- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 009287: Correct name of neo4j datatype class
by GitHub 24 Jun '17

24 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 23 Jun '17

23 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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[galaxyproject/galaxy] 268ee7: Improve resilience of tool url building
by GitHub 22 Jun '17

22 Jun '17

Branch: refs/heads/release_17.05 Home: https://github.com/galaxyproject/galaxy Commit: 268ee7f1b7e65dde514098e0779b80b7589d26b5 https://github.com/galaxyproject/galaxy/commit/268ee7f1b7e65dde514098e0779b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-06-21 (Wed, 21 Jun 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M static/maps/mvc/tool/tool-form-base.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tool-form-base.js Log Message: ----------- Improve resilience of tool url building Commit: 69e76f98fa90782c37a2697de0204e4ff7945f09 https://github.com/galaxyproject/galaxy/commit/69e76f98fa90782c37a2697de020… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-06-21 (Wed, 21 Jun 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M static/maps/mvc/tool/tool-form-base.js.map M static/scripts/mvc/tool/tool-form-base.js Log Message: ----------- Remove redundancy of tool_id parameter Commit: a498390bef74301816945551a9832f38747fd4fc https://github.com/galaxyproject/galaxy/commit/a498390bef74301816945551a983… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-06-21 (Wed, 21 Jun 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.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: ----------- Fix basic version changes for reloaded tools Commit: 9dca211e2fe59eaad1f7b95c8d51608b2afa05af https://github.com/galaxyproject/galaxy/commit/9dca211e2fe59eaad1f7b95c8d51… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-06-22 (Thu, 22 Jun 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M static/maps/mvc/tool/tool-form-base.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tool-form-base.js Log Message: ----------- Merge pull request #4214 from guerler/revise_tool_url [17.05] Improve resilience of tool url building Compare: https://github.com/galaxyproject/galaxy/compare/f7ba7295102c...9dca211e2fe5

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[galaxyproject/usegalaxy-playbook] 8ae4c0: Data rewrites for Bridges on Main
by GitHub 22 Jun '17

22 Jun '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 8ae4c0768d9e012e329cc71bd0d64eadba174a8b https://github.com/galaxyproject/usegalaxy-playbook/commit/8ae4c0768d9e012e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-06-22 (Thu, 22 Jun 2017) Changed paths: A files/galaxy/usegalaxy.org/config/pulsar_bridges_actions.yml M files/galaxy/usegalaxy.org/var/integrated_tool_panel.xml M files/galaxy/usegalaxy.org/var/shed_tool_data_table_conf.xml M production/group_vars/galaxyservers.yml Log Message: ----------- Data rewrites for Bridges on Main

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[galaxyproject/usegalaxy-playbook] c06cee: Run RNA Star on Bridges on Test, configure data pa...
by GitHub 22 Jun '17

22 Jun '17

Branch: refs/heads/reorg Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: c06cee0e218843b77ca86bab23007f16cfaa106a https://github.com/galaxyproject/usegalaxy-playbook/commit/c06cee0e218843b7… 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/bridges_select.py A env/test/files/galaxy/config/pulsar_bridges_actions.yml M env/test/group_vars/galaxyservers/vars.yml M env/test/templates/galaxy/config/job_conf.xml.j2 Log Message: ----------- Run RNA Star on Bridges on Test, configure data path rewrites.

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[galaxyproject/usegalaxy-playbook] 3fbe6d: Run RNA Star on multi partition on TEst
by GitHub 21 Jun '17

21 Jun '17

Branch: refs/heads/reorg Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 3fbe6d1d53f295cbe7b7a877db72d4a4c706ec4c https://github.com/galaxyproject/usegalaxy-playbook/commit/3fbe6d1d53f295cb… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-06-21 (Wed, 21 Jun 2017) Changed paths: M env/test/templates/galaxy/config/job_conf.xml.j2 Log Message: ----------- Run RNA Star on multi partition on TEst

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[galaxyproject/galaxy] 490d73: Fix left/right panel hiding
by GitHub 21 Jun '17

21 Jun '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 490d738ba4efea392297941ceb266fa428ca2323 https://github.com/galaxyproject/galaxy/commit/490d738ba4efea392297941ceb26… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-06-20 (Tue, 20 Jun 2017) Changed paths: M client/galaxy/scripts/layout/page.js M static/maps/layout/page.js.map 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 M static/scripts/layout/page.js Log Message: ----------- Fix left/right panel hiding Commit: ecdaa04dfd14c1497f3db85409b4c0add8c91022 https://github.com/galaxyproject/galaxy/commit/ecdaa04dfd14c1497f3db85409b4… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-06-21 (Wed, 21 Jun 2017) Changed paths: M client/galaxy/scripts/layout/page.js M static/maps/layout/page.js.map 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 M static/scripts/layout/page.js Log Message: ----------- Merge pull request #4210 from guerler/fix_panel_hiding Fix left/right panel hiding Compare: https://github.com/galaxyproject/galaxy/compare/9b9e2aa22742...ecdaa04dfd14

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[galaxyproject/galaxy] a407a9: Removing run mako from workflows
by GitHub 21 Jun '17

