galaxy-commits June 2017

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[galaxyproject/galaxy] 4ee184: Running a word count on a compressed fastq file no...
by GitHub 26 Jun '17

26 Jun '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4ee184899215931213e088b381c1d91c930e8775 https://github.com/galaxyproject/galaxy/commit/4ee184899215931213e088b381c1… Author: Devon Ryan <dpryan79(a)gmail.com> Date: 2017-06-26 (Mon, 26 Jun 2017) Changed paths: M tools/filters/wc_gnu.xml Log Message: ----------- Running a word count on a compressed fastq file now runs wc on the uncompressed file Commit: 8a6ef0585861ad457184797b5a14e42698277d33 https://github.com/galaxyproject/galaxy/commit/8a6ef0585861ad457184797b5a14… Author: Devon Ryan <dpryan79(a)gmail.com> Date: 2017-06-26 (Mon, 26 Jun 2017) Changed paths: M tools/filters/wc_gnu.xml Log Message: ----------- Single quote file names Commit: ce1316d6808ef758c61ddb85ad77ec3acf2c7048 https://github.com/galaxyproject/galaxy/commit/ce1316d6808ef758c61ddb85ad77… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-06-26 (Mon, 26 Jun 2017) Changed paths: M tools/filters/wc_gnu.xml Log Message: ----------- Merge pull request #4226 from dpryan79/CompressedFastqLines_implement4144 Running a word count on a compressed fastq file now runs wc on the un… Compare: https://github.com/galaxyproject/galaxy/compare/3ec2c7831def...ce1316d6808e

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[galaxyproject/galaxy] 0bfa1d: Fix Registry.get_datatype_by_extension() to return...
by GitHub 26 Jun '17

26 Jun '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 0bfa1df72f8d0d140dea400ea6ad7f854714817e https://github.com/galaxyproject/galaxy/commit/0bfa1df72f8d0d140dea400ea6ad… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-06-26 (Mon, 26 Jun 2017) Changed paths: M lib/galaxy/datatypes/registry.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/wrappers.py M test/functional/tools/sample_datatypes_conf.xml Log Message: ----------- Fix Registry.get_datatype_by_extension() to return None if ext is unknown Without this fix, the Cheetah expression: $dataset.is_of_type('unknown_ext') in a tool command would be equivalent to: $dataset.is_of_type('txt') meaning that if the dataset datatype is a subclass of Text, the expression would evaluate to True without any warning. xref. https://github.com/galaxyproject/tools-iuc/issues/1373 Also add missing `xml` datatype to `test/functional/tools/sample_datatypes_conf.xml` which is needed by 3 test tools. Commit: 02ffcd5c8f9f30f38581d89f8b913bb587b88e6d https://github.com/galaxyproject/galaxy/commit/02ffcd5c8f9f30f38581d89f8b91… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-06-26 (Mon, 26 Jun 2017) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M lib/galaxy/datatypes/registry.py Log Message: ----------- Fix import order and Python3 compatibility for lib/galaxy/datatypes/registry.py xref. https://github.com/galaxyproject/galaxy/issues/1715 Commit: e8c23136406fd4acd6c2b902e107dfea21a73762 https://github.com/galaxyproject/galaxy/commit/e8c23136406fd4acd6c2b902e107… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-06-26 (Mon, 26 Jun 2017) Changed paths: M lib/galaxy/datatypes/data.py M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Small fixes Commit: 3ec2c7831defa0486a8b3eb5a88a12458d5b5d1b https://github.com/galaxyproject/galaxy/commit/3ec2c7831defa0486a8b3eb5a88a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-06-26 (Mon, 26 Jun 2017) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/registry.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/wrappers.py M test/functional/tools/sample_datatypes_conf.xml Log Message: ----------- Merge pull request #4224 from nsoranzo/fix_get_datatype_by_extension Fix Registry.get_datatype_by_extension() to return None if ext is unknown Compare: https://github.com/galaxyproject/galaxy/compare/73faf7c8b6e0...3ec2c7831def

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[galaxyproject/galaxy] 009287: Correct name of neo4j datatype class
by GitHub 23 Jun '17

