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[galaxyproject/galaxy] 1c82d0: adds Aequatus visualisation plugin
by GitHub 21 Dec '18

21 Dec '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1c82d08ab5c216ad568ec1d51d3398ffb0214c18 https://github.com/galaxyproject/galaxy/commit/1c82d08ab5c216ad568ec1d51d33… Author: anilthanki <thanki.anil(a)gmail.com> Date: 2018-12-20 (Thu, 20 Dec 2018) Changed paths: A config/plugins/visualizations/aequatus/README.md A config/plugins/visualizations/aequatus/config/aequatus.xml A config/plugins/visualizations/aequatus/static/aequatus-vis/LICENSE A config/plugins/visualizations/aequatus/static/aequatus-vis/README.md A config/plugins/visualizations/aequatus/static/aequatus-vis/_config.yml A config/plugins/visualizations/aequatus/static/aequatus-vis/scripts/cigarUtils.js A config/plugins/visualizations/aequatus/static/aequatus-vis/scripts/d3_tree.js A config/plugins/visualizations/aequatus/static/aequatus-vis/scripts/drawCIGARs.js A config/plugins/visualizations/aequatus/static/aequatus-vis/scripts/drawGene.js A config/plugins/visualizations/aequatus/static/aequatus-vis/scripts/drawGeneExonOnly.js A config/plugins/visualizations/aequatus/static/aequatus-vis/scripts/geneView.js A config/plugins/visualizations/aequatus/static/aequatus-vis/scripts/init.js A config/plugins/visualizations/aequatus/static/aequatus-vis/scripts/jquery/jquery-ui-1.12.1.min.css A config/plugins/visualizations/aequatus/static/aequatus-vis/scripts/jquery/jquery.svg.css A config/plugins/visualizations/aequatus/static/aequatus-vis/scripts/jquery/js/jquery-3.3.1.min.js A config/plugins/visualizations/aequatus/static/aequatus-vis/scripts/jquery/js/jquery-migrate-1.4.1.min.js A config/plugins/visualizations/aequatus/static/aequatus-vis/scripts/jquery/js/jquery-ui-1.12.1.min.js A config/plugins/visualizations/aequatus/static/aequatus-vis/scripts/jquery/js/jquery.cookie.js A config/plugins/visualizations/aequatus/static/aequatus-vis/scripts/jquery/js/jquery.svg.js A config/plugins/visualizations/aequatus/static/aequatus-vis/scripts/newick.js A config/plugins/visualizations/aequatus/static/aequatus-vis/scripts/scriptaculous/prototype.js A config/plugins/visualizations/aequatus/static/aequatus-vis/scripts/util.js A config/plugins/visualizations/aequatus/static/aequatus-vis/styles/font-awesome-5.6.1/css/fontawesome.min.css A config/plugins/visualizations/aequatus/static/aequatus-vis/styles/font-awesome-5.6.1/css/solid.min.css A config/plugins/visualizations/aequatus/static/aequatus-vis/styles/font-awesome-5.6.1/webfonts/FontAwesome.otf A config/plugins/visualizations/aequatus/static/aequatus-vis/styles/font-awesome-5.6.1/webfonts/fa-solid-900.eot A config/plugins/visualizations/aequatus/static/aequatus-vis/styles/font-awesome-5.6.1/webfonts/fa-solid-900.svg A config/plugins/visualizations/aequatus/static/aequatus-vis/styles/font-awesome-5.6.1/webfonts/fa-solid-900.ttf A config/plugins/visualizations/aequatus/static/aequatus-vis/styles/font-awesome-5.6.1/webfonts/fa-solid-900.woff A config/plugins/visualizations/aequatus/static/aequatus-vis/styles/font-awesome-5.6.1/webfonts/fa-solid-900.woff2 A config/plugins/visualizations/aequatus/static/aequatus-vis/styles/font-awesome-5.6.1/webfonts/fontawesome-webfont.eot A config/plugins/visualizations/aequatus/static/aequatus-vis/styles/font-awesome-5.6.1/webfonts/fontawesome-webfont.svg A config/plugins/visualizations/aequatus/static/aequatus-vis/styles/font-awesome-5.6.1/webfonts/fontawesome-webfont.ttf