galaxy-commits June 2017

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[galaxyproject/galaxy] e5010a: Prepare backbone route for datasets endpoint
by GitHub 12 Jun '17

12 Jun '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e5010ad8ef82b5dd5b91d2303a582cb30ff51b0a https://github.com/galaxyproject/galaxy/commit/e5010ad8ef82b5dd5b91d2303a58… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-06-07 (Wed, 07 Jun 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js Log Message: ----------- Prepare backbone route for datasets endpoint Commit: 04775ab4d8fc64aaa036e0f26377029c3a65d574 https://github.com/galaxyproject/galaxy/commit/04775ab4d8fc64aaa036e0f26377… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-06-07 (Wed, 07 Jun 2017) Changed paths: M client/galaxy/scripts/layout/menu.js M static/maps/layout/menu.js.map M static/scripts/layout/menu.js Log Message: ----------- Redirect menu link to new dataset grid endpoint Commit: 5421dbd606eafd0106c2974a154c78eb93e17b72 https://github.com/galaxyproject/galaxy/commit/5421dbd606eafd0106c2974a154c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-06-07 (Wed, 07 Jun 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/dataset.py Log Message: ----------- Transform controller endpoint to dictionary mode Commit: a26ee06cf997f2438042555b23a85e66cfadeb7e https://github.com/galaxyproject/galaxy/commit/a26ee06cf997f2438042555b23a8… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-06-07 (Wed, 07 Jun 2017) Changed paths: M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Add client endpoint to backend Commit: eea8841f533a41f781db7472b190bdc87487bd41 https://github.com/galaxyproject/galaxy/commit/eea8841f533a41f781db7472b190… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-06-07 (Wed, 07 Jun 2017) Changed paths: M client/galaxy/scripts/layout/menu.js M static/maps/layout/menu.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.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: ----------- Fix grid element target Commit: 2bbe5e04988f5bd642514dcc82576257f945a1a2 https://github.com/galaxyproject/galaxy/commit/2bbe5e04988f5bd642514dcc8257… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-06-07 (Wed, 07 Jun 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.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: ----------- Fix router url, pack scripts Commit: 14345a423266abe7b6fa4f31ffd2af5893eb39c2 https://github.com/galaxyproject/galaxy/commit/14345a423266abe7b6fa4f31ffd2… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-06-07 (Wed, 07 Jun 2017) Changed paths: R templates/webapps/galaxy/dataset/grid.mako Log Message: ----------- Remove mako file Commit: b0fb99c080ad03453d66def1d3083f2aaf436e84 https://github.com/galaxyproject/galaxy/commit/b0fb99c080ad03453d66def1d308… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-06-07 (Wed, 07 Jun 2017) Changed paths: M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/webapps/galaxy/controllers/dataset.py Log Message: ----------- Add refresh handling Commit: 8aa23f047972b10942a88f629b2c93c656e045be https://github.com/galaxyproject/galaxy/commit/8aa23f047972b10942a88f629b2c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-06-07 (Wed, 07 Jun 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/dataset.py Log Message: ----------- Add note on missing highlighting handling Commit: a5d99ce516bb35bc17dc1c9606c979567f79489c https://github.com/galaxyproject/galaxy/commit/a5d99ce516bb35bc17dc1c9606c9… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-06-07 (Wed, 07 Jun 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/dataset.py Log Message: ----------- Remove custom grid mako name from grid definition Commit: b25bf5946e50dfa9acd17cb32ed057d538da1148 https://github.com/galaxyproject/galaxy/commit/b25bf5946e50dfa9acd17cb32ed0… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-06-08 (Thu, 08 Jun 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/grid/grid-view.js A client/galaxy/scripts/mvc/page/page-list.js M config/datatypes_conf.xml.sample M config/galaxy.ini.sample M lib/galaxy/datatypes/data.py A lib/galaxy/datatypes/plant_tribes.py M lib/galaxy/datatypes/text.py M lib/galaxy/webapps/galaxy/controllers/page.py M static/maps/layout/menu.js.map M static/maps/mvc/grid/grid-view.js.map A static/maps/mvc/page/page-list.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.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/grid/grid-view.js A static/scripts/mvc/page/page-list.js M templates/sharing_base.mako M templates/webapps/galaxy/page/editor.mako R templates/webapps/galaxy/page/index.mako Log Message: ----------- Merge branch 'dev' into grid_datasets Commit: 707c66a6ab4cb4b552affaaf1f03aaf9c6b99a47 https://github.com/galaxyproject/galaxy/commit/707c66a6ab4cb4b552affaaf1f03… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-06-12 (Mon, 12 Jun 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/layout/menu.js M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/dataset.py 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/layout/menu.js R templates/webapps/galaxy/dataset/grid.mako Log Message: ----------- Merge branch 'grid_datasets' into dev Commit: d36c4053cd16a31ecd77bdc726cfb52179088e4f https://github.com/galaxyproject/galaxy/commit/d36c4053cd16a31ecd77bdc726cf… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-06-12 (Mon, 12 Jun 2017) Changed paths: M static/scripts/bundled/admin.bundled.js.map 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.map Log Message: ----------- Merge and repack. Compare: https://github.com/galaxyproject/galaxy/compare/2178cffaed03...d36c4053cd16