21 Jun '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a407a99ae3b8a83879b5f4629c8c07d7cfa3945b https://github.com/galaxyproject/galaxy/commit/a407a99ae3b8a83879b5f4629c8c… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-05-29 (Mon, 29 May 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/panels/tool-panel.js M client/galaxy/scripts/mvc/workflow/workflow.js M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M static/maps/mvc/workflow/workflow.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/workflow/workflow.js R templates/webapps/galaxy/workflow/run.mako Log Message: ----------- Removing run mako from workflows Commit: 094dbe92c3e33d0184cc3691f3d9f66cb7e2b697 https://github.com/galaxyproject/galaxy/commit/094dbe92c3e33d0184cc3691f3d9… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-05-30 (Tue, 30 May 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/mvc/workflow/workflow.js M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M static/maps/mvc/workflow/workflow.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/workflow/workflow.js Log Message: ----------- Adding basic elements for import workflow Commit: 6dba0c74f266483ef0a67d5d8f25f5ced1bbed37 https://github.com/galaxyproject/galaxy/commit/6dba0c74f266483ef0a67d5d8f25… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-05-30 (Tue, 30 May 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js A client/galaxy/scripts/mvc/workflow/workflow-configure-menu.js M client/galaxy/scripts/mvc/workflow/workflow.js M client/galaxy/style/less/base.less M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/drmaa.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/workflow.py A static/maps/mvc/workflow/workflow-configure-menu.js.map M static/maps/mvc/workflow/workflow.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 A static/scripts/mvc/workflow/workflow-configure-menu.js M static/scripts/mvc/workflow/workflow.js M static/style/blue/base.css R templates/webapps/galaxy/workflow/configure_menu.mako Log Message: ----------- Merging with dev Commit: 764933bf3417c734ee2f5554ae122ddca1f3655a https://github.com/galaxyproject/galaxy/commit/764933bf3417c734ee2f5554ae12… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-06-01 (Thu, 01 Jun 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow.js M lib/galaxy/webapps/galaxy/controllers/workflow.py M static/maps/mvc/workflow/workflow.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/workflow/workflow.js Log Message: ----------- Adding import functionality Commit: 62bd742808e5c45a00cb64ac7ef962f936e57351 https://github.com/galaxyproject/galaxy/commit/62bd742808e5c45a00cb64ac7ef9… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-06-01 (Thu, 01 Jun 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow.js M lib/galaxy/webapps/galaxy/controllers/workflow.py M static/maps/mvc/workflow/workflow.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/workflow/workflow.js Log Message: ----------- Moving common functions out of view and adding messages for client actions for importing workflow Commit: 07ea4c04347956fd5e177b052c86a63568aa28a7 https://github.com/galaxyproject/galaxy/commit/07ea4c04347956fd5e177b052c86… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-06-06 (Tue, 06 Jun 2017) Changed paths: M .ci/flake8_lint_include_list.txt M README.rst M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/collection/collection-view.js M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/grid/grid-template.js M client/galaxy/scripts/mvc/grid/grid-view.js M client/galaxy/scripts/mvc/history/hda-li.js M client/galaxy/scripts/mvc/history/hdca-li.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/workflow/workflow.js M client/galaxy/style/less/base.less M client/webpack.config.js M config/job_conf.xml.sample_advanced M contrib/galaxy.debian-init M contrib/galaxy_supervisor.conf M doc/Makefile R doc/patch.py M doc/source/admin/authentication.md M doc/source/admin/special_topics/mulled_containers.rst R doc/source/api/api.rst R doc/source/api/ts_api.rst M doc/source/dev/build_a_job_runner.rst M doc/source/lib/galaxy.actions.rst M doc/source/lib/galaxy.auth.providers.rst M doc/source/lib/galaxy.auth.rst A doc/source/lib/galaxy.containers.rst M doc/source/lib/galaxy.dataset_collections.rst M doc/source/lib/galaxy.dataset_collections.types.rst M doc/source/lib/galaxy.datatypes.converters.rst M doc/source/lib/galaxy.datatypes.dataproviders.rst M doc/source/lib/galaxy.datatypes.display_applications.rst M doc/source/lib/galaxy.datatypes.rst M doc/source/lib/galaxy.datatypes.util.rst M 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static/scripts/mvc/collection/collection-view.js M static/scripts/mvc/dataset/dataset-li.js M static/scripts/mvc/form/form-input.js M static/scripts/mvc/grid/grid-template.js M static/scripts/mvc/grid/grid-view.js M static/scripts/mvc/history/hda-li.js M static/scripts/mvc/history/hdca-li.js M static/scripts/mvc/tool/tool-form-composite.js M static/scripts/mvc/workflow/workflow.js M static/style/blue/base.css M static/welcome.html.sample M templates/grid_base.mako R templates/webapps/galaxy/page/list_published.mako M test/api/test_dataset_collections.py M test/base/populators.py M test/functional/tools/sample_datatypes_conf.xml M test/qunit/test-data/bootstrapped.js M test/qunit/tests/galaxy-app-base.js Log Message: ----------- Resolving conflicts and merging with dev Commit: 207249a4665470288fe77ae9d532e3cb07d4ce32 https://github.com/galaxyproject/galaxy/commit/207249a4665470288fe77ae9d532… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-06-06 (Tue, 06 Jun 2017) Changed paths: 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 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/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/user/user-preferences.js M static/scripts/mvc/workflow/workflow-configure-menu.js M static/scripts/mvc/workflow/workflow.js Log Message: ----------- Moving configure menu call to user preferences Commit: 77327d27b5f526f0b1ddd4375d32e57e83453169 https://github.com/galaxyproject/galaxy/commit/77327d27b5f526f0b1ddd4375d32… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-06-07 (Wed, 07 Jun 2017) Changed paths: R templates/webapps/galaxy/workflow/import.mako Log Message: ----------- Removing import.mako file Commit: 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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: ----------- Merging with dev Commit: 1caf29d7591ff3787de330de58003fd9f0c0b6e1 https://github.com/galaxyproject/galaxy/commit/1caf29d7591ff3787de330de5800… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-06-07 (Wed, 07 Jun 2017) Changed paths: M client/galaxy/scripts/apps/analysis.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: ----------- Removing extra link for custom_builds in analysis.js Commit: 3573f4d59f3d177a0b91b06ce192e1711aaf4a0d https://github.com/galaxyproject/galaxy/commit/3573f4d59f3d177a0b91b06ce192… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-06-07 (Wed, 07 Jun 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow.js M static/maps/mvc/workflow/workflow.