23 Jun '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 00928743bfa363bf74429b65948cec14d6985a75 https://github.com/galaxyproject/galaxy/commit/00928743bfa363bf74429b65948c… Author: pvanheus <pvh(a)webbedfeet.co.za> Date: 2017-06-23 (Fri, 23 Jun 2017) Changed paths: M config/plugins/interactive_environments/neo/config/neo.xml Log Message: ----------- Correct name of neo4j datatype class Its neo4j.Neo4jDB: https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/datatypes/neo4j… Commit: 73faf7c8b6e07dee3d277c510dd70604bc85ae98 https://github.com/galaxyproject/galaxy/commit/73faf7c8b6e07dee3d277c510dd7… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-06-24 (Sat, 24 Jun 2017) Changed paths: M config/plugins/interactive_environments/neo/config/neo.xml Log Message: ----------- Merge pull request #4223 from pvanheus/patch-3 Correct name of neo4j datatype class Compare: https://github.com/galaxyproject/galaxy/compare/a910763cd8f0...73faf7c8b6e0

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[galaxyproject/usegalaxy-playbook] c3f315: Quick and dirty dynamic rule changes for RNA STAR
by GitHub 23 Jun '17

23 Jun '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: c3f315583d3449bd6269f0d6edbdd64300ca0efb https://github.com/galaxyproject/usegalaxy-playbook/commit/c3f315583d3449bd… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-06-23 (Fri, 23 Jun 2017) Changed paths: M files/galaxy/common/dynamic_rules/multi_dynamic_walltime.py M files/galaxy/usegalaxy.org/config/job_resource_params_conf.xml M templates/galaxy/usegalaxy.org/config/job_conf.xml.j2 Log Message: ----------- Quick and dirty dynamic rule changes for RNA STAR Commit: d3d2a4733f1fe844089a077bf029a703e159ec67 https://github.com/galaxyproject/usegalaxy-playbook/commit/d3d2a4733f1fe844… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-06-23 (Fri, 23 Jun 2017) Changed paths: M files/galaxy/usegalaxy.org/var/integrated_tool_panel.xml M files/galaxy/usegalaxy.org/var/shed_tool_data_table_conf.xml Log Message: ----------- Main mutable configs Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/8ae4c0768d9e...…

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[galaxyproject/usegalaxy-playbook] 49a63a: Hack RNA STAR into the terrible One Dynamic Rule T...
by GitHub 22 Jun '17

22 Jun '17

Branch: refs/heads/reorg Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 49a63ad338ca092dd8739bc1d650d645e00bc6fd https://github.com/galaxyproject/usegalaxy-playbook/commit/49a63ad338ca092d… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-06-22 (Thu, 22 Jun 2017) Changed paths: M env/common/files/galaxy/dynamic_rules/multi_dynamic_walltime.py M env/test/files/galaxy/config/job_resource_params_conf.xml M env/test/templates/galaxy/config/job_conf.xml.j2 Log Message: ----------- Hack RNA STAR into the terrible One Dynamic Rule To Rule Them All

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[galaxyproject/galaxy] 67b798: Add missing lines for fixing Singularity volumes.
by GitHub 22 Jun '17

22 Jun '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 67b798f3832277708e884cb6ababeaaa947e9825 https://github.com/galaxyproject/galaxy/commit/67b798f3832277708e884cb6abab… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-06-20 (Tue, 20 Jun 2017) Changed paths: M lib/galaxy/tools/deps/containers.py Log Message: ----------- Add missing lines for fixing Singularity volumes. These should have been included in https://github.com/galaxyproject/galaxy/pull/4180. Commit: a910763cd8f07c8863af177294bfacf5eb7df536 https://github.com/galaxyproject/galaxy/commit/a910763cd8f07c8863af177294bf… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-06-22 (Thu, 22 Jun 2017) Changed paths: M lib/galaxy/tools/deps/containers.py Log Message: ----------- Merge pull request #4208 from jmchilton/singularity_volume_fix_2 Add missing lines for fixing Singularity volumes. Compare: https://github.com/galaxyproject/galaxy/compare/c18479b79c7e...a910763cd8f0

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[galaxyproject/galaxy] 3f29f1: Visualizations grid
by GitHub 22 Jun '17