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[galaxyproject/galaxy] ec3428: Bring in all recent mulled container changes from ...
by GitHub 12 Jun '17

12 Jun '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ec34287afdf63e4712dc76bd29f718a26e04e17e https://github.com/galaxyproject/galaxy/commit/ec34287afdf63e4712dc76bd29f7… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-06-08 (Thu, 08 Jun 2017) Changed paths: M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/mulled/invfile.lua 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_search.py M lib/galaxy/tools/deps/mulled/util.py Log Message: ----------- Bring in all recent mulled container changes from galaxy-lib. - Update mulled container resolution to use a version 2 (v2) hashing function. https://github.com/galaxyproject/galaxy-lib/pull/63 - When building images with mulled, always cleanup build directory. https://github.com/galaxyproject/galaxy-lib/pull/55/files and https://github.com/galaxyproject/galaxy-lib/pull/61 - Expose an offline search option in library Conda search utility. https://github.com/galaxyproject/galaxy-lib/pull/60 - Fix first use of mulled-build-* for auto-install of Involucro. https://github.com/galaxyproject/galaxy-lib/pull/59/commits/c5e7778f51d735a… - Fix up and improve logic related to rebuilding mulled containers. https://github.com/galaxyproject/galaxy-lib/pull/59/commits/faf528997c36f8a… - Fix mulled-build-files to properly handle tab separated files. https://github.com/galaxyproject/galaxy-lib/pull/59/commits/10b1cf3addf03e1… - Various other mulled-build-file enhancements. https://github.com/galaxyproject/galaxy-lib/pull/59/commits/70314e3e65921a5… https://github.com/galaxyproject/galaxy-lib/pull/59/commits/21b4bc58013dc53… https://github.com/galaxyproject/galaxy-lib/pull/59/commits/74abe8a107044e1… https://github.com/galaxyproject/galaxy-lib/pull/58 - Correct mulled-search default namespace from mulled to biocontainers. https://github.com/galaxyproject/galaxy-lib/pull/57 - Add ability to specify a new base image when building mulled images. https://github.com/galaxyproject/galaxy-lib/pull/56 - Update the default mulled target namespace from the older mulled to the new biocontainers. Commit: 51219f0db0734bfe62a1ba26bf45aca3833541f0 https://github.com/galaxyproject/galaxy/commit/51219f0db0734bfe62a1ba26bf45… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-06-08 (Thu, 08 Jun 2017) Changed paths: A test/functional/tools/mulled_example_multi_versionless.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Add a test tool for mulled containers with versionless requirements. Commit: 065eb716c40b781fe75577c94da3f23bb0b5c4f6 https://github.com/galaxyproject/galaxy/commit/065eb716c40b781fe75577c94da3… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-06-10 (Sat, 10 Jun 2017) Changed paths: M lib/galaxy/tools/deps/mulled/invfile.lua M lib/galaxy/tools/deps/mulled/mulled_build.py Log Message: ----------- Merged downstream galaxy-lib mulled enhancement and fixes. - Singularity support for building mulled containers https://github.com/galaxyproject/galaxy-lib/pull/64 - Hack to fix previous mulled v2 changes for single requirement tools https://github.com/galaxyproject/galaxy-lib/pull/65. Commit: 2178cffaed030bf3e821cd89a299431a63fec7c1 https://github.com/galaxyproject/galaxy/commit/2178cffaed030bf3e821cd89a299… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-06-12 (Mon, 12 Jun 2017) Changed paths: M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/mulled/invfile.lua 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_search.py M lib/galaxy/tools/deps/mulled/util.py A test/functional/tools/mulled_example_multi_versionless.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #4173 from jmchilton/galaxy-lib-mulled-update Improved Mulled Containers Compare: https://github.com/galaxyproject/galaxy/compare/3bff7f36d1a9...2178cffaed03