A config/plugins/visualizations/aequatus/static/aequatus-vis/styles/font-awesome-5.6.1/webfonts/fontawesome-webfont.woff A config/plugins/visualizations/aequatus/static/aequatus-vis/styles/style.css A config/plugins/visualizations/aequatus/static/scripts/controls.js A config/plugins/visualizations/aequatus/static/scripts/popup.js A config/plugins/visualizations/aequatus/static/scripts/readSQLite.js A config/plugins/visualizations/aequatus/static/scripts/sql.js A config/plugins/visualizations/aequatus/static/scripts/worker.js A config/plugins/visualizations/aequatus/static/scripts/worker.sql.js A config/plugins/visualizations/aequatus/static/styles/aequatus.css A config/plugins/visualizations/aequatus/templates/aequatus.mako M lib/galaxy/datatypes/binary.py Log Message: ----------- adds Aequatus visualisation plugin updates Aequatus control panel-settings font size Update README.md fix path to aequatus static scripts updates with upstream removes console removes installation guide removes demo removes duplicates removes d3.js removes bootstrap prunes font-awesome removes less of font-awesome removes scss of font-awesome uses font-swesome min removes bootstrap removes leftandright css class updates jQuery and changes css class for popup updates jQuery updates fontawesome to 5.6.1 restore galaxy.yml.sample add missing resource update paths after updating font remove console log switch to minified jquery ui Commit: e4e2d9c09a45375faeb3e52d16beac87d4df1f99 https://github.com/galaxyproject/galaxy/commit/e4e2d9c09a45375faeb3e52d16be… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-12-21 (Fri, 21 Dec 2018) Changed paths: A config/plugins/visualizations/aequatus/README.md A config/plugins/visualizations/aequatus/config/aequatus.xml A config/plugins/visualizations/aequatus/static/aequatus-vis/LICENSE A config/plugins/visualizations/aequatus/static/aequatus-vis/README.md A config/plugins/visualizations/aequatus/static/aequatus-vis/_config.yml A config/plugins/visualizations/aequatus/static/aequatus-vis/scripts/cigarUtils.js A config/plugins/visualizations/aequatus/static/aequatus-vis/scripts/d3_tree.js A config/plugins/visualizations/aequatus/static/aequatus-vis/scripts/drawCIGARs.js A config/plugins/visualizations/aequatus/static/aequatus-vis/scripts/drawGene.js A config/plugins/visualizations/aequatus/static/aequatus-vis/scripts/drawGeneExonOnly.js A config/plugins/visualizations/aequatus/static/aequatus-vis/scripts/geneView.js A config/plugins/visualizations/aequatus/static/aequatus-vis/scripts/init.js A config/plugins/visualizations/aequatus/static/aequatus-vis/scripts/jquery/jquery-ui-1.12.1.min.css A config/plugins/visualizations/aequatus/static/aequatus-vis/scripts/jquery/jquery.svg.css A config/plugins/visualizations/aequatus/static/aequatus-vis/scripts/jquery/js/jquery-3.3.1.min.js A config/plugins/visualizations/aequatus/static/aequatus-vis/scripts/jquery/js/jquery-migrate-1.4.1.min.js A config/plugins/visualizations/aequatus/static/aequatus-vis/scripts/jquery/js/jquery-ui-1.12.1.min.js A config/plugins/visualizations/aequatus/static/aequatus-vis/scripts/jquery/js/jquery.cookie.js A config/plugins/visualizations/aequatus/static/aequatus-vis/scripts/jquery/js/jquery.svg.js A config/plugins/visualizations/aequatus/static/aequatus-vis/scripts/newick.js A config/plugins/visualizations/aequatus/static/aequatus-vis/scripts/scriptaculous/prototype.js