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/workflow/workflow.js Log Message: ----------- Removing usused imports in workflow.js Commit: 785e3e557aeee7071905f1aa3d88c1ae1653ec9b https://github.com/galaxyproject/galaxy/commit/785e3e557aeee7071905f1aa3d88… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-06-09 (Fri, 09 Jun 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/panels/tool-panel.js M client/galaxy/scripts/mvc/workflow/workflow.js M client/galaxy/scripts/utils/utils.js M lib/galaxy/webapps/galaxy/controllers/workflow.py M static/maps/mvc/workflow/workflow.js.map M static/maps/utils/utils.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/workflow/workflow.js M static/scripts/utils/utils.js Log Message: ----------- Fixing PR review comments Commit: b52042ef8ebe250a1124071a98f4de486e5dc737 https://github.com/galaxyproject/galaxy/commit/b52042ef8ebe250a1124071a98f4… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-06-09 (Fri, 09 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: ----------- Merging with dev Commit: 5cc46a95c9c9a54ae390496b52c7efc8ac25cf0d https://github.com/galaxyproject/galaxy/commit/5cc46a95c9c9a54ae390496b52c7… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-06-10 (Sat, 10 Jun 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js M lib/galaxy/webapps/galaxy/controllers/workflow.py 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: ----------- Fixing PR review comments Commit: 6d9a911ea9200d3339635c0f4370f18001271f8b https://github.com/galaxyproject/galaxy/commit/6d9a911ea9200d3339635c0f4370… Author: anuprulez 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lib/galaxy/tools/deps/singularity_util.py 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 A test/functional/tools/mulled_example_multi_versionless.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merging with dev Commit: 659c039601a474eba86156a6957dd48560630fa1 https://github.com/galaxyproject/galaxy/commit/659c039601a474eba86156a6957d… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-06-19 (Mon, 19 Jun 2017) Changed paths: M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/layout/panel.js M client/galaxy/scripts/mvc/history/history-view-edit-current.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/style/less/base.less M static/maps/layout/page.js.map M static/maps/layout/panel.js.map M static/maps/mvc/history/history-view-edit-current.js.map M static/maps/mvc/tool/tool-form-base.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/page.js M static/scripts/layout/panel.js M static/scripts/mvc/history/history-view-edit-current.js M static/scripts/mvc/tool/tool-form-base.js M static/style/blue/base.css Log Message: ----------- Revise panel/iframe handling, align naming, rely on empty to trigger removal of previous view Repack Move inline styles, use consistent naming Commit: 2c4c7147e075f036ee703a89eb6de7f39c4e10dd https://github.com/galaxyproject/galaxy/commit/2c4c7147e075f036ee703a89eb6d… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-06-19 (Mon, 19 Jun 2017) 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/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tool-form-composite.js Log Message: ----------- Revise and fix resize handler Commit: 21312138a47cb0c3f958c318500937b11df31d49 https://github.com/galaxyproject/galaxy/commit/21312138a47cb0c3f958c3185009… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-06-19 (Mon, 19 Jun 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M static/maps/mvc/tool/tool-form-base.js.map M static/scripts/bundled/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/tool/tool-form-base.js Log Message: ----------- Fix deferred form destructor Commit: 71498cabfdb9e988e3035915a8be647b88db1ef8 https://github.com/galaxyproject/galaxy/commit/71498cabfdb9e988e3035915a8be… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-06-19 (Mon, 19 Jun 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M static/maps/mvc/tool/tool-form-base.js.map M static/scripts/mvc/tool/tool-form-base.js Log Message: ----------- Fix log statement Commit: d031758d7323c39ed3176c158355f9d697266ef1 https://github.com/galaxyproject/galaxy/commit/d031758d7323c39ed3176c158355… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-06-19 (Mon, 19 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: f4e4c08bab6b8ecf39a69844a904e2fa1c3e4459 https://github.com/galaxyproject/galaxy/commit/f4e4c08bab6b8ecf39a69844a904… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-06-19 (Mon, 19 Jun 2017) Changed paths: M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/layout/panel.js M client/galaxy/scripts/mvc/history/history-view-edit-current.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/style/less/base.less M static/maps/layout/page.js.map M static/maps/layout/panel.js.map M static/maps/mvc/history/history-view-edit-current.js.map M static/maps/mvc/tool/tool-form-base.js.map M static/maps/mvc/tool/tool-form-composite.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/page.js M static/scripts/layout/panel.js M static/scripts/mvc/history/history-view-edit-current.js M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/tool/tool-form-composite.js M static/style/blue/base.css Log Message: ----------- Merge pull request #36 from guerler/fix_cleanup Fixes deferred removal of previous views, augments center panel handling Commit: 837a5c85fcf9c6906843fe413aaf10f27ef21af4 https://github.com/galaxyproject/galaxy/commit/837a5c85fcf9c6906843fe413aaf… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-06-19 (Mon, 19 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: ----------- Merging changes with static files Commit: 8a09836ba79e7f7b08f51a8d7db7c416b03bd44f https://github.com/galaxyproject/galaxy/commit/8a09836ba79e7f7b08f51a8d7db7… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-06-19 (Mon, 19 Jun 2017) Changed paths: M .gitignore M client/galaxy/scripts/layout/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/webhooks.js M client/galaxy/scripts/onload.js 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/config.py 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 scripts/api/library_upload_dir.py M static/maps/layout/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/webhooks.js.map M static/maps/onload.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/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/webhooks.js M static/scripts/onload.js M templates/js-app.mako M test/functional/webhooks/phdcomics/helper/__init__.py M test/functional/webhooks/trans_object/helper/__init__.py Log Message: ----------- Merging with dev Commit: 9b9e2aa2274202c9afe336724c78142408c94a77 https://github.com/galaxyproject/galaxy/commit/9b9e2aa2274202c9afe336724c78… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-06-20 (Tue, 20 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/page.js M client/galaxy/scripts/layout/panel.js M client/galaxy/scripts/mvc/history/history-view-edit-current.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 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static/scripts/bundled/login.bundled.js.map M static/scripts/layout/page.js M static/scripts/layout/panel.js M static/scripts/mvc/history/history-view-edit-current.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/workflow/import.mako R templates/webapps/galaxy/workflow/run.mako Log Message: ----------- Merge remote-tracking branch 'bgruening/convertworkflowmako' into dev Compare: https://github.com/galaxyproject/galaxy/compare/6a0401e08ebc...9b9e2aa22742