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[galaxyproject/galaxy] 413f47: Implement singularity support.
by GitHub 10 Jun '17

10 Jun '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 413f47652098cddafa406be3cef546c757249847 https://github.com/galaxyproject/galaxy/commit/413f47652098cddafa406be3cef5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-06-09 (Fri, 09 Jun 2017) Changed paths: M config/job_conf.xml.sample_advanced M lib/galaxy/tools/deps/containers.py A lib/galaxy/tools/deps/singularity_util.py Log Message: ----------- Implement singularity support. See http://singularity.lbl.gov/ for more information on Singularity and see job_conf.xml.sample_advanced for information on setting up job runners to exploit singularity. The biggest current caveat is probably that currently these container images need to be setup manually by the admin and the paths hard-coded for each tool in job_conf.xml. There are people who do such manual setups for Docker (https://github.com/phnmnl/container-galaxy-k8s-runtime/blob/develop/config/…) - so it wouldn't be surprising if someone wanted to set this up for singularity as well. That said I'm sure this will be followed up by magic to fetch and convert Docker containers and leverage published singularity containers (such as mulled can now produce (https://github.com/galaxyproject/galaxy-lib/pull/64). Commit: 3bff7f36d1a9014e0ea7123f0a156e8924070f3d https://github.com/galaxyproject/galaxy/commit/3bff7f36d1a9014e0ea7123f0a15… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-06-10 (Sat, 10 Jun 2017) Changed paths: M config/job_conf.xml.sample_advanced M lib/galaxy/tools/deps/containers.py A lib/galaxy/tools/deps/singularity_util.py Log Message: ----------- Merge pull request #4175 from jmchilton/singularity Implement Singularity Support Compare: https://github.com/galaxyproject/galaxy/compare/625feb1bb654...3bff7f36d1a9

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[galaxyproject/galaxy] 1ce673: Switch pages grid controller endpoint to dictionar...
by GitHub 08 Jun '17