A config/plugins/visualizations/aequatus/static/aequatus-vis/scripts/util.js A config/plugins/visualizations/aequatus/static/aequatus-vis/styles/font-awesome-5.6.1/css/fontawesome.min.css A config/plugins/visualizations/aequatus/static/aequatus-vis/styles/font-awesome-5.6.1/css/solid.min.css A config/plugins/visualizations/aequatus/static/aequatus-vis/styles/font-awesome-5.6.1/webfonts/FontAwesome.otf A config/plugins/visualizations/aequatus/static/aequatus-vis/styles/font-awesome-5.6.1/webfonts/fa-solid-900.eot A config/plugins/visualizations/aequatus/static/aequatus-vis/styles/font-awesome-5.6.1/webfonts/fa-solid-900.svg A config/plugins/visualizations/aequatus/static/aequatus-vis/styles/font-awesome-5.6.1/webfonts/fa-solid-900.ttf A config/plugins/visualizations/aequatus/static/aequatus-vis/styles/font-awesome-5.6.1/webfonts/fa-solid-900.woff A config/plugins/visualizations/aequatus/static/aequatus-vis/styles/font-awesome-5.6.1/webfonts/fa-solid-900.woff2 A config/plugins/visualizations/aequatus/static/aequatus-vis/styles/font-awesome-5.6.1/webfonts/fontawesome-webfont.eot A config/plugins/visualizations/aequatus/static/aequatus-vis/styles/font-awesome-5.6.1/webfonts/fontawesome-webfont.svg A config/plugins/visualizations/aequatus/static/aequatus-vis/styles/font-awesome-5.6.1/webfonts/fontawesome-webfont.ttf A config/plugins/visualizations/aequatus/static/aequatus-vis/styles/font-awesome-5.6.1/webfonts/fontawesome-webfont.woff A config/plugins/visualizations/aequatus/static/aequatus-vis/styles/style.css A config/plugins/visualizations/aequatus/static/scripts/controls.js A config/plugins/visualizations/aequatus/static/scripts/popup.js A config/plugins/visualizations/aequatus/static/scripts/readSQLite.js A config/plugins/visualizations/aequatus/static/scripts/sql.js A config/plugins/visualizations/aequatus/static/scripts/worker.js A config/plugins/visualizations/aequatus/static/scripts/worker.sql.js A config/plugins/visualizations/aequatus/static/styles/aequatus.css A config/plugins/visualizations/aequatus/templates/aequatus.mako M lib/galaxy/datatypes/binary.py Log Message: ----------- Merge pull request #6484 from anilthanki/aequatus-vis Adds Aequatus visualisation plugin Compare: https://github.com/galaxyproject/galaxy/compare/e8d95fba71a4...e4e2d9c09a45 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] fbf671: added store library to exported libs in bundleEntr...
by GitHub 21 Dec '18

21 Dec '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: fbf67196fff08a8c7a04d23703082cd77893e815 https://github.com/galaxyproject/galaxy/commit/fbf67196fff08a8c7a04d2370308… Author: Mason <nerdinacan(a)gmail.com> Date: 2018-12-21 (Fri, 21 Dec 2018) Changed paths: M client/galaxy/scripts/apps/extended.js Log Message: ----------- added store library to exported libs in bundleEntries Commit: e8d95fba71a44b128dd873c336d95b7e551607a7 https://github.com/galaxyproject/galaxy/commit/e8d95fba71a44b128dd873c336d9… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-12-21 (Fri, 21 Dec 2018) Changed paths: M client/galaxy/scripts/apps/extended.js Log Message: ----------- Merge pull request #7149 from Nerdinacan/include_store_in_bundleEntries added store library to exported libs in bundleEntries Compare: https://github.com/galaxyproject/galaxy/compare/9de86adc06dc...e8d95fba71a4 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 9bbdb3: Remove unneeded session flushes and adds when coll...