22 Jun '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 3f29f13d3b1e373710bcf3400cc38c21966dcf75 https://github.com/galaxyproject/galaxy/commit/3f29f13d3b1e373710bcf3400cc3… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-06-16 (Fri, 16 Jun 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/layout/menu.js M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M static/maps/layout/menu.js.map 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.map M static/scripts/layout/menu.js R templates/webapps/galaxy/visualization/list_published.mako Log Message: ----------- Visualizations grid Commit: 90d6262ef9b1c7b5ce107f3a3c1d0c3ae125e916 https://github.com/galaxyproject/galaxy/commit/90d6262ef9b1c7b5ce107f3a3c1d… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-06-16 (Fri, 16 Jun 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/layout/menu.js M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/workflow.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/workflow/list_published.mako Log Message: ----------- Published workflows Commit: bf65490a14a6808abef32fe0d5ea0dd335553c91 https://github.com/galaxyproject/galaxy/commit/bf65490a14a6808abef32fe0d5ea… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-06-21 (Wed, 21 Jun 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/panels/tool-panel.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/layout/panel.js M client/galaxy/scripts/mvc/grid/grid-view.js A client/galaxy/scripts/mvc/history/history-list.js M client/galaxy/scripts/mvc/history/history-view-edit-current.js M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/user/user-preferences.js M client/galaxy/scripts/mvc/workflow/workflow-configure-menu.js M client/galaxy/scripts/mvc/workflow/workflow.js M client/galaxy/scripts/utils/utils.js M client/galaxy/style/less/base.less M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/deps/mulled/invfile.lua M lib/galaxy/tools/deps/mulled/mulled_build.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M scripts/api/library_upload_dir.py M static/maps/layout/menu.js.map M static/maps/layout/page.js.map M static/maps/layout/panel.js.map M static/maps/mvc/grid/grid-view.js.map A static/maps/mvc/history/history-list.js.map M static/maps/mvc/history/history-view-edit-current.js.map M static/maps/mvc/history/options-menu.js.map M static/maps/mvc/tool/tool-form-base.js.map M static/maps/mvc/tool/tool-form-composite.js.map M static/maps/mvc/user/user-preferences.js.map M static/maps/mvc/workflow/workflow-configure-menu.js.map M static/maps/mvc/workflow/workflow.js.map M static/maps/utils/utils.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 M static/scripts/layout/page.js M static/scripts/layout/panel.js M static/scripts/mvc/grid/grid-view.js A static/scripts/mvc/history/history-list.js M static/scripts/mvc/history/history-view-edit-current.js M static/scripts/mvc/history/options-menu.js M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/tool/tool-form-composite.js M static/scripts/mvc/user/user-preferences.js M static/scripts/mvc/workflow/workflow-configure-menu.js M static/scripts/mvc/workflow/workflow.js M static/scripts/utils/utils.js M static/style/blue/base.css R templates/webapps/galaxy/history/grid.mako R templates/webapps/galaxy/history/grid_js.mako R templates/webapps/galaxy/workflow/import.mako R templates/webapps/galaxy/workflow/run.mako Log Message: ----------- Merge branch 'dev' into grids_published Commit: c18479b79c7e7d3496a1aa91cda2e83e13a429c6 https://github.com/galaxyproject/galaxy/commit/c18479b79c7e7d3496a1aa91cda2… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-06-22 (Thu, 22 Jun 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/layout/menu.js M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M static/maps/layout/menu.js.map 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.map M static/scripts/layout/menu.js R templates/webapps/galaxy/visualization/list_published.mako R templates/webapps/galaxy/workflow/list_published.mako Log Message: ----------- Merge remote-tracking branch 'guerler/grids_published' into dev Compare: https://github.com/galaxyproject/galaxy/compare/27e843bfc131...c18479b79c7e

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[galaxyproject/usegalaxy-playbook] 5f46d0: Manually upgraded Test galaxy-lib on Jetstream fro...
by GitHub 22 Jun '17

22 Jun '17

Branch: refs/heads/reorg Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 5f46d03b2050f4bdb89ca8364c3ea4a72314cd9c https://github.com/galaxyproject/usegalaxy-playbook/commit/5f46d03b2050f4bd… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-06-22 (Thu, 22 Jun 2017) Log Message: ----------- Manually upgraded Test galaxy-lib on Jetstream from 16.7.7 to 17.9.1. No committable changes.

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[galaxyproject/galaxy] 19231b: Reduce opening of search overlay to one step - jus...
by GitHub 22 Jun '17