08 Jun '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1ce673828749835c220ad45d81f6753bd24ee011 https://github.com/galaxyproject/galaxy/commit/1ce673828749835c220ad45d81f6… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-06-05 (Mon, 05 Jun 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/page.py Log Message: ----------- Switch pages grid controller endpoint to dictionary mode Commit: 0a03039e35861975c07273d7c8a27e3c4a2471d3 https://github.com/galaxyproject/galaxy/commit/0a03039e35861975c07273d7c8a2… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-06-05 (Mon, 05 Jun 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/mvc/grid/grid-view.js M lib/galaxy/webapps/galaxy/controllers/page.py M static/maps/mvc/grid/grid-view.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.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/grid/grid-view.js Log Message: ----------- Add page list viewer, move sharing feature out of operations Commit: aac37045d53f3ab7cc718dabaa734cb752c5b2d4 https://github.com/galaxyproject/galaxy/commit/aac37045d53f3ab7cc718dabaa73… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-06-05 (Mon, 05 Jun 2017) Changed paths: M client/galaxy/scripts/layout/menu.js A client/galaxy/scripts/mvc/page/page-list.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/layout/menu.js Log Message: ----------- Redirect masthead link to client route Commit: 9784c1d698c7fd0d7a573f44460e4c2fbd00501a https://github.com/galaxyproject/galaxy/commit/9784c1d698c7fd0d7a573f44460e… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-06-05 (Mon, 05 Jun 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/page.py Log Message: ----------- Redirect create submission Commit: 3208325b2e2e2a23e50fb94f7827d336486d6e11 https://github.com/galaxyproject/galaxy/commit/3208325b2e2e2a23e50fb94f7827… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-06-05 (Mon, 05 Jun 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/page.py Log Message: ----------- Properly redirect after editing a page Commit: abe3b1e326ba56d878fafe095fcaa8ffa0fa3566 https://github.com/galaxyproject/galaxy/commit/abe3b1e326ba56d878fafe095fca… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-06-06 (Tue, 06 Jun 2017) Changed paths: M client/galaxy/scripts/mvc/page/page-list.js M lib/galaxy/webapps/galaxy/controllers/page.py M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.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: ----------- Add shared by other, load rendering through model Commit: aa85d00615edcc28b94e00ac95efe803d90ee009 https://github.com/galaxyproject/galaxy/commit/aa85d00615edcc28b94e00ac95ef… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-06-06 (Tue, 06 Jun 2017) Changed paths: M client/galaxy/scripts/mvc/page/page-list.js 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: ----------- Add shared pages table Commit: 26fdf8b8fd200af439f4ba8b2138d3209c617ba4 https://github.com/galaxyproject/galaxy/commit/26fdf8b8fd200af439f4ba8b2138… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-06-06 (Tue, 06 Jun 2017) Changed paths: M client/galaxy/scripts/mvc/page/page-list.js 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: ----------- Display only link for shared pages since viewing is the only operation Commit: 81592f3c32de7fb05d260996aaaafa0866f4a3e6 https://github.com/galaxyproject/galaxy/commit/81592f3c32de7fb05d260996aaaa… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-06-06 (Tue, 06 Jun 2017) Changed paths: R templates/webapps/galaxy/page/index.mako Log Message: ----------- Remove pages grid mako Commit: 53cfedaaeaba2bba803a4040e161539e6d6660b7 https://github.com/galaxyproject/galaxy/commit/53cfedaaeaba2bba803a4040e161… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-06-06 (Tue, 06 Jun 2017) Changed paths: M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.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: ----------- Pack scripts Commit: 7f97d5016e2638084fedd2f2cca3f2b78a67ba6c https://github.com/galaxyproject/galaxy/commit/7f97d5016e2638084fedd2f2cca3… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-06-06 (Tue, 06 Jun 2017) Changed paths: M client/galaxy/scripts/mvc/page/page-list.js 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: ----------- Revise template Commit: 37bdf694d182caff4e5df8cb10f12bb39037e7e7 https://github.com/galaxyproject/galaxy/commit/37bdf694d182caff4e5df8cb10f1… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-06-06 (Tue, 06 Jun 2017) Changed paths: M templates/webapps/galaxy/page/editor.mako Log Message: ----------- Redirect close in page editor to new client route Commit: 5d85515c09b667a8d6c6bc1ebb0511de60aea05b https://github.com/galaxyproject/galaxy/commit/5d85515c09b667a8d6c6bc1ebb05… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-06-06 (Tue, 06 Jun 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/page.py M templates/sharing_base.mako Log Message: ----------- Fix sharing base mako urls for new client side controller endpoints Commit: aedb72606abb5365a2f80a49c274ad5635b3556f https://github.com/galaxyproject/galaxy/commit/aedb72606abb5365a2f80a49c274… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-06-07 (Wed, 07 Jun 2017) Changed paths: A static/maps/mvc/page/page-list.js.map A static/scripts/mvc/page/page-list.js Log Message: ----------- Add packed files Commit: e3109d8d946e147b2fdd740bd3fe946a8d1151ac https://github.com/galaxyproject/galaxy/commit/e3109d8d946e147b2fdd740bd3fe… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-06-07 (Wed, 07 Jun 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-slider.js M client/galaxy/style/less/ui.less M config/job_conf.xml.sample_advanced M config/plugins/webhooks/demo/search/config/searchover.yaml M config/plugins/webhooks/demo/tool_list/config/tool_list.yml M lib/galaxy/app.py M lib/galaxy/datatypes/text.py M lib/galaxy/jobs/__init__.py A lib/galaxy/tools/cache.py R lib/galaxy/tools/toolbox/cache.py M static/maps/mvc/ui/ui-slider.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-slider.js M static/style/blue/base.css M test/api/test_dataset_collections.py M test/functional/webhooks/trans_object/config/trans_object.yaml M test/qunit/tests/ui_tests.html M test/qunit/tests/ui_tests.js A test/unit/jobs/conditional_runners_job_conf.xml M test/unit/jobs/test_job_configuration.py M test/unit/tools/test_toolbox.py Log Message: ----------- Merge branch 'dev' into grid_pages Commit: 625feb1bb6549b712b7c2fc652155cd8a8785e90 https://github.com/galaxyproject/galaxy/commit/625feb1bb6549b712b7c2fc65215… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-06-08 (Thu, 08 Jun 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/grid/grid-view.js A client/galaxy/scripts/mvc/page/page-list.js M lib/galaxy/webapps/galaxy/controllers/page.py M static/maps/layout/menu.js.map M static/maps/mvc/grid/grid-view.js.map A static/maps/mvc/page/page-list.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.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/grid/grid-view.js A static/scripts/mvc/page/page-list.js M templates/sharing_base.mako M templates/webapps/galaxy/page/editor.mako R templates/webapps/galaxy/page/index.mako Log Message: ----------- Merge pull request #4157 from guerler/grid_pages Remove saved pages grid mako Compare: https://github.com/galaxyproject/galaxy/compare/848bcd8587a1...625feb1bb654

