b344461bd428a0ef314b3ec985e1a60d9 https://github.com/galaxyproject/galaxy/commit/c693b69b344461bd428a0ef314b3… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-02-05 (Fri, 05 Feb 2016) Changed paths: M doc/source/admin/framework_dependencies.rst Log Message: ----------- Merge pull request #1677 from natefoo/admin-docs [16.01] Improve documentation about binary-compatibility.cfg Compare: https://github.com/galaxyproject/galaxy/compare/9ead68aeca67...c693b69b3444

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[galaxyproject/galaxy] 61f168: A slightly different check for Galaxy object defin...
by GitHub 05 Feb '16

05 Feb '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 61f168d34b748da0994be2d0d1c8c77af27c4520 https://github.com/galaxyproject/galaxy/commit/61f168d34b748da0994be2d0d1c8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-02-04 (Thu, 04 Feb 2016) Changed paths: M client/galaxy/scripts/mvc/tours.js M static/maps/mvc/tours.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tours.js Log Message: ----------- A slightly different check for Galaxy object definition that doesn't assume a window-attached Galaxy context, only a parent. Minor cleanup. Commit: 33ebeb801d235af58a6e1152056d52e9ee5bfac6 https://github.com/galaxyproject/galaxy/commit/33ebeb801d235af58a6e1152056d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-02-04 (Thu, 04 Feb 2016) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/layout/menu.js M static/maps/layout/menu.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 Log Message: ----------- Use backbone routing for a tours URL, since there's no serverside endpoint. Commit: ab5f1536171dba6fc2f8afaae9c0154d46e1dd5b https://github.com/galaxyproject/galaxy/commit/ab5f1536171dba6fc2f8afaae9c0… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-02-04 (Thu, 04 Feb 2016) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/mvc/tours.js M client/galaxy/scripts/onload.js M static/maps/mvc/tours.js.map M static/maps/onload.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/tours.js M static/scripts/onload.js Log Message: ----------- Clientside routing for tour kickoff, swapping from ?tour_id=foo approach. Commit: dfceb5c144de556e10659a8d876237188bd4595f https://github.com/galaxyproject/galaxy/commit/dfceb5c144de556e10659a8d8762… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-02-04 (Thu, 04 Feb 2016) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/tours.js M client/galaxy/scripts/onload.js M static/maps/layout/menu.js.map M static/maps/mvc/tours.js.map M static/maps/onload.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/tours.js M static/scripts/onload.js Log Message: ----------- Merge pull request #1671 from dannon/tour_fixes_and_cleanup Tour improvements and bugfixes Compare: https://github.com/galaxyproject/galaxy/compare/d93f095c7f56...dfceb5c144de

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[galaxyproject/infrastructure-playbook] f16b24: Modify access list
by GitHub 04 Feb '16

04 Feb '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: f16b24f8ff84d74da8e21de0cd2db012678801f1 https://github.com/galaxyproject/infrastructure-playbook/commit/f16b24f8ff8… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-04 (Thu, 04 Feb 2016) Changed paths: M galaxyenv/secret_host_vars/athena.galaxyproject.org.yml Log Message: ----------- Modify access list

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