August 2016 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 33c402: Fix misplaced parenthesis
by GitHub 10 Aug '16

10 Aug '16

Branch: refs/heads/release_16.04 Home: https://github.com/galaxyproject/galaxy Commit: 33c4025fabc057a412c2da662b3606afc0726902 https://github.com/galaxyproject/galaxy/commit/33c4025fabc057a412c2da662b36… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-08-10 (Wed, 10 Aug 2016) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py Log Message: ----------- Fix misplaced parenthesis Reported by @dpryan79 in https://github.com/galaxyproject/tools-iuc/issues/906#issuecomment-238844304 Commit: f4cb63d6f27f68814bd6131f43c1eee6fa8d099e https://github.com/galaxyproject/galaxy/commit/f4cb63d6f27f68814bd6131f43c1… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-08-10 (Wed, 10 Aug 2016) Changed paths: M .ci/flake8_blacklist.txt M tox.ini Log Message: ----------- Pin flake8 version Do not pin when forward-merging to dev branch. Also ignore .tox/ and eggs/ as in #2650 . Commit: 68f718d53bc6bcc44c8ccbe14c79a9fb79c3b9fc https://github.com/galaxyproject/galaxy/commit/68f718d53bc6bcc44c8ccbe14c79… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-08-10 (Wed, 10 Aug 2016) Changed paths: M .ci/flake8_blacklist.txt M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py M tox.ini Log Message: ----------- Merge pull request #2767 from nsoranzo/release_16.01_handle_complex_repository_dependency_for_package [16.01] Fix misplaced parenthesis Commit: f2f62f340ecd92ebdde51e6d13d5145a6f40cc9e https://github.com/galaxyproject/galaxy/commit/f2f62f340ecd92ebdde51e6d13d5… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-08-10 (Wed, 10 Aug 2016) Changed paths: M .ci/flake8_blacklist.txt M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py M tox.ini Log Message: ----------- Merge branch 'release_16.01' into release_16.04 Conflicts: .ci/flake8_blacklist.txt tox.ini Compare: https://github.com/galaxyproject/galaxy/compare/a7664f00f92a...f2f62f340ecd

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[galaxyproject/galaxy] 33c402: Fix misplaced parenthesis
by GitHub 10 Aug '16

10 Aug '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: 33c4025fabc057a412c2da662b3606afc0726902 https://github.com/galaxyproject/galaxy/commit/33c4025fabc057a412c2da662b36… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-08-10 (Wed, 10 Aug 2016) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py Log Message: ----------- Fix misplaced parenthesis Reported by @dpryan79 in https://github.com/galaxyproject/tools-iuc/issues/906#issuecomment-238844304 Commit: f4cb63d6f27f68814bd6131f43c1eee6fa8d099e https://github.com/galaxyproject/galaxy/commit/f4cb63d6f27f68814bd6131f43c1… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-08-10 (Wed, 10 Aug 2016) Changed paths: M .ci/flake8_blacklist.txt M tox.ini Log Message: ----------- Pin flake8 version Do not pin when forward-merging to dev branch. Also ignore .tox/ and eggs/ as in #2650 . Commit: 68f718d53bc6bcc44c8ccbe14c79a9fb79c3b9fc https://github.com/galaxyproject/galaxy/commit/68f718d53bc6bcc44c8ccbe14c79… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-08-10 (Wed, 10 Aug 2016) Changed paths: M .ci/flake8_blacklist.txt M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py M tox.ini Log Message: ----------- Merge pull request #2767 from nsoranzo/release_16.01_handle_complex_repository_dependency_for_package [16.01] Fix misplaced parenthesis Compare: https://github.com/galaxyproject/galaxy/compare/f4631d2e59af...68f718d53bc6

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[galaxyproject/infrastructure-playbook] 0484e5: Allow Jenkins slaves ssh access to orval
by GitHub 10 Aug '16