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[galaxyproject/galaxy] 72eb48: Move PlantTribes datatypes to a separate file, wil...
by GitHub 08 Jun '17

08 Jun '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 72eb4858db6b5683515b7bb89bd0e2d4f58f372d https://github.com/galaxyproject/galaxy/commit/72eb4858db6b5683515b7bb89bd0… Author: Greg Von Kuster <ghv2(a)psu.edu> Date: 2017-06-01 (Thu, 01 Jun 2017) Changed paths: M config/datatypes_conf.xml.sample A lib/galaxy/datatypes/plant_tribes.py M lib/galaxy/datatypes/text.py Log Message: ----------- Move PlantTribes datatypes to a separate file, will replace PR 3999 Commit: 0c2af94adee5f725f93ee086095497cb0ebbfeb4 https://github.com/galaxyproject/galaxy/commit/0c2af94adee5f725f93ee0860954… Author: Greg Von Kuster <ghv2(a)psu.edu> Date: 2017-06-01 (Thu, 01 Jun 2017) Changed paths: M lib/galaxy/datatypes/plant_tribes.py Log Message: ----------- Fix Smat sniff method Commit: 1b7a386e6cad75ec68bd624aef3f8f7c9445838b https://github.com/galaxyproject/galaxy/commit/1b7a386e6cad75ec68bd624aef3f… Author: Greg Von Kuster <ghv2(a)psu.edu> Date: 2017-06-05 (Mon, 05 Jun 2017) Changed paths: M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/plant_tribes.py Log Message: ----------- Move ability to view directory contents in base display_data() function Commit: 507dc9d7fc7d7aff1b32da1d6bdf0c752b60fc24 https://github.com/galaxyproject/galaxy/commit/507dc9d7fc7d7aff1b32da1d6bdf… Author: Greg Von Kuster <ghv2(a)psu.edu> Date: 2017-06-05 (Mon, 05 Jun 2017) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Fix the Smat sniffer Commit: 848bcd8587a1aa466b63a074a17225a38678d70f https://github.com/galaxyproject/galaxy/commit/848bcd8587a1aa466b63a074a172… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-06-08 (Thu, 08 Jun 2017) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/data.py A lib/galaxy/datatypes/plant_tribes.py M lib/galaxy/datatypes/text.py Log Message: ----------- Merge pull request #4137 from gregvonkuster/ptformats4 Move PlantTribes datatypes to a separate file with enhancements and fixes Compare: https://github.com/galaxyproject/galaxy/compare/2b3cd15c774f...848bcd8587a1