by GitHub 21 Dec '18

21 Dec '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 9bbdb34fb6f0676675851691280f261a3f37bb9e https://github.com/galaxyproject/galaxy/commit/9bbdb34fb6f0676675851691280f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-12-19 (Wed, 19 Dec 2018) Changed paths: M lib/galaxy/tools/parameters/output_collect.py Log Message: ----------- Remove unneeded session flushes and adds when collecting primary datasets. Commit: 9de86adc06dc3fa0d071d84252fd9c9b4befd2a0 https://github.com/galaxyproject/galaxy/commit/9de86adc06dc3fa0d071d84252fd… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-12-21 (Fri, 21 Dec 2018) Changed paths: M lib/galaxy/tools/parameters/output_collect.py Log Message: ----------- Merge pull request #7134 from jmchilton/remove_flushes Remove unneeded session flushes and adds when discovering outputs. Compare: https://github.com/galaxyproject/galaxy/compare/3af7a5c1a754...9de86adc06dc **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

1 0

[galaxyproject/galaxy] 3af7a5: Client format I intended to lump into display appl...
by GitHub 21 Dec '18

21 Dec '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 3af7a5c1a754a72c3dab94fde0eb1cc3476405fe https://github.com/galaxyproject/galaxy/commit/3af7a5c1a754a72c3dab94fde0eb… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-12-21 (Fri, 21 Dec 2018) Changed paths: M client/galaxy/scripts/components/admin/AdminServices.js M client/galaxy/scripts/components/admin/DisplayApplications.vue Log Message: ----------- Client format I intended to lump into display applications merge. **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] de3b7b: Add display applications api endpoint
by GitHub 21 Dec '18

21 Dec '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: de3b7bb55fd4949456bfb61637cb67b1fd367d6e https://github.com/galaxyproject/galaxy/commit/de3b7bb55fd4949456bfb61637cb… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-12-11 (Tue, 11 Dec 2018) Changed paths: A lib/galaxy/webapps/galaxy/api/display_applications.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Add display applications api endpoint Commit: 6546e35bff27a60b09bf30ca68c2beb62a61acd4 https://github.com/galaxyproject/galaxy/commit/6546e35bff27a60b09bf30ca68c2… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-12-11 (Tue, 11 Dec 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/display_applications.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Add reload feature to display applications api endpoint Commit: eb0c0ad9ab204cee83233523c01b11aa040a6388 https://github.com/galaxyproject/galaxy/commit/eb0c0ad9ab204cee83233523c01b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-12-11 (Tue, 11 Dec 2018) Changed paths: M client/galaxy/scripts/apps/admin.js A client/galaxy/scripts/components/admin/DisplayApplications.vue M lib/galaxy/webapps/galaxy/api/display_applications.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Add display application vue component Commit: 727ab11480962ec31387cc6934c0fcec14a4ead0 https://github.com/galaxyproject/galaxy/commit/727ab11480962ec31387cc6934c0… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-12-11 (Tue, 11 Dec 2018) Changed paths: M client/galaxy/scripts/apps/panels/admin-panel.js Log Message: ----------- Fix spacing in admin app router Commit: 35d2cd9bf62a748bc3dd5963a3246b5a5a7e2a18 https://github.com/galaxyproject/galaxy/commit/35d2cd9bf62a748bc3dd5963a324… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-12-11 (Tue, 11 Dec 2018) Changed paths: M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/components/admin/DisplayApplications.vue Log Message: ----------- Load display application data and display number of available applications Commit: 505e4288eebabf4ff3a317a90785cc6906941e53 https://github.com/galaxyproject/galaxy/commit/505e4288eebabf4ff3a317a90785… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-12-11 (Tue, 11 Dec 2018) Changed paths: M client/galaxy/scripts/components/admin/DisplayApplications.vue Log Message: ----------- Add display application vue component Commit: 218a02f3dccd8ccb5c6aa3df6c81764cb5e7a793 https://github.com/galaxyproject/galaxy/commit/218a02f3dccd8ccb5c6aa3df6c81… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-12-11 (Tue, 11 Dec 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py R templates/webapps/galaxy/admin/view_display_applications.mako