10 Aug '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 0484e5580305df888a8313ec19c13ea916412223 https://github.com/galaxyproject/infrastructure-playbook/commit/0484e558030… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-08-10 (Wed, 10 Aug 2016) Changed paths: M galaxyenv/secret_group_vars/all.yml Log Message: ----------- Allow Jenkins slaves ssh access to orval

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[galaxyproject/galaxy] e5e398: Fix message style by removing float attribute
by GitHub 10 Aug '16

10 Aug '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e5e398faf7be73a575d349e3fcba6731426ac226 https://github.com/galaxyproject/galaxy/commit/e5e398faf7be73a575d349e3fcba… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-09 (Tue, 09 Aug 2016) Changed paths: M client/galaxy/style/less/ui.less M static/style/blue/base.css Log Message: ----------- Fix message style by removing float attribute Commit: 5d57b4474181cb7266ddd0e70447eb49bc5200dc https://github.com/galaxyproject/galaxy/commit/5d57b4474181cb7266ddd0e70447… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-08-10 (Wed, 10 Aug 2016) Changed paths: M client/galaxy/style/less/ui.less M static/style/blue/base.css Log Message: ----------- Merge pull request #2762 from guerler/fix_message_float Fix message style by removing float attribute Compare: https://github.com/galaxyproject/galaxy/compare/e5e2996f6b7b...5d57b4474181

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[galaxyproject/galaxy] a1eb9b: Add lazy loading for step forms
by GitHub 09 Aug '16