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[galaxyproject/galaxy] 324904: Fix older GIE config sample description.
by GitHub 07 Jun '17

07 Jun '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 324904238512dea23f1b2fffbb43e024b3fbbed4 https://github.com/galaxyproject/galaxy/commit/324904238512dea23f1b2fffbb43… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-06-07 (Wed, 07 Jun 2017) Changed paths: M config/galaxy.ini.sample Log Message: ----------- Fix older GIE config sample description. Commit: 2b3cd15c774f986e3f2824ebd1522c5cc3848f26 https://github.com/galaxyproject/galaxy/commit/2b3cd15c774f986e3f2824ebd152… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-06-07 (Wed, 07 Jun 2017) Changed paths: M config/galaxy.ini.sample Log Message: ----------- Merge pull request #4164 from jmchilton/gei_desc_update Fix older GIE config sample description. Compare: https://github.com/galaxyproject/galaxy/compare/d75cec160302...2b3cd15c774f

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[galaxyproject/galaxy] 3c5044: Add model handler for sliders
by GitHub 07 Jun '17

07 Jun '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 3c5044f01bd735229f1d4ef45217b6e8205ab568 https://github.com/galaxyproject/galaxy/commit/3c5044f01bd735229f1d4ef45217… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-06-04 (Sun, 04 Jun 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-slider.js M static/maps/mvc/ui/ui-slider.js.map M static/scripts/mvc/ui/ui-slider.js Log Message: ----------- Add model handler for sliders Commit: 1c5c400f9565182bfbf5f56dab55c3e3992c761e https://github.com/galaxyproject/galaxy/commit/1c5c400f9565182bfbf5f56dab55… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-06-04 (Sun, 04 Jun 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-slider.js M static/maps/mvc/ui/ui-slider.js.map M static/scripts/mvc/ui/ui-slider.js Log Message: ----------- Add consistent render caller Commit: 167a26129f09a3c8bd176547d72263d780ae172f https://github.com/galaxyproject/galaxy/commit/167a26129f09a3c8bd176547d722… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-06-04 (Sun, 04 Jun 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-slider.js Log Message: ----------- Align tabs Commit: 6fe034f23dbe49ecddaf9dea571c401d7c41e2d1 https://github.com/galaxyproject/galaxy/commit/6fe034f23dbe49ecddaf9dea571c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-06-04 (Sun, 04 Jun 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-slider.js M static/maps/mvc/ui/ui-slider.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.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/ui/ui-slider.js Log Message: ----------- Add value to model Commit: d632e4081da0ec68fd07dd9738ea09ff52a103c4 https://github.com/galaxyproject/galaxy/commit/d632e4081da0ec68fd07dd9738ea… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-06-04 (Sun, 04 Jun 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-slider.js M static/maps/mvc/ui/ui-slider.js.map M static/scripts/mvc/ui/ui-slider.js Log Message: ----------- Remove duplicate selector Commit: f5bb52257221b9c3058dba80f4b1b34e2e294cdd https://github.com/galaxyproject/galaxy/commit/f5bb52257221b9c3058dba80f4b1… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-06-04 (Sun, 04 Jun 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-slider.js M client/galaxy/style/less/ui.less M static/maps/mvc/ui/ui-slider.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-slider.js M static/style/blue/base.css M test/qunit/tests/ui_tests.html M test/qunit/tests/ui_tests.js Log Message: ----------- Use style classes to produce left floating text field Commit: 6605681c1dc07cb97c7112d97ddef9eecfec7e85 https://github.com/galaxyproject/galaxy/commit/6605681c1dc07cb97c7112d97dde… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-06-05 (Mon, 05 Jun 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-slider.js M static/maps/mvc/ui/ui-slider.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.