Log Message: ----------- Remove legacy display applications mako and controller endpoints Commit: 4b097acffe77ab8348b4497cc9032011e2469825 https://github.com/galaxyproject/galaxy/commit/4b097acffe77ab8348b4497cc903… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-12-11 (Tue, 11 Dec 2018) Changed paths: M client/galaxy/scripts/components/admin/DisplayApplications.vue M lib/galaxy/webapps/galaxy/api/display_applications.py Log Message: ----------- Submit reload requests to new display application api endpoint Commit: b3f4d9b699e7a137dce7d130fe629aa01fc81292 https://github.com/galaxyproject/galaxy/commit/b3f4d9b699e7a137dce7d130fe62… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-12-11 (Tue, 11 Dec 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/display_applications.py Log Message: ----------- Remove debug outputs Commit: e8739a6cf530426bcd6f8c1c3964d7c31fb2a487 https://github.com/galaxyproject/galaxy/commit/e8739a6cf530426bcd6f8c1c3964… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-12-11 (Tue, 11 Dec 2018) Changed paths: M client/galaxy/scripts/components/admin/DisplayApplications.vue Log Message: ----------- Use bootstrap vues table component to render display applications table Commit: 39870a0d06647cf378ceae8b99065fbb09a8eefb https://github.com/galaxyproject/galaxy/commit/39870a0d06647cf378ceae8b9906… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-12-11 (Tue, 11 Dec 2018) Changed paths: M client/galaxy/scripts/components/admin/DisplayApplications.vue M lib/galaxy/webapps/galaxy/api/display_applications.py Log Message: ----------- Highlight reloaded/failed display application rows individually Commit: f68fa47f295f3d743d7de97521fcf97f78cf0248 https://github.com/galaxyproject/galaxy/commit/f68fa47f295f3d743d7de97521fc… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-12-11 (Tue, 11 Dec 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/display_applications.py Log Message: ----------- Fix linting Commit: 06deee06a48ae263a8ad396aac210ff9093ad6c6 https://github.com/galaxyproject/galaxy/commit/06deee06a48ae263a8ad396aac21… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-12-12 (Wed, 12 Dec 2018) Changed paths: M client/galaxy/scripts/components/admin/DisplayApplications.vue M test/selenium_tests/test_admin_app.py Log Message: ----------- Fix selenium test case for display application visibility Commit: 5b677cfd52e35e4b325dcd7fe426446c9c695262 https://github.com/galaxyproject/galaxy/commit/5b677cfd52e35e4b325dcd7fe426… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-12-13 (Thu, 13 Dec 2018) Changed paths: M client/galaxy/scripts/components/admin/DisplayApplications.vue M test/selenium_tests/test_admin_app.py Log Message: ----------- Fix selenium test, add missing applications message Commit: e3ef379674784f766d94c8e126f3744af4f5c9a7 https://github.com/galaxyproject/galaxy/commit/e3ef379674784f766d94c8e126f3… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-12-13 (Thu, 13 Dec 2018) Changed paths: M client/galaxy/scripts/components/admin/DisplayApplications.vue Log Message: ----------- Show warning message after requesting display applications Commit: f5a3ab464743a0d47672c00ce611520d846d6241 https://github.com/galaxyproject/galaxy/commit/f5a3ab464743a0d47672c00ce611… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-12-13 (Thu, 13 Dec 2018) Changed paths: A client/galaxy/scripts/components/admin/AdminServices.js M client/galaxy/scripts/components/admin/DisplayApplications.vue Log Message: ----------- Separate api requests from vue component for admin services Commit: 255418d158fd0d4a77bd9e56f18c15ec56bac02d https://github.com/galaxyproject/galaxy/commit/255418d158fd0d4a77bd9e56f18c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-12-13 (Thu, 13 Dec 2018) Changed paths: M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Fix comment header for display applications api Commit: f5b7553fea0f08c1bb37ce43172b91feed15bb44 https://github.com/galaxyproject/galaxy/commit/f5b7553fea0f08c1bb37ce43172b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-12-17 (Mon, 17 Dec 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/display_applications.py Log Message: ----------- Add require admin to display applications api Commit: a00d013fd14ecc1eca59b8d572c1ec5a673bce74 https://github.com/galaxyproject/galaxy/commit/a00d013fd14ecc1eca59b8d572c1… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-12-18 (Tue, 18 Dec 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/display_applications.py Log Message: ----------- Remove admin requirment from index endpoint of display applications Commit: e237bcfd16d6a72e78afe1405e4eaeb05a91af20 https://github.com/galaxyproject/galaxy/commit/e237bcfd16d6a72e78afe1405e4e… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-12-19 (Wed, 19 Dec 2018) Changed paths: M client/galaxy/scripts/components/admin/DisplayApplications.vue Log Message: ----------- Use b-alert instead of basic bootstrap alert messages Commit: 558aca71d69ea81746013489be52ee5813ecc43c https://github.com/galaxyproject/galaxy/commit/558aca71d69ea81746013489be52… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-12-19 (Wed, 19 Dec 2018) Changed paths: M client/galaxy/scripts/components/admin/DisplayApplications.vue Log Message: ----------- Replace default links with bootstrap vue buttons Commit: 3c2858ab0c9d79de18e28abfcef89de789e2c70c https://github.com/galaxyproject/galaxy/commit/3c2858ab0c9d79de18e28abfcef8… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-12-21 (Fri, 21 Dec 2018) Changed paths: M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/panels/admin-panel.js A client/galaxy/scripts/components/admin/AdminServices.js A client/galaxy/scripts/components/admin/DisplayApplications.vue A lib/galaxy/webapps/galaxy/api/display_applications.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin.py R templates/webapps/galaxy/admin/view_display_applications.mako M test/selenium_tests/test_admin_app.py Log Message: ----------- Merge pull request #7097 from guerler/display_applications Replace display applications mako with vue component Compare: https://github.com/galaxyproject/galaxy/compare/38687ff15a09...3c2858ab0c9d **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 5d8e0b: Correct code error in 'build job runner' tutorial
by GitHub 21 Dec '18

21 Dec '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 5d8e0bb049a5ffdc0197a1e8436f358d4352ce09 https://github.com/galaxyproject/galaxy/commit/5d8e0bb049a5ffdc0197a1e8436f… Author: Sergey Golitsynskiy <sgolitsynskiy(a)gmail.com> Date: 2018-12-21 (Fri, 21 Dec 2018) Changed paths: M doc/source/dev/build_a_job_runner.rst Log Message: ----------- Correct code error in 'build job runner' tutorial When __init__ is called, **kwargs (most likely) will not contain the 'runner_param_specs' key. And if so, calling update() on kwargs['runner_param_specs'] will cause an error. Check if key exists, then update or create. Commit: 0bd861aec759edb86a86e5e599e5b208dec48e43 https://github.com/galaxyproject/galaxy/commit/0bd861aec759edb86a86e5e599e5… Author: Sergey Golitsynskiy <sgolitsynskiy(a)gmail.com> Date: 2018-12-21 (Fri, 21 Dec 2018) Changed paths: M doc/source/dev/build_a_job_runner.rst Log Message: ----------- Code style improvement to previous commit Commit: 38687ff15a092477a798891eed572c7680e4d037 https://github.com/galaxyproject/galaxy/commit/38687ff15a092477a798891eed57… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-12-21 (Fri, 21 Dec 2018) Changed paths: M doc/source/dev/build_a_job_runner.rst Log Message: ----------- Merge pull request #7148 from ic4f/dev Correct code error in 'build job runner' tutorial Compare: https://github.com/galaxyproject/galaxy/compare/288453d4d017...38687ff15a09 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/usegalaxy-playbook] dbcc6f: Update test toolshed.
by GitHub 21 Dec '18

21 Dec '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: dbcc6f4f189fc5e801b35b20989ee5e577cf9a7e https://github.com/galaxyproject/usegalaxy-playbook/commit/dbcc6f4f189fc5e8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-12-21 (Fri, 21 Dec 2018) Changed paths: M env/testtoolshed/group_vars/toolshedservers/vars.yml Log Message: ----------- Update test toolshed. **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 4fbaa1: Add simple stub for mash sketch files
by GitHub 20 Dec '18

20 Dec '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4fbaa161232f1b8e12b23788e258def10e6aa156 https://github.com/galaxyproject/galaxy/commit/4fbaa161232f1b8e12b23788e258… Author: Dan Fornika <dfornika(a)gmail.com> Date: 2018-12-07 (Fri, 07 Dec 2018) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py Log Message: ----------- Add simple stub for mash sketch files Commit: 7d5