09 Aug '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a1eb9b75c230823bb861c55d2ca6c9f2e2cbb251 https://github.com/galaxyproject/galaxy/commit/a1eb9b75c230823bb861c55d2ca6… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-09 (Tue, 09 Aug 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/style/less/ui.less M static/maps/mvc/tool/tool-form-composite.js.map M static/scripts/mvc/tool/tool-form-composite.js M static/style/blue/base.css Log Message: ----------- Add lazy loading for step forms Commit: 737b90506b0054ccb635b566e63da69cd06b04c5 https://github.com/galaxyproject/galaxy/commit/737b90506b0054ccb635b566e63d… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-09 (Tue, 09 Aug 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M static/maps/mvc/tool/tool-form-composite.js.map M static/scripts/mvc/tool/tool-form-composite.js Log Message: ----------- Fix scroll handling listener Commit: 69e47b2d276d20201da9aac18e96ba86a7a7db8c https://github.com/galaxyproject/galaxy/commit/69e47b2d276d20201da9aac18e96… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-09 (Tue, 09 Aug 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M static/maps/mvc/tool/tool-form-composite.js.map M static/scripts/mvc/tool/tool-form-composite.js Log Message: ----------- Fix highlighting upon server response Commit: d9fa01fb2fe2f4afd657247b9f4a5593167f252e https://github.com/galaxyproject/galaxy/commit/d9fa01fb2fe2f4afd657247b9f4a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-09 (Tue, 09 Aug 2016) Changed paths: M static/maps/mvc/tool/tool-form-composite.js.map M static/scripts/mvc/tool/tool-form-composite.js Log Message: ----------- Auto append all steps after initialization Commit: 2c43b93a1252fa4049b6dd69a7e7b4e03059c4b7 https://github.com/galaxyproject/galaxy/commit/2c43b93a1252fa4049b6dd69a7e7… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-09 (Tue, 09 Aug 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M static/maps/mvc/tool/tool-form-composite.js.map M static/scripts/mvc/tool/tool-form-composite.js Log Message: ----------- Auto append all steps after initialization Commit: a37f99fdb86917ee8e264b63d5966a47da5e02a6 https://github.com/galaxyproject/galaxy/commit/a37f99fdb86917ee8e264b63d596… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-09 (Tue, 09 Aug 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M static/maps/mvc/tool/tool-form-composite.js.map M static/scripts/mvc/tool/tool-form-composite.js Log Message: ----------- Queue form preparation in background, hide progress bar until execute has been clicked Commit: d79653e312dd77145258ad18a11dbfaefbc3b686 https://github.com/galaxyproject/galaxy/commit/d79653e312dd77145258ad18a11d… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-09 (Tue, 09 Aug 2016) Changed paths: M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M static/maps/mvc/form/form-parameters.js.map M static/maps/mvc/tool/tool-form-composite.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-parameters.js M static/scripts/mvc/tool/tool-form-composite.js M static/scripts/mvc/ui/ui-select-default.js Log Message: ----------- Use classic select fields for non-data inputs for options in workflow form Commit: fa02860b2f06f3d303717fce3a4442cfb42f7bbb https://github.com/galaxyproject/galaxy/commit/fa02860b2f06f3d303717fce3a44… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-09 (Tue, 09 Aug 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M static/maps/mvc/tool/tool-form-composite.js.map M static/scripts/mvc/tool/tool-form-composite.js Log Message: ----------- Disable workflow parameter form when attempting execution Commit: 808d410be0c90542efadd2af01497eabc8008059 https://github.com/galaxyproject/galaxy/commit/808d410be0c90542efadd2af0149… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-09 (Tue, 09 Aug 2016) Changed paths: M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/style/less/ui.less M static/maps/mvc/form/form-input.js.map 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-input.js M static/scripts/mvc/form/form-section.js M static/style/blue/base.css Log Message: ----------- Use local div container instead of table view to build the tool form Commit: 671c9406f2ed2ae4b18cfe173d729ad97755b697 https://github.com/galaxyproject/galaxy/commit/671c9406f2ed2ae4b18cfe173d72… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-09 (Tue, 09 Aug 2016) Changed paths: M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/ui/ui-portlet.js M client/galaxy/style/less/ui.less M static/maps/mvc/form/form-input.js.map M static/maps/mvc/form/form-section.js.map M static/maps/mvc/form/form-view.js.map M static/maps/mvc/ui/ui-portlet.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-section.js M static/scripts/mvc/form/form-view.js M static/scripts/mvc/ui/ui-portlet.js M static/style/blue/base.css Log Message: ----------- Revise portlet handling, fix table removal issues Commit: 0f86cf27fec817278b218956f678137744ee102f https://github.com/galaxyproject/galaxy/commit/0f86cf27fec817278b218956f678… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-09 (Tue, 09 Aug 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M static/maps/mvc/tool/tool-form-composite.js.map M static/scripts/mvc/tool/tool-form-composite.js Log Message: ----------- Add placeholder input and information for subworkflows Commit: cfdc7296eba5934de7fbcacf8de58140704423bd https://github.com/galaxyproject/galaxy/commit/cfdc7296eba5934de7fbcacf8de5… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-09 (Tue, 09 Aug 2016) Changed paths: M client/galaxy/style/less/ui.less M static/style/blue/base.css Log Message: ----------- Remove unused margin, fix elements using floating features Commit: a9d498d0f4bf8be08f721f5c95c0e4798e7865d2 https://github.com/galaxyproject/galaxy/commit/a9d498d0f4bf8be08f721f5c95c0… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-09 (Tue, 09 Aug 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M static/maps/mvc/tool/tool-form-composite.js.map M static/scripts/mvc/tool/tool-form-composite.js Log Message: ----------- Fix post job action label style Commit: f7bbcdd1a37856ed4e44f091be8030f9099d238d https://github.com/galaxyproject/galaxy/commit/f7bbcdd1a37856ed4e44f091be80… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-09 (Tue, 09 Aug 2016) Changed paths: M test/qunit/test-data/fakeserver.js M test/qunit/tests/form_tests.js Log Message: ----------- Fix and extend form test cases Commit: e5e2996f6b7b87b3ac28407abd83de03ff374617 https://github.com/galaxyproject/galaxy/commit/e5e2996f6b7b87b3ac28407abd83… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-09 (Tue, 09 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 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 pull request #2720 from guerler/lazy_load_steps Load steps in background, show progress bar upon workflow execution, avoid nested tables Compare: https://github.com/galaxyproject/galaxy/compare/231e36da926b...e5e2996f6b7b

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[galaxyproject/galaxy] 53633a: Add a few watching makefile targets for quick iter...
by GitHub 09 Aug '16