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/ui/ui-slider.js M test/qunit/tests/ui_tests.js Log Message: ----------- Move slider building out of render, cannot be rebuild Commit: adebe0521cdc1d1c74aae5386b0caf83451b601c https://github.com/galaxyproject/galaxy/commit/adebe0521cdc1d1c74aae5386b0c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-06-05 (Mon, 05 Jun 2017) Changed paths: M test/qunit/tests/ui_tests.js Log Message: ----------- Remove space from test case Commit: 49a60016b56bca5ad6a3a7484db6d2c7e2fb12bb https://github.com/galaxyproject/galaxy/commit/49a60016b56bca5ad6a3a7484db6… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-06-05 (Mon, 05 Jun 2017) Changed paths: M test/qunit/tests/ui_tests.js Log Message: ----------- Add test cases Commit: b7530fbbc981e8fe5e93db7d56560339f3a64f47 https://github.com/galaxyproject/galaxy/commit/b7530fbbc981e8fe5e93db7d5656… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-06-05 (Mon, 05 Jun 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-slider.js M static/maps/mvc/ui/ui-slider.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-slider.js Log Message: ----------- Remove inconsistent change caller Commit: 7274bb641bcf23f5bac55d857f0402e33ca94423 https://github.com/galaxyproject/galaxy/commit/7274bb641bcf23f5bac55d857f04… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-06-05 (Mon, 05 Jun 2017) Changed paths: M client/galaxy/scripts/mvc/collection/collection-view.js M config/job_conf.xml.sample_advanced M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/data.py M lib/galaxy/jobs/runners/chronos.py M lib/galaxy/managers/collections_util.py M lib/galaxy/webapps/galaxy/api/history_contents.py M lib/galaxy/webapps/galaxy/buildapp.py M static/maps/mvc/collection/collection-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.map M static/scripts/mvc/collection/collection-view.js M test/api/test_dataset_collections.py M test/base/populators.py Log Message: ----------- Merge branch 'dev' into slider_upgrade Commit: a2e14c6c6ecf9ce752f79311584ce69b8bd8d4ca https://github.com/galaxyproject/galaxy/commit/a2e14c6c6ecf9ce752f79311584c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-06-05 (Mon, 05 Jun 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-slider.js M static/maps/mvc/ui/ui-slider.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-slider.js Log Message: ----------- Resolve previously existing issue with pasting float values into integer fields Commit: d75cec160302029a9aa56e5ef12c4ddaed009b0e https://github.com/galaxyproject/galaxy/commit/d75cec160302029a9aa56e5ef12c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-06-07 (Wed, 07 Jun 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-slider.js M client/galaxy/style/less/ui.less M static/maps/mvc/ui/ui-slider.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-slider.js M static/style/blue/base.css M test/qunit/tests/ui_tests.html M test/qunit/tests/ui_tests.js Log Message: ----------- Merge pull request #4149 from guerler/slider_upgrade Slider enhancement, shared event listeners Compare: https://github.com/galaxyproject/galaxy/compare/865b2249cec5...d75cec160302

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[galaxyproject/galaxy] 0b1a33: Set content type to application/json for JSON text...
by GitHub 06 Jun '17

06 Jun '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 0b1a3354216b4a7b9554648d0581360036ffa94e https://github.com/galaxyproject/galaxy/commit/0b1a3354216b4a7b9554648d0581… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-06-06 (Tue, 06 Jun 2017) Changed paths: M lib/galaxy/datatypes/text.py Log Message: ----------- Set content type to application/json for JSON text types. Commit: 865b2249cec5365f72d3f18be595bf7b75cf6c82 https://github.com/galaxyproject/galaxy/commit/865b2249cec5365f72d3f18be595… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-06-06 (Tue, 06 Jun 2017) Changed paths: M lib/galaxy/datatypes/text.py Log Message: ----------- Merge pull request #4160 from dannon/json_contenttype Set content type to application/json for JSON text types. Compare: https://github.com/galaxyproject/galaxy/compare/ee4826fbc4ae...865b2249cec5