1 0

[galaxyproject/galaxy] 325863: Add histories route to analaysis app
by GitHub 20 Jun '17

20 Jun '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 3258635c159acfa3cd4ab33e1484b20b9bced9c1 https://github.com/galaxyproject/galaxy/commit/3258635c159acfa3cd4ab33e1484… 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: ----------- Add histories route to analaysis app Commit: 0fa6f144d013ecac7bcd268f100b07c2c7811ffe https://github.com/galaxyproject/galaxy/commit/0fa6f144d013ecac7bcd268f100b… 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 masthead link Commit: 15206d1dec8547b0ee23a5f8412478f79a6689e0 https://github.com/galaxyproject/galaxy/commit/15206d1dec8547b0ee23a5f84124… 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 route to backend app Commit: 6af0126e60fcffc8afa3d57c8a1d9490822bdfa4 https://github.com/galaxyproject/galaxy/commit/6af0126e60fcffc8afa3d57c8a1d… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-06-07 (Wed, 07 Jun 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Change controller response from mako to json Commit: 658483ba5e50516d3bbef8f22411534a483a1aa6 https://github.com/galaxyproject/galaxy/commit/658483ba5e50516d3bbef8f22411… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-06-07 (Wed, 07 Jun 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/history.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: ----------- Fix refresh handler Commit: 23d086a9894d6ea67bf19ca0f74147f62e76c801 https://github.com/galaxyproject/galaxy/commit/23d086a9894d6ea67bf19ca0f741… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-06-07 (Wed, 07 Jun 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Fix sharing operation Commit: d7d33323952d81352259bc745d749b8583a3cd16 https://github.com/galaxyproject/galaxy/commit/d7d33323952d81352259bc745d74… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-06-07 (Wed, 07 Jun 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Remove custom mako name from definition Commit: 9ed0326b150e71b781994c4d2def42f71fdb48d0 https://github.com/galaxyproject/galaxy/commit/9ed0326b150e71b781994c4d2def… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-06-07 (Wed, 07 Jun 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Fix rename operation Commit: c987e5fa375ce66f383482a7b30c23e71610d2a2 https://github.com/galaxyproject/galaxy/commit/c987e5fa375ce66f383482a7b30c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-06-07 (Wed, 07 Jun 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Revise view operation Commit: 843ed9e6a9d2f7545919b71b057068ffb52f4d01 https://github.com/galaxyproject/galaxy/commit/843ed9e6a9d2f7545919b71b0570… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-06-07 (Wed, 07 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 Commit: 49ae97d3a368d1352f591a8d5a6bde96307af27d https://github.com/galaxyproject/galaxy/commit/49ae97d3a368d1352f591a8d5a6b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-06-07 (Wed, 07 Jun 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Remove uncommented copy statement Commit: 0fb1059bf74bbd4ba7f12cdd0f1104141242290b https://github.com/galaxyproject/galaxy/commit/0fb1059bf74bbd4ba7f12cdd0f11… 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 R templates/webapps/galaxy/history/grid.mako R templates/webapps/galaxy/history/grid_js.mako Log Message: ----------- Insert custom history-list view to accomodate copy dialog hack Commit: 01cab673e7dcca0e7d463e3aa4982e49fa632e27 https://github.com/galaxyproject/galaxy/commit/01cab673e7dcca0e7d463e3aa498… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-06-07 (Wed, 07 Jun 2017) Changed paths: A static/maps/mvc/history/history-list.js.map A static/scripts/mvc/history/history-list.js Log Message: ----------- Add packed files Commit: e3a4bf5d9ed02fe22a6732637511490d0a086f8d https://github.com/galaxyproject/galaxy/commit/e3a4bf5d9ed02fe22a6732637511… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-06-07 (Wed, 07 Jun 2017) Changed paths: A client/galaxy/scripts/mvc/history/history-list.js Log Message: ----------- Add history list module Commit: 84adc659bc67b6b65206ad7f9e9ee10916237f30 https://github.com/galaxyproject/galaxy/commit/84adc659bc67b6b65206ad7f9e9e… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-06-07 (Wed, 07 Jun 2017) Changed paths: M client/galaxy/scripts/mvc/grid/grid-view.js M client/galaxy/scripts/mvc/history/history-list.js M static/maps/mvc/grid/grid-view.js.map M static/maps/mvc/history/history-list.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/grid/grid-view.js M static/scripts/mvc/history/history-list.js Log Message: ----------- Augment grid view event handler to allow custom client side operations Commit: d931df2ca9d107d07af1c97a3d5de326f8ef378b https://github.com/galaxyproject/galaxy/commit/d931df2ca9d107d07af1c97a3d5d… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-06-07 (Wed, 07 Jun 2017) Changed paths: M client/galaxy/scripts/mvc/history/history-list.js M static/maps/mvc/history/history-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/mvc/history/history-list.js Log Message: ----------- Reimplement copy operation Commit: c3305581426fc2b344499079a5f94a65c9f5400a https://github.com/galaxyproject/galaxy/commit/c3305581426fc2b344499079a5f9… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-06-07 (Wed, 07 Jun 2017) Changed paths: M client/galaxy/scripts/mvc/history/options-menu.js M static/maps/mvc/history/options-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.map M static/scripts/mvc/history/options-menu.js Log Message: ----------- Reroute link form history panel to saved grids Commit: 72d038504128a5b8e7ce721375b254b18805c450 https://github.com/galaxyproject/galaxy/commit/72d038504128a5b8e7ce721375b2… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-06-07 (Wed, 07 Jun 2017) Changed paths: M client/galaxy/scripts/mvc/history/options-menu.js M static/maps/mvc/history/options-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.map M static/scripts/mvc/history/options-menu.js Log Message: ----------- Fix target handling Commit: b9461eba40fbc3e8d3129fff94b954f2618c5ddf https://github.com/galaxyproject/galaxy/commit/b9461eba40fbc3e8d3129fff94b9… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-06-13 (Tue, 13 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 config/job_conf.xml.sample_advanced M lib/galaxy/config.py M lib/galaxy/datatypes/data.py A lib/galaxy/datatypes/plant_tribes.py M lib/galaxy/datatypes/text.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/deps/docker_util.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 lib/galaxy/tools/deps/singularity_util.py M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/dataset.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/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 R templates/webapps/galaxy/dataset/grid.mako M templates/webapps/galaxy/page/editor.mako R templates/webapps/galaxy/page/index.mako A test/functional/tools/mulled_example_multi_versionless.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge branch 'dev' into grid_histories Commit: c2ebb5776bc26d62179fbc7ffe07bb7bec4288cf https://github.com/galaxyproject/galaxy/commit/c2ebb5776bc26d62179fbc7ffe07… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-06-14 (Wed, 14 Jun 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js M lib/galaxy/webapps/galaxy/buildapp.py 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: ----------- Use explicit routes Commit: 434d944e5da46cf889b74a6759f3cce88c2f6aa4 https://github.com/galaxyproject/galaxy/commit/434d944e5da46cf889b74a6759f3… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-06-14 (Wed, 14 Jun 2017) Changed paths: M .gitignore M client/galaxy/scripts/layout/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/webhooks.js M client/galaxy/scripts/onload.js 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 static/maps/layout/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/webhooks.js.map M static/maps/onload.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/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/webhooks.js M static/scripts/onload.js M templates/js-app.mako M test/functional/webhooks/phdcomics/helper/__init__.py M test/functional/webhooks/trans_object/helper/__init__.py Log Message: ----------- Merge branch 'dev' into grid_histories Commit: 6a0401e08ebce9797901812c57d7fca69a887c0b https://github.com/galaxyproject/galaxy/commit/6a0401e08ebce9797901812c57d7… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-06-20 (Tue, 20 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/history/history-list.js M client/galaxy/scripts/mvc/history/options-menu.js M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/history.py M static/maps/layout/menu.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/options-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.map M static/scripts/layout/menu.js M static/scripts/mvc/grid/grid-view.js A static/scripts/mvc/history/history-list.js M static/scripts/mvc/history/options-menu.js R templates/webapps/galaxy/history/grid.mako R templates/webapps/galaxy/history/grid_js.mako Log Message: ----------- Merge pull request #4167 from guerler/grid_histories Remove histories grid mako Compare: https://github.com/galaxyproject/galaxy/compare/89851e4c7154...6a0401e08ebc

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[galaxyproject/galaxy] 76c6b6: Fix mulled Docker resolution.
by GitHub 19 Jun '17

19 Jun '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 76c6b6f5bae1fbf7b2b564ecdb46a556590a6daa https://github.com/galaxyproject/galaxy/commit/76c6b6f5bae1fbf7b2b564ecdb46… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-06-19 (Mon, 19 Jun 2017) Changed paths: M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/containers.py Log Message: ----------- Fix mulled Docker resolution. I broke a bunch of Docker stuff when I abstracted it out for Singularity - things like ignoring namespaces because Singularity doesn't use that concept. Also fetching mulled-v2 images from quay.io was broken - I didn't notice this because previously there were no published images mulit-container images. Commit: ea1cf742f0f8e2f6277762c540e0173dbaf45964 https://github.com/galaxyproject/galaxy/commit/ea1cf742f0f8e2f6277762c540e0… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-06-19 (Mon, 19 Jun 2017) Changed paths: M lib/galaxy/tools/deps/mulled/invfile.lua M lib/galaxy/tools/deps/mulled/mulled_build.py Log Message: ----------- Bring in Singularity fixes from galaxy-lib. xref https://github.com/galaxyproject/galaxy-lib/pull/67 Commit: 89851e4c7154b451c02f83e1561a65ded45ae502 https://github.com/galaxyproject/galaxy/commit/89851e4c7154b451c02f83e1561a… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-06-19 (Mon, 19 Jun 2017) Changed paths: 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 Log Message: ----------- Merge pull request #4207 from jmchilton/mulled_container_fixes Various mulled container fixes. Compare: https://github.com/galaxyproject/galaxy/compare/2a5dc90003c6...89851e4c7154

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[galaxyproject/galaxy] b32c1c: Check name export in legacy export section
by GitHub 19 Jun '17

19 Jun '17

Branch: refs/heads/release_17.05 Home: https://github.com/galaxyproject/galaxy Commit: b32c1cf1a3143804b0c4f12f6f7235a87801a74d https://github.com/galaxyproject/galaxy/commit/b32c1cf1a3143804b0c4f12f6f72… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-06-16 (Fri, 16 Jun 2017) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Check name export in legacy export section Commit: f7ba7295102c9ce9969c634ee89e26f02c2801ea https://github.com/galaxyproject/galaxy/commit/f7ba7295102c9ce9969c634ee89e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-06-19 (Mon, 19 Jun 2017) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Merge pull request #4203 from guerler/fix_name_export [17.05] Check name type in legacy export section Compare: https://github.com/galaxyproject/galaxy/compare/d39b955e8a5d...f7ba7295102c