22 Jun '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 19231b73f356c568cd85cba9962f6dc1d27a0d0a https://github.com/galaxyproject/galaxy/commit/19231b73f356c568cd85cba9962f… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-06-20 (Tue, 20 Jun 2017) Changed paths: M client/galaxy/scripts/layout/menu.js M config/plugins/webhooks/demo/search/config/searchover.yaml M config/plugins/webhooks/demo/search/static/script.js M static/maps/layout/menu.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/layout/menu.js Log Message: ----------- Reduce opening of search overlay to one step - just click on the magnifier Commit: 6704872cd9e1121855274187b6c85b86a7c7f9d5 https://github.com/galaxyproject/galaxy/commit/6704872cd9e1121855274187b6c8… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-06-21 (Wed, 21 Jun 2017) Changed paths: M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/utils/utils.js M static/maps/layout/menu.js.map M static/maps/utils/utils.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/utils/utils.js Log Message: ----------- Moving the creation of script and style tags to Utils Commit: e9b132bd5345a4fb7637db9fa1fbc5de40ad0adc https://github.com/galaxyproject/galaxy/commit/e9b132bd5345a4fb7637db9fa1fb… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-06-21 (Wed, 21 Jun 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/panels/tool-panel.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/layout/panel.js M client/galaxy/scripts/mvc/grid/grid-view.js A client/galaxy/scripts/mvc/history/history-list.js M client/galaxy/scripts/mvc/history/history-view-edit-current.js M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/user/user-preferences.js M client/galaxy/scripts/mvc/workflow/workflow-configure-menu.js M client/galaxy/scripts/mvc/workflow/workflow.js M client/galaxy/scripts/utils/utils.js M client/galaxy/style/less/base.less M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M static/maps/layout/menu.js.map M static/maps/layout/page.js.map M static/maps/layout/panel.js.map M static/maps/mvc/grid/grid-view.js.map A static/maps/mvc/history/history-list.js.map M static/maps/mvc/history/history-view-edit-current.js.map M static/maps/mvc/history/options-menu.js.map M static/maps/mvc/tool/tool-form-base.js.map M static/maps/mvc/tool/tool-form-composite.js.map M static/maps/mvc/user/user-preferences.js.map M static/maps/mvc/workflow/workflow-configure-menu.js.map M static/maps/mvc/workflow/workflow.js.map M static/maps/utils/utils.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 M static/scripts/layout/page.js M static/scripts/layout/panel.js M static/scripts/mvc/grid/grid-view.js A static/scripts/mvc/history/history-list.js M static/scripts/mvc/history/history-view-edit-current.js M static/scripts/mvc/history/options-menu.js M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/tool/tool-form-composite.js M static/scripts/mvc/user/user-preferences.js M static/scripts/mvc/workflow/workflow-configure-menu.js M static/scripts/mvc/workflow/workflow.js M static/scripts/utils/utils.js M static/style/blue/base.css R templates/webapps/galaxy/history/grid.mako R templates/webapps/galaxy/history/grid_js.mako R templates/webapps/galaxy/workflow/import.mako R templates/webapps/galaxy/workflow/run.mako Log Message: ----------- Merging with dev Commit: 9cec283b5a7209a6d2e461cdb08714e173de4704 https://github.com/galaxyproject/galaxy/commit/9cec283b5a7209a6d2e461cdb087… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-06-22 (Thu, 22 Jun 2017) Changed paths: M config/plugins/webhooks/demo/search/config/searchover.yaml M config/plugins/webhooks/demo/search/static/script.js 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: ----------- make the overlay icon toggleable, change wording Commit: 27e843bfc131ff1c86a916d246961dff3c3ae807 https://github.com/galaxyproject/galaxy/commit/27e843bfc131ff1c86a916d24696… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-06-22 (Thu, 22 Jun 2017) Changed paths: M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/utils/utils.js M config/plugins/webhooks/demo/search/config/searchover.yaml M config/plugins/webhooks/demo/search/static/script.js M static/maps/layout/menu.js.map M static/maps/utils/utils.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/utils/utils.js Log Message: ----------- Merge pull request #4213 from bgruening/improve_search_plugin Improve search plugin Compare: https://github.com/galaxyproject/galaxy/compare/739fb083f080...27e843bfc131

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[galaxyproject/galaxy] 842d14: Upgrade IE to Neo4j:3.1
by GitHub 22 Jun '17