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[galaxyproject/galaxy] d14eb9: Add the ability to control job conf plugin loading...
by GitHub 06 Jun '17

06 Jun '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d14eb9e63c222345cff111b8fe888a74a968d4bc https://github.com/galaxyproject/galaxy/commit/d14eb9e63c222345cff111b8fe88… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-06-06 (Tue, 06 Jun 2017) Changed paths: M config/job_conf.xml.sample_advanced M lib/galaxy/jobs/__init__.py A test/unit/jobs/conditional_runners_job_conf.xml M test/unit/jobs/test_job_configuration.py Log Message: ----------- Add the ability to control job conf plugin loading from environment variables. All job configuration parameters can be set using environment variables but currently the actual loading of the plugin cannot. This is problematic for setting up single job confs for multiple environemnts (like done with docker-galaxy-stable) when using plugins that may hang waiting for resources (such as Kubernetes for the K8 runner or a MQ for Pulsar for instance) or may require library dependencies not be setup in every environment the job configuration is deployed in. xref https://github.com/bgruening/docker-galaxy-stable/pull/328 Rebased with advice from @bgruening. Commit: ee4826fbc4aeb09bcf01e501759f9774e61244b1 https://github.com/galaxyproject/galaxy/commit/ee4826fbc4aeb09bcf01e501759f… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-06-06 (Tue, 06 Jun 2017) Changed paths: M config/job_conf.xml.sample_advanced M lib/galaxy/jobs/__init__.py A test/unit/jobs/conditional_runners_job_conf.xml M test/unit/jobs/test_job_configuration.py Log Message: ----------- Merge pull request #4154 from jmchilton/dynamic_disable_runners Add the ability to control job conf plugin loading from environment variables. Compare: https://github.com/galaxyproject/galaxy/compare/ae76200b08b6...ee4826fbc4ae

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[galaxyproject/galaxy] 0b1eaf: fix - remove extra slash
by GitHub 06 Jun '17

06 Jun '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 0b1eaf3269ed5ccbfba7807826e822b38f57778e https://github.com/galaxyproject/galaxy/commit/0b1eaf3269ed5ccbfba7807826e8… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-06-06 (Tue, 06 Jun 2017) Changed paths: M config/plugins/webhooks/demo/search/config/searchover.yaml M config/plugins/webhooks/demo/tool_list/config/tool_list.yml M test/functional/webhooks/trans_object/config/trans_object.yaml Log Message: ----------- fix - remove extra slash Commit: d39b955e8a5d6c54852d3b32cd9cd1e7e2d3e519 https://github.com/galaxyproject/galaxy/commit/d39b955e8a5d6c54852d3b32cd9c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-06-06 (Tue, 06 Jun 2017) Changed paths: M config/plugins/webhooks/demo/search/config/searchover.yaml M config/plugins/webhooks/demo/tool_list/config/tool_list.yml M test/functional/webhooks/trans_object/config/trans_object.yaml Log Message: ----------- Merge pull request #4158 from martenson/webhooks-fix-prefix [17.05] fix webhooks loading url Commit: ae76200b08b6e74a58a414c6fe3ae641717523b9 https://github.com/galaxyproject/galaxy/commit/ae76200b08b6e74a58a414c6fe3a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-06-06 (Tue, 06 Jun 2017) Changed paths: M config/plugins/webhooks/demo/search/config/searchover.yaml M config/plugins/webhooks/demo/tool_list/config/tool_list.yml M test/functional/webhooks/trans_object/config/trans_object.yaml Log Message: ----------- Merge remote-tracking branch 'upstream/release_17.05' into dev Compare: https://github.com/galaxyproject/galaxy/compare/fae508b48f40...ae76200b08b6

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