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[galaxyproject/infrastructure-playbook] 8c4b4f: Add singularity user to orval
by GitHub 19 Jun '17

19 Jun '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 8c4b4fe9ae5908dc02e0da65d523f55d3e345140 https://github.com/galaxyproject/infrastructure-playbook/commit/8c4b4fe9ae5… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-06-19 (Mon, 19 Jun 2017) Changed paths: M galaxyenv/host_vars/orval.galaxyproject.org.yml M galaxyenv/secret_group_vars/all.yml M galaxyenv/secret_host_vars/orval.galaxyproject.org.yml Log Message: ----------- Add singularity user to orval

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[galaxyproject/usegalaxy-playbook] 5b00fa: Fixes for Data Managers, plus allocate 128GB of me...
by GitHub 16 Jun '17

16 Jun '17

Branch: refs/heads/reorg Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 5b00fa5d5c55915aaac7f440b1f074216be6a148 https://github.com/galaxyproject/usegalaxy-playbook/commit/5b00fa5d5c55915a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-06-16 (Fri, 16 Jun 2017) Changed paths: M env/common/templates/supervisor/galaxy_datamanager.j2 M env/test/files/galaxy/var/integrated_tool_panel.xml M env/test/files/galaxy/var/shed_data_manager_conf.xml M env/test/files/galaxy/var/shed_tool_conf.xml M env/test/files/galaxy/var/shed_tool_data_table_conf.xml M env/test/group_vars/galaxyservers/vars.yml M env/test/templates/galaxy/config/job_conf.xml.j2 Log Message: ----------- Fixes for Data Managers, plus allocate 128GB of memory for the RNA STAR DM

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[galaxyproject/galaxy] 3384e1: correction of a typo leading to incomplete format ...
by GitHub 16 Jun '17

16 Jun '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 3384e13744981a25f34433e80b3093cf3b495018 https://github.com/galaxyproject/galaxy/commit/3384e13744981a25f34433e80b30… Author: Frederic Sapet <frederic.sapet(a)biogemma.com> Date: 2017-06-16 (Fri, 16 Jun 2017) Changed paths: M scripts/api/library_upload_dir.py Log Message: ----------- correction of a typo leading to incomplete format string Commit: 2a5dc90003c6c787e2008140fa6b92cab387362c https://github.com/galaxyproject/galaxy/commit/2a5dc90003c6c787e2008140fa6b… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-06-16 (Fri, 16 Jun 2017) Changed paths: M scripts/api/library_upload_dir.py Log Message: ----------- Merge pull request #4199 from FredericBGA/library_upload_dir Debug of script library_upload_dir.py Compare: https://github.com/galaxyproject/galaxy/compare/95a879c5e782...2a5dc90003c6

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[galaxyproject/usegalaxy-playbook] 1a3bfc: I forget why these variable names have changed but...
by GitHub 15 Jun '17

15 Jun '17

Branch: refs/heads/reorg Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 1a3bfcec003a4827b75c28cc02a233fe65d952a1 https://github.com/galaxyproject/usegalaxy-playbook/commit/1a3bfcec003a4827… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-06-15 (Thu, 15 Jun 2017) Changed paths: M env/test/group_vars/galaxyservers/vars.yml Log Message: ----------- I forget why these variable names have changed but apparently I didn't finish changing them

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[galaxyproject/usegalaxy-playbook] 8f9080: Disable conda copying for per-job envs since all e...
by GitHub 15 Jun '17

15 Jun '17

Branch: refs/heads/reorg Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 8f9080fbb5039af509b30a28a13c9af42f9054e8 https://github.com/galaxyproject/usegalaxy-playbook/commit/8f9080fbb5039af5… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-06-15 (Thu, 15 Jun 2017) Changed paths: M env/test/group_vars/galaxyservers/vars.yml Log Message: ----------- Disable conda copying for per-job envs since all envs are now mulled. always_symlink has also been enabled in _condarc

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[galaxyproject/galaxy] ebfdb5: Lint updateucsc.sh.sample
by GitHub 14 Jun '17

14 Jun '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ebfdb598f63bd06925670e7c1764e1d1da740d05 https://github.com/galaxyproject/galaxy/commit/ebfdb598f63bd06925670e7c1764… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-06-14 (Wed, 14 Jun 2017) Changed paths: M cron/updateucsc.sh.sample Log Message: ----------- Lint updateucsc.sh.sample Commit: 404b855dd278760c625a6515279da6908ab9f9c6 https://github.com/galaxyproject/galaxy/commit/404b855dd278760c625a6515279d… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-06-14 (Wed, 14 Jun 2017) Changed paths: M cron/updateucsc.sh.sample Log Message: ----------- Make updateucsc.sh.sample usable without any change Commit: 95a879c5e78283228c335e7c6d6e8e97916f1db1 https://github.com/galaxyproject/galaxy/commit/95a879c5e78283228c335e7c6d6e… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-06-14 (Wed, 14 Jun 2017) Changed paths: M cron/updateucsc.sh.sample Log Message: ----------- Merge pull request #4192 from nsoranzo/updateucsc.sh Make updateucsc.sh.sample usable without any change Compare: https://github.com/galaxyproject/galaxy/compare/579b8b025cc5...95a879c5e782

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[galaxyproject/galaxy] 5a83e5: upload tool's test data into the History panel
by GitHub 14 Jun '17