09 Aug '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 53633a0ac5defebb2c0b82a85eb6b52671c0b10c https://github.com/galaxyproject/galaxy/commit/53633a0ac5defebb2c0b82a85eb6… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-09 (Tue, 09 Aug 2016) Changed paths: M Makefile Log Message: ----------- Add a few watching makefile targets for quick iterative development of the client. Execute in parallel, which is super handy, using something like `make -j webpack-watch grunt-watch-style grunt-watch-develop`. Make sure to rerun the root `make client` before committing though! Commit: 483eb45e506b5431f35765da2e52111b2457a0f3 https://github.com/galaxyproject/galaxy/commit/483eb45e506b5431f35765da2e52… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-09 (Tue, 09 Aug 2016) Changed paths: M Makefile Log Message: ----------- Add a single target. Execute with `make -j client-develop`. Commit: 231e36da926b55066183f37a096beaa9ef9791d0 https://github.com/galaxyproject/galaxy/commit/231e36da926b55066183f37a096b… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-08-09 (Tue, 09 Aug 2016) Changed paths: M Makefile Log Message: ----------- Merge pull request #2757 from dannon/dev_makefile_update Add makefile targets for running client-build watch modes Compare: https://github.com/galaxyproject/galaxy/compare/1d0c37e91a6d...231e36da926b

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[galaxyproject/infrastructure-playbook] 80980f: Additional Jenkins installs
by GitHub 09 Aug '16

09 Aug '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 80980f28fdc9f1d9c5ee4db48a02fb845504a81b https://github.com/galaxyproject/infrastructure-playbook/commit/80980f28fdc… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-08-09 (Tue, 09 Aug 2016) Changed paths: M galaxyenv/group_vars/jenkinsservers.yml M galaxyenv/group_vars/jenkinsslaves.yml M galaxyenv/host_vars/n4.galaxyproject.org.yml Log Message: ----------- Additional Jenkins installs

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[galaxyproject/galaxy] 370346: List toolshed deps in 'Dependency Resolver Details...
by GitHub 09 Aug '16