22 Jun '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 842d14a0e6fb9d4226012b91ad104b387bd36988 https://github.com/galaxyproject/galaxy/commit/842d14a0e6fb9d4226012b91ad10… Author: Thoba Lose <lose.thoba(a)gmail.com> Date: 2017-06-13 (Tue, 13 Jun 2017) Changed paths: M config/plugins/interactive_environments/neo/config/allowed_images.yml.sample M config/plugins/interactive_environments/neo/config/neo.ini.sample Log Message: ----------- Upgrade IE to Neo4j:3.1 Commit: 3461b2654045f36c446556858416db3c60175027 https://github.com/galaxyproject/galaxy/commit/3461b2654045f36c446556858416… Author: Thoba Lose <lose.thoba(a)gmail.com> Date: 2017-06-21 (Wed, 21 Jun 2017) Changed paths: M .gitignore M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/panels/tool-panel.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/layout/panel.js M client/galaxy/scripts/mvc/grid/grid-view.js A client/galaxy/scripts/mvc/history/history-list.js M client/galaxy/scripts/mvc/history/history-view-edit-current.js M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/scripts/mvc/user/user-preferences.js M client/galaxy/scripts/mvc/webhooks.js M client/galaxy/scripts/mvc/workflow/workflow-configure-menu.js M client/galaxy/scripts/mvc/workflow/workflow.js M client/galaxy/scripts/onload.js M client/galaxy/scripts/utils/utils.js M client/galaxy/style/less/base.less M config/plugins/webhooks/demo/tool_list/helper/__init__.py A config/plugins/webhooks/demo/tour_generator/config/tour_generator.yml A config/plugins/webhooks/demo/tour_generator/helper/__init__.py A config/plugins/webhooks/demo/tour_generator/static/script.js A config/plugins/webhooks/demo/tour_generator/static/styles.css M cron/updateucsc.sh.sample M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/containers.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_files.py M lib/galaxy/tools/deps/mulled/mulled_build_tool.py M lib/galaxy/webapps/galaxy/api/webhooks.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M scripts/api/library_upload_dir.py M static/maps/layout/menu.js.map M static/maps/layout/page.js.map M static/maps/layout/panel.js.map M static/maps/mvc/grid/grid-view.js.map A static/maps/mvc/history/history-list.js.map M static/maps/mvc/history/history-view-edit-current.js.map M static/maps/mvc/history/options-menu.js.map M static/maps/mvc/tool/tool-form-base.js.map M static/maps/mvc/tool/tool-form-composite.js.map M static/maps/mvc/tool/tool-form.js.map M static/maps/mvc/user/user-preferences.js.map M static/maps/mvc/webhooks.js.map M static/maps/mvc/workflow/workflow-configure-menu.js.map M static/maps/mvc/workflow/workflow.js.map M static/maps/onload.js.map M static/maps/utils/utils.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 M static/scripts/layout/page.js M static/scripts/layout/panel.js M static/scripts/mvc/grid/grid-view.js A static/scripts/mvc/history/history-list.js M static/scripts/mvc/history/history-view-edit-current.js M static/scripts/mvc/history/options-menu.js M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/tool/tool-form-composite.js M static/scripts/mvc/tool/tool-form.js M static/scripts/mvc/user/user-preferences.js M static/scripts/mvc/webhooks.js M static/scripts/mvc/workflow/workflow-configure-menu.js M static/scripts/mvc/workflow/workflow.js M static/scripts/onload.js M static/scripts/utils/utils.js M static/style/blue/base.css M templates/js-app.mako R templates/webapps/galaxy/history/grid.mako R templates/webapps/galaxy/history/grid_js.mako R templates/webapps/galaxy/workflow/import.mako R templates/webapps/galaxy/workflow/run.mako M test/functional/webhooks/phdcomics/helper/__init__.py M test/functional/webhooks/trans_object/helper/__init__.py Log Message: ----------- Merge branch 'dev' of github.com:galaxyproject/galaxy into neo4j-ie Commit: 009f44c25f9c4ebb467f7c6ceb30b605a0fae923 https://github.com/galaxyproject/galaxy/commit/009f44c25f9c4ebb467f7c6ceb30… Author: Thoba Lose <lose.thoba(a)gmail.com> Date: 2017-06-22 (Thu, 22 Jun 2017) Changed paths: M .gitignore M config/plugins/interactive_environments/neo/config/allowed_images.yml.sample Log Message: ----------- using sanbi-sa image. Commit: 739fb083f0801d4dfd85fdff0355df1920ea0b1b https://github.com/galaxyproject/galaxy/commit/739fb083f0801d4dfd85fdff0355… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-06-22 (Thu, 22 Jun 2017) Changed paths: M .gitignore M config/plugins/interactive_environments/neo/config/allowed_images.yml.sample M config/plugins/interactive_environments/neo/config/neo.ini.sample Log Message: ----------- Merge pull request #4216 from thobalose/neo4j-ie Upgrading Neo4j IE to 3.1 Compare: https://github.com/galaxyproject/galaxy/compare/ecdaa04dfd14...739fb083f080

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