14 Jun '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 5a83e56168369a3fccde6aae34015ffc21721188 https://github.com/galaxyproject/galaxy/commit/5a83e56168369a3fccde6aae3401… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2017-03-05 (Sun, 05 Mar 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/scripts/mvc/webhooks.js M client/galaxy/scripts/onload.js M client/galaxy/scripts/utils/uploadbox.js M config/plugins/visualizations/charts/static/repository/utilities/jobs.js M config/plugins/webhooks/demo/phdcomics/helper/__init__.py M config/plugins/webhooks/demo/trans_object/helper/__init__.py A config/plugins/webhooks/tour_generator/config/tour_generator.yml A config/plugins/webhooks/tour_generator/helper/__init__.py A config/plugins/webhooks/tour_generator/static/script.js A config/plugins/webhooks/tour_generator/static/styles.css M lib/galaxy/webapps/galaxy/api/webhooks.py M lib/galaxy/webapps/galaxy/buildapp.py M static/maps/mvc/tool/tool-form-base.js.map M static/maps/mvc/tool/tool-form.js.map M static/maps/mvc/webhooks.js.map M static/maps/onload.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/tool/tool-form.js M static/scripts/mvc/webhooks.js M static/scripts/onload.js Log Message: ----------- upload tool's test data into the History panel Commit: 4fdb554629e10e4fd20a99806c9b2e8e883cb844 https://github.com/galaxyproject/galaxy/commit/4fdb554629e10e4fd20a99806c9b… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2017-04-05 (Wed, 05 Apr 2017) Changed paths: M .gitignore M config/galaxy.ini.sample 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 R config/plugins/webhooks/tour_generator/config/tour_generator.yml R config/plugins/webhooks/tour_generator/helper/__init__.py R config/plugins/webhooks/tour_generator/static/script.js R config/plugins/webhooks/tour_generator/static/styles.css Log Message: ----------- generate tool tours Commit: bef2e2fc00030dbcdf32acc3dcfe30175db80506 https://github.com/galaxyproject/galaxy/commit/bef2e2fc00030dbcdf32acc3dcfe… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2017-04-07 (Fri, 07 Apr 2017) Changed paths: M config/plugins/webhooks/demo/tour_generator/helper/__init__.py M config/plugins/webhooks/demo/tour_generator/static/script.js Log Message: ----------- deal with different input types + bugfixes Commit: c7f3de9713c07ba51f61f7a2761e1a685b68d4eb https://github.com/galaxyproject/galaxy/commit/c7f3de9713c07ba51f61f7a2761e… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2017-04-08 (Sat, 08 Apr 2017) Changed paths: M client/galaxy/scripts/onload.js M config/plugins/webhooks/demo/tour_generator/helper/__init__.py M config/plugins/webhooks/demo/tour_generator/static/script.js M static/maps/onload.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/onload.js Log Message: ----------- improve frontend script + bugfixes Commit: 73e90fc7f53fff6c9fdf901b9b06a66a801f0c6c https://github.com/galaxyproject/galaxy/commit/73e90fc7f53fff6c9fdf901b9b06… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2017-04-08 (Sat, 08 Apr 2017) Changed paths: M .ci/flake8_blacklist.txt M .ci/flake8_lint_include_list.txt M .ci/jenkins/selenium/run_galaxy.bash M .ci/jenkins/selenium/run_tests.sh M .ci/py3_sources.txt M CONTRIBUTING.md M 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tool-data/shared/ucsc/ucsc_build_sites.txt.sample M tools/data_source/upload.py M tools/evolution/add_scores.xml M tools/extract/extract_genomic_dna.xml M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_feature_count.py R tools/filters/gff/sort_gtf.py M tools/filters/pasteWrapper.xml M tools/filters/trimmer.py M tools/filters/trimmer.xml M tools/maf/genebed_maf_to_fasta.xml M tools/maf/interval2maf.xml M tools/maf/interval2maf_pairwise.xml M tools/maf/interval_maf_to_merged_fasta.xml M tools/maf/macros.xml M tools/maf/maf_by_block_number.xml M tools/maf/maf_filter.xml M tools/maf/maf_limit_size.xml M tools/maf/maf_limit_to_species.xml M tools/maf/maf_reverse_complement.xml M tools/maf/maf_split_by_species.xml M tools/maf/maf_stats.xml M tools/maf/maf_thread_for_species.xml M tools/maf/maf_to_bed.xml M tools/maf/maf_to_fasta.xml M tools/maf/maf_to_interval.xml M tools/maf/vcf_to_maf_customtrack.xml M tools/metag_tools/shrimp_color_wrapper.xml M tools/metag_tools/shrimp_wrapper.xml M tools/next_gen_conversion/fastq_gen_conv.xml M tools/plotting/bar_chart.xml M tools/stats/aggregate_binned_scores_in_intervals.xml M tox.ini Log Message: ----------- Merge branch 'dev' into auto_tour_generation # Conflicts: # static/maps/mvc/tool/tool-form-base.js.map # static/maps/mvc/tool/tool-form.js.map # static/scripts/bundled/analysis.bundled.js # static/scripts/bundled/analysis.bundled.js.map # static/scripts/bundled/libs.bundled.js # static/scripts/bundled/libs.bundled.js.map # static/scripts/bundled/login.bundled.js # static/scripts/bundled/login.bundled.js.map # static/scripts/mvc/tool/tool-form-base.js # static/scripts/mvc/tool/tool-form.js Commit: a3037742cf0a6521651dad63b5c9c466d0031da4 https://github.com/galaxyproject/galaxy/commit/a3037742cf0a6521651dad63b5c9… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2017-04-08 (Sat, 08 Apr 2017) Changed paths: M config/plugins/webhooks/demo/tool_list/helper/__init__.py M config/plugins/webhooks/demo/tour_generator/static/script.js M static/maps/mvc/tool/tool-form-base.js.map M static/maps/mvc/tool/tool-form.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/tool/tool-form.js Log Message: ----------- bugfixes after the previous merge Commit: ebcb2627dfa920d0b491191a961374fb3d091248 https://github.com/galaxyproject/galaxy/commit/ebcb2627dfa920d0b491191a9613… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2017-04-08 (Sat, 08 Apr 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/webhooks.js M static/maps/mvc/tool/tool-form-composite.js.map M static/maps/mvc/webhooks.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tool-form-composite.js M static/scripts/mvc/webhooks.js Log Message: ----------- tiny changes Commit: ebf1f3903caeeae7e712666228c34958cbfc4094 https://github.com/galaxyproject/galaxy/commit/ebf1f3903caeeae7e712666228c3… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2017-04-08 (Sat, 08 Apr 2017) Changed paths: M config/plugins/webhooks/demo/tour_generator/static/script.js M lib/galaxy/webapps/galaxy/api/webhooks.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- bugfixes and small improvements Commit: 934a26c195a983f64889bac6e25498ec16328e53 https://github.com/galaxyproject/galaxy/commit/934a26c195a983f64889bac6e254… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2017-04-20 (Thu, 20 Apr 2017) Changed paths: M client/galaxy/scripts/onload.js M config/plugins/webhooks/demo/tour_generator/helper/__init__.py M config/plugins/webhooks/demo/tour_generator/static/script.js M static/maps/onload.