09 Aug '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 370346ad9e7e828a5048382ccdc048c7bad2152a https://github.com/galaxyproject/galaxy/commit/370346ad9e7e828a5048382ccdc0… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-08-08 (Mon, 08 Aug 2016) Changed paths: M lib/galaxy/tools/deps/resolvers/galaxy_packages.py M lib/galaxy/tools/deps/resolvers/tool_shed_packages.py M lib/galaxy/tools/deps/views.py M lib/tool_shed/util/shed_util_common.py Log Message: ----------- List toolshed deps in 'Dependency Resolver Details' This should make it easier to understand/predict for admins how tool dependencies will be resolved during tool execution. Commit: 7f0d323aca5c0ea546f4186d3364d68441217e97 https://github.com/galaxyproject/galaxy/commit/7f0d323aca5c0ea546f4186d3364… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-08-08 (Mon, 08 Aug 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/views.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/tool_shed/util/shed_util_common.py Log Message: ----------- Include toolshed resolved packages in tool requirements API Commit: b0bd9a3326285e20adfa74de891777137766b0c5 https://github.com/galaxyproject/galaxy/commit/b0bd9a3326285e20adfa74de8917… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-08-08 (Mon, 08 Aug 2016) Changed paths: M test/unit/tools/test_tool_deps.py Log Message: ----------- Adjust test for new GalaxyPackageDependency signature Commit: 45d357e7c39b6564915dfc037439c546011c9c2b https://github.com/galaxyproject/galaxy/commit/45d357e7c39b6564915dfc037439… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-08-08 (Mon, 08 Aug 2016) Changed paths: M lib/galaxy/tools/deps/resolvers/galaxy_packages.py M lib/galaxy/tools/deps/resolvers/tool_shed_packages.py Log Message: ----------- Introduce ToolShedDependency as subclass of GalaxyPackageDependency Commit: 0bfa56f010f38b4f151c1f3257478a926ea7cc38 https://github.com/galaxyproject/galaxy/commit/0bfa56f010f38b4f151c1f325747… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-08-08 (Mon, 08 Aug 2016) Changed paths: M lib/galaxy/tools/deps/resolvers/galaxy_packages.py Log Message: ----------- Fix list of public objects Commit: f8fef3269729358de20c688d02b3aca339d8eeaa https://github.com/galaxyproject/galaxy/commit/f8fef3269729358de20c688d02b3… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-08-09 (Tue, 09 Aug 2016) Changed paths: M lib/galaxy/tools/deps/resolvers/galaxy_packages.py M lib/galaxy/tools/deps/resolvers/tool_shed_packages.py Log Message: ----------- Change DependencyType class variable to dependency_type Commit: 7e3d7ced81d70ac1544f4d94bdb22a7a8e3986c6 https://github.com/galaxyproject/galaxy/commit/7e3d7ced81d70ac1544f4d94bdb2… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-08-09 (Tue, 09 Aug 2016) Changed paths: M lib/galaxy/tools/deps/views.py Log Message: ----------- Avoid changes in requested_requirements Commit: a72f9d88650719ed2c4a149861eee3321c4d6e07 https://github.com/galaxyproject/galaxy/commit/a72f9d88650719ed2c4a149861ee… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-08-09 (Tue, 09 Aug 2016) Changed paths: M lib/galaxy/tools/deps/views.py Log Message: ----------- Pass installed_tool_dependencies as a parameter Commit: a297a0467116f007dcd7b952fd64c4caa2048492 https://github.com/galaxyproject/galaxy/commit/a297a0467116f007dcd7b952fd64… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-08-09 (Tue, 09 Aug 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/resolvers/galaxy_packages.py M lib/galaxy/tools/deps/resolvers/tool_shed_packages.py M lib/galaxy/tools/deps/views.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M test/unit/tools/test_tool_deps.py Log Message: ----------- Merge pull request #2750 from mvdbeek/list_resolver_toolshed_packages List resolver toolshed packages Commit: 1d0c37e91a6d9f334698c09caa1f594fb1075874 https://github.com/galaxyproject/galaxy/commit/1d0c37e91a6d9f334698c09caa1f… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-08-09 (Tue, 09 Aug 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/resolvers/galaxy_packages.py M lib/galaxy/tools/deps/resolvers/tool_shed_packages.py M lib/galaxy/tools/deps/views.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M test/unit/tools/test_tool_deps.py Log Message: ----------- Merge branch 'release_16.07' into dev Compare: https://github.com/galaxyproject/galaxy/compare/0b98601779e3...1d0c37e91a6d

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[galaxyproject/galaxy] 38dcf9: History UI: remove list:list hdca initialize
by GitHub 09 Aug '16

09 Aug '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 38dcf911b818780e3b9af1ba9013361bf17f8cc6 https://github.com/galaxyproject/galaxy/commit/38dcf911b818780e3b9af1ba9013… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-08-09 (Tue, 09 Aug 2016) Changed paths: M client/galaxy/scripts/mvc/history/hdca-model.js M static/maps/mvc/history/hdca-model.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/hdca-model.js Log Message: ----------- History UI: remove list:list hdca initialize It's unneeded now that client-side type ids are created on the server. Commit: 0b98601779e33f1e0db2babb0d704e69d938a269 https://github.com/galaxyproject/galaxy/commit/0b98601779e33f1e0db2babb0d70… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-08-09 (Tue, 09 Aug 2016) Changed paths: M client/galaxy/scripts/mvc/history/hdca-model.js M static/maps/mvc/history/hdca-model.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/hdca-model.js Log Message: ----------- Merge pull request #2758 from carlfeberhard/fix.list-o-lists History UI: remove list:list hdca initialize Compare: https://github.com/galaxyproject/galaxy/compare/8c1be9123151...0b98601779e3

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[galaxyproject/galaxy] 370346: List toolshed deps in 'Dependency Resolver Details...
by GitHub 09 Aug '16

09 Aug '16

Branch: refs/heads/release_16.07 Home: https://github.com/galaxyproject/galaxy Commit: 370346ad9e7e828a5048382ccdc048c7bad2152a https://github.com/galaxyproject/galaxy/commit/370346ad9e7e828a5048382ccdc0… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-08-08 (Mon, 08 Aug 2016) Changed paths: M lib/galaxy/tools/deps/resolvers/galaxy_packages.py M lib/galaxy/tools/deps/resolvers/tool_shed_packages.py M lib/galaxy/tools/deps/views.py M lib/tool_shed/util/shed_util_common.py Log Message: ----------- List toolshed deps in 'Dependency Resolver Details' This should make it easier to understand/predict for admins how tool dependencies will be resolved during tool execution. Commit: 7f0d323aca5c0ea546f4186d3364d68441217e97 https://github.com/galaxyproject/galaxy/commit/7f0d323aca5c0ea546f4186d3364… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-08-08 (Mon, 08 Aug 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/views.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/tool_shed/util/shed_util_common.py Log Message: ----------- Include toolshed resolved packages in tool requirements API Commit: b0bd9a3326285e20adfa74de891777137766b0c5 https://github.com/galaxyproject/galaxy/commit/b0bd9a3326285e20adfa74de8917… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-08-08 (Mon, 08 Aug 2016) Changed paths: M test/unit/tools/test_tool_deps.py Log Message: ----------- Adjust test for new GalaxyPackageDependency signature Commit: 45d357e7c39b6564915dfc037439c546011c9c2b https://github.com/galaxyproject/galaxy/commit/45d357e7c39b6564915dfc037439… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-08-08 (Mon, 08 Aug 2016) Changed paths: M lib/galaxy/tools/deps/resolvers/galaxy_packages.py M lib/galaxy/tools/deps/resolvers/tool_shed_packages.py Log Message: ----------- Introduce ToolShedDependency as subclass of GalaxyPackageDependency Commit: 0bfa56f010f38b4f151c1f3257478a926ea7cc38 https://github.com/galaxyproject/galaxy/commit/0bfa56f010f38b4f151c1f325747… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-08-08 (Mon, 08 Aug 2016) Changed paths: M lib/galaxy/tools/deps/resolvers/galaxy_packages.py Log Message: ----------- Fix list of public objects Commit: f8fef3269729358de20c688d02b3aca339d8eeaa https://github.com/galaxyproject/galaxy/commit/f8fef3269729358de20c688d02b3… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-08-09 (Tue, 09 Aug 2016) Changed paths: M lib/galaxy/tools/deps/resolvers/galaxy_packages.py M lib/galaxy/tools/deps/resolvers/tool_shed_packages.py Log Message: ----------- Change DependencyType class variable to dependency_type Commit: 7e3d7ced81d70ac1544f4d94bdb22a7a8e3986c6 https://github.com/galaxyproject/galaxy/commit/7e3d7ced81d70ac1544f4d94bdb2… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-08-09 (Tue, 09 Aug 2016) Changed paths: M lib/galaxy/tools/deps/views.py Log Message: ----------- Avoid changes in requested_requirements Commit: a72f9d88650719ed2c4a149861eee3321c4d6e07 https://github.com/galaxyproject/galaxy/commit/a72f9d88650719ed2c4a149861ee… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-08-09 (Tue, 09 Aug 2016) Changed paths: M lib/galaxy/tools/deps/views.py Log Message: ----------- Pass installed_tool_dependencies as a parameter Commit: a297a0467116f007dcd7b952fd64c4caa2048492 https://github.com/galaxyproject/galaxy/commit/a297a0467116f007dcd7b952fd64… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-08-09 (Tue, 09 Aug 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/resolvers/galaxy_packages.py M lib/galaxy/tools/deps/resolvers/tool_shed_packages.py M lib/galaxy/tools/deps/views.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M test/unit/tools/test_tool_deps.py Log Message: ----------- Merge pull request #2750 from mvdbeek/list_resolver_toolshed_packages List resolver toolshed packages Compare: https://github.com/galaxyproject/galaxy/compare/77b7e65d2b12...a297a0467116

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