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map M static/scripts/onload.js Log Message: ----------- improve the generator + bugfixes Commit: dc29a1a637c0274bceeb817ab64638a17464db6b https://github.com/galaxyproject/galaxy/commit/dc29a1a637c0274bceeb817ab646… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2017-04-20 (Thu, 20 Apr 2017) Changed paths: M config/plugins/webhooks/demo/tour_generator/helper/__init__.py M config/plugins/webhooks/demo/tour_generator/static/script.js Log Message: ----------- add support for the 'conditional' input type Commit: 68ab3cfcac72cb759fc7941624d5a8e6a9ddb23e https://github.com/galaxyproject/galaxy/commit/68ab3cfcac72cb759fc7941624d5… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2017-04-25 (Tue, 25 Apr 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/scripts/mvc/webhooks.js M client/galaxy/scripts/onload.js M client/galaxy/scripts/utils/uploadbox.js M config/plugins/visualizations/charts/static/repository/utilities/jobs.js A config/plugins/webhooks/tour_generator/config/tour_generator.yml A config/plugins/webhooks/tour_generator/helper/__init__.py A config/plugins/webhooks/tour_generator/static/script.js A config/plugins/webhooks/tour_generator/static/styles.css M lib/galaxy/webapps/galaxy/api/webhooks.py M lib/galaxy/webapps/galaxy/buildapp.py M static/maps/mvc/webhooks.js.map M static/maps/onload.js.map M static/scripts/mvc/webhooks.js M static/scripts/onload.js M test/functional/webhooks/phdcomics/helper/__init__.py M test/functional/webhooks/trans_object/helper/__init__.py Log Message: ----------- upload tool's test data into the History panel Commit: bb2c467c379a2780578e44551d9a447259256437 https://github.com/galaxyproject/galaxy/commit/bb2c467c379a2780578e44551d9a… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2017-04-25 (Tue, 25 Apr 2017) Changed paths: M .gitignore 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 R config/plugins/webhooks/tour_generator/config/tour_generator.yml R config/plugins/webhooks/tour_generator/helper/__init__.py R config/plugins/webhooks/tour_generator/static/script.js R config/plugins/webhooks/tour_generator/static/styles.css Log Message: ----------- generate tool tours Commit: e9accf5459d0a311cec590dcdeb4f07533d3a9aa https://github.com/galaxyproject/galaxy/commit/e9accf5459d0a311cec590dcdeb4… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2017-04-25 (Tue, 25 Apr 2017) Changed paths: M config/plugins/webhooks/demo/tour_generator/helper/__init__.py M config/plugins/webhooks/demo/tour_generator/static/script.js Log Message: ----------- deal with different input types + bugfixes Commit: 5227e7b632ef3add1f8f0289c4caf6e926e53de6 https://github.com/galaxyproject/galaxy/commit/5227e7b632ef3add1f8f0289c4ca… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2017-04-25 (Tue, 25 Apr 2017) Changed paths: M client/galaxy/scripts/onload.js M config/plugins/webhooks/demo/tour_generator/helper/__init__.py M config/plugins/webhooks/demo/tour_generator/static/script.js M static/maps/onload.js.map M static/scripts/onload.js Log Message: ----------- improve frontend script + bugfixes Commit: 31277edc6109aa97ab34ce6d851ade314b340dfa https://github.com/galaxyproject/galaxy/commit/31277edc6109aa97ab34ce6d851a… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2017-04-25 (Tue, 25 Apr 2017) Changed paths: M config/plugins/webhooks/demo/tool_list/helper/__init__.py M config/plugins/webhooks/demo/tour_generator/static/script.js M static/maps/mvc/tool/tool-form-base.js.map M static/maps/mvc/tool/tool-form.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/tool/tool-form.js Log Message: ----------- bugfixes after the previous merge Commit: e1f7875351c826bf503d00d6a43f3c415c601858 https://github.com/galaxyproject/galaxy/commit/e1f7875351c826bf503d00d6a43f… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2017-04-25 (Tue, 25 Apr 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/webhooks.js M static/maps/mvc/tool/tool-form-composite.js.map M static/maps/mvc/webhooks.js.map M static/scripts/mvc/tool/tool-form-composite.js M static/scripts/mvc/webhooks.js Log Message: ----------- tiny changes Commit: d6109ee1e81cb7b744309fca7cb7c0ef57ba6eb2 https://github.com/galaxyproject/galaxy/commit/d6109ee1e81cb7b744309fca7cb7… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2017-04-25 (Tue, 25 Apr 2017) Changed paths: M config/plugins/webhooks/demo/tour_generator/static/script.js M lib/galaxy/webapps/galaxy/api/webhooks.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- bugfixes and small improvements Commit: e64cff4647ec2806b9b548274c363b7d022b6730 https://github.com/galaxyproject/galaxy/commit/e64cff4647ec2806b9b548274c36… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2017-04-25 (Tue, 25 Apr 2017) Changed paths: M client/galaxy/scripts/onload.js M config/plugins/webhooks/demo/tour_generator/helper/__init__.py M config/plugins/webhooks/demo/tour_generator/static/script.js M static/maps/onload.js.map M static/scripts/bundled/login.bundled.js.map M static/scripts/onload.js Log Message: ----------- improve the generator + bugfixes Commit: d253d7aa468bc9fe5d48ecea3be74059b9252300 https://github.com/galaxyproject/galaxy/commit/d253d7aa468bc9fe5d48ecea3be7… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2017-04-25 (Tue, 25 Apr 2017) Changed paths: M config/plugins/webhooks/demo/tour_generator/helper/__init__.py M config/plugins/webhooks/demo/tour_generator/static/script.js Log Message: ----------- add support for the 'conditional' input type Commit: 65a31e0e5dd7efd7c69a434100ff7d93eabee91c https://github.com/galaxyproject/galaxy/commit/65a31e0e5dd7efd7c69a434100ff… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2017-04-25 (Tue, 25 Apr 2017) Changed paths: M config/plugins/webhooks/demo/tour_generator/helper/__init__.py M config/plugins/webhooks/demo/tour_generator/static/script.js M lib/galaxy/webapps/galaxy/api/webhooks.py Log Message: ----------- improve conditional input type message Commit: 17bb071721b83d63b3edf49ab1c509e4efb781ff https://github.com/galaxyproject/galaxy/commit/17bb071721b83d63b3edf49ab1c5… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2017-04-25 (Tue, 25 Apr 2017) Changed paths: M client/galaxy/scripts/onload.js M config/plugins/webhooks/demo/tour_generator/helper/__init__.py M config/plugins/webhooks/demo/tour_generator/static/script.js M static/maps/onload.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/onload.js Log Message: ----------- improve and simplify the main script Commit: 19567f48b846219a48eceb8d1a58cd29a659d5ba https://github.com/galaxyproject/galaxy/commit/19567f48b846219a48eceb8d1a58… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2017-04-25 (Tue, 25 Apr 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/webhooks.py M static/scripts/bundled/login.bundled.js Log Message: ----------- make client Commit: 64e91ddb8f0baf7a63c015bb7438fe19bd40bc7d https://github.com/galaxyproject/galaxy/commit/64e91ddb8f0baf7a63c015bb7438… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2017-04-25 (Tue, 25 Apr 2017) Changed paths: 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 Log Message: ----------- make client Commit: ed4fa0425efc9b719e923f6d0959e8098fd9b8e7 https://github.com/galaxyproject/galaxy/commit/ed4fa0425efc9b719e923f6d0959… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2017-04-26 (Wed, 26 Apr 2017) Changed paths: M config/plugins/webhooks/demo/tour_generator/static/script.js Log Message: ----------- fix a bug when a tour coudn't be ended after executing a tool Commit: 47a5f17089b696208cb5f432ade866c1d953601d https://github.com/galaxyproject/galaxy/commit/47a5f17089b696208cb5f432ade8… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2017-04-26 (Wed, 26 Apr 2017) Changed paths: M config/plugins/webhooks/demo/tour_generator/helper/__init__.py M config/plugins/webhooks/demo/tour_generator/static/script.js Log Message: ----------- many improvements - show warning messages (not errors) - upload test datasets with a correct type according to the tool's .xml file (no 'auto' detection) - add more checks to improve the overall stability - fix tour messages - other bugfixes Commit: 542e396ddf48a8d9159ee0aa1e5137f307a6b8f4 https://github.com/galaxyproject/galaxy/commit/542e396ddf48a8d9159ee0aa1e51… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2017-04-26 (Wed, 26 Apr 2017) Changed paths: M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/onload.js M config/plugins/webhooks/demo/tour_generator/config/tour_generator.yml M static/maps/layout/menu.js.map M static/maps/mvc/tool/tool-form-base.js.map M static/maps/onload.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/menu.js M static/scripts/mvc/tool/tool-form-base.js M static/scripts/onload.js Log Message: ----------- introduce two new entry points: onload and tool-menu Commit: ce017c3fec9f1edd0d7858f408302b6962073657 https://github.com/galaxyproject/galaxy/commit/ce017c3fec9f1edd0d7858f40830… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2017-05-01 (Mon, 01 May 2017) Changed paths: M config/plugins/webhooks/demo/tour_generator/helper/__init__.py M config/plugins/webhooks/demo/tour_generator/static/script.js Log Message: ----------- upload conditional test datasets Commit: c42941da04c94acec13598c8d6f8425c938ad548 https://github.com/galaxyproject/galaxy/commit/c42941da04c94acec13598c8d6f8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-05-05 (Fri, 05 May 2017) Changed paths: M client/galaxy/scripts/onload.js M config/plugins/webhooks/demo/tour_generator/config/tour_generator.yml M config/plugins/webhooks/demo/tour_generator/static/script.js M static/maps/onload.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map M static/scripts/onload.js M templates/js-app.mako Log Message: ----------- Remove global Toastr addition, allow external requires through standard js-app entrypoint. Commit: d90a30f5eaf57eb0e3a1ba370406f393a066f96d https://github.com/galaxyproject/galaxy/commit/d90a30f5eaf57eb0e3a1ba370406… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-05-05 (Fri, 05 May 2017) Changed paths: M client/galaxy/scripts/onload.js M config/plugins/webhooks/demo/tour_generator/config/tour_generator.yml M config/plugins/webhooks/demo/tour_generator/static/script.js M static/maps/onload.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map M static/scripts/onload.js M templates/js-app.mako Log Message: ----------- Merge pull request #4 from dannon/auto_tour_generation Toastr Loading fixes. Commit: ef0809c2eb95fb9bd740718a287d6548ceea0f3a https://github.com/galaxyproject/galaxy/commit/ef0809c2eb95fb9bd740718a287d… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-05-05 (Fri, 05 May 2017) Changed paths: M client/galaxy/scripts/utils/uploadbox.js M config/plugins/visualizations/charts/static/repository/utilities/jobs.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 Log Message: ----------- remove unnecessary whitespace fixes from otherwise untouched files Commit: 96d03c7c35eacb1d0e4bbf8675c51b3b429e53a1 https://github.com/galaxyproject/galaxy/commit/96d03c7c35eacb1d0e4bbf8675c5… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2017-05-18 (Thu, 18 May 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/webhooks.js M config/plugins/webhooks/demo/tour_generator/config/tour_generator.yml M config/plugins/webhooks/demo/tour_generator/helper/__init__.py M config/plugins/webhooks/demo/tour_generator/static/script.js M static/maps/mvc/tool/tool-form-composite.js.map M static/maps/mvc/webhooks.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/tool/tool-form-composite.js M static/scripts/mvc/webhooks.js Log Message: ----------- pass tool version along with the id Commit: a8251fe656b3d7e1dabe98ad3fd2eff2cd2898d5 https://github.com/galaxyproject/galaxy/commit/a8251fe656b3d7e1dabe98ad3fd2… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-06-13 (Tue, 13 Jun 2017) Changed paths: M .gitignore Log Message: ----------- Remove .idea and .vscode from .gitignore (these are editor specific files that contributors can add to their personal global .gitignores) Commit: d77962213872244daecc39ea6f9a1d130cce474b https://github.com/galaxyproject/galaxy/commit/d77962213872244daecc39ea6f9a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-06-14 (Wed, 14 Jun 2017) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/flake8_wrapper_docstrings.sh M .ci/jenkins/selenium/run_tests.sh M .gitignore M .travis.yml M CITATION M CONTRIBUTORS.md M Makefile M README.rst A client/galaxy/scripts/admin.toolshed.js A client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/analysis.js R client/galaxy/scripts/apps/history-panel.js M client/galaxy/scripts/apps/login.js A client/galaxy/scripts/apps/panels/admin-panel.js A client/galaxy/scripts/apps/panels/history-panel.js A client/galaxy/scripts/apps/panels/tool-panel.js R client/galaxy/scripts/apps/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 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Commit: 26f214257337c4546b9783bda8df9ac7e15b4444 https://github.com/galaxyproject/galaxy/commit/26f214257337c4546b9783bda8df… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-06-14 (Wed, 14 Jun 2017) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/flake8_wrapper_docstrings.sh M .ci/jenkins/selenium/run_tests.sh M .gitignore M .travis.yml M CITATION M CONTRIBUTORS.md M Makefile M README.rst A client/galaxy/scripts/admin.toolshed.js A client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/analysis.js R client/galaxy/scripts/apps/history-panel.js M client/galaxy/scripts/apps/login.js A client/galaxy/scripts/apps/panels/admin-panel.js A client/galaxy/scripts/apps/panels/history-panel.js A client/galaxy/scripts/apps/panels/tool-panel.js R client/galaxy/scripts/apps/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/citation/citation-view.js M 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test/selenium_tests/framework.py M test/selenium_tests/test_history_sharing.py M test/selenium_tests/test_login.py M test/selenium_tests/test_registration.py M test/selenium_tests/test_tool_form.py M test/selenium_tests/test_workflow_management.py M test/selenium_tests/test_workflow_run.py A test/unit/jobs/conditional_runners_job_conf.xml M test/unit/jobs/test_job_configuration.py M test/unit/tools/test_toolbox.py M tools/data_source/upload.py M tox.ini Log Message: ----------- Merge pull request #5 from dannon/auto_tour_generation Fixes .gitignore, merges dev. Commit: 579b8b025cc5242f1e32563cfb78ac3c354703d6 https://github.com/galaxyproject/galaxy/commit/579b8b025cc5242f1e32563cfb78… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-06-14 (Wed, 14 Jun 2017) Changed paths: M .gitignore M client/galaxy/scripts/layout/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/webhooks.js M client/galaxy/scripts/onload.js 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 lib/galaxy/webapps/galaxy/api/webhooks.py M static/maps/layout/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/webhooks.js.map M static/maps/onload.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/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/webhooks.js M static/scripts/onload.js M templates/js-app.mako M test/functional/webhooks/phdcomics/helper/__init__.py M test/functional/webhooks/trans_object/helper/__init__.py Log Message: ----------- Merge pull request #4019 from anatskiy/auto_tour_generation Tool-Describing-Tours Compare: https://github.com/galaxyproject/galaxy/compare/f58f372a26c4...579b8b025cc5

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[galaxyproject/galaxy] f7f28d: Build mulled images for Singularity on demand...
by GitHub 14 Jun '17

14 Jun '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f7f28d606a17bc4020678d498895b3acdb955a9b https://github.com/galaxyproject/galaxy/commit/f7f28d606a17bc4020678d498895… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-06-14 (Wed, 14 Jun 2017) Changed paths: 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 Log Message: ----------- Build mulled images for Singularity on demand... ... if a cached container for the tool in question cannot be found. This mirrors behavior for Docker and can be disabled by setting up a custom containers resolution file. This should also enable easy testing of tools with Planemo using Singularity. Commit: f58f372a26c43f1ef55e8193a324769285ba728a https://github.com/galaxyproject/galaxy/commit/f58f372a26c43f1ef55e8193a324… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-06-14 (Wed, 14 Jun 2017) Changed paths: 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 Log Message: ----------- Merge pull request #4185 from jmchilton/singularity_mulled_build Build mulled images for Singularity on demand... Compare: https://github.com/galaxyproject/galaxy/compare/3e36af050ff1...f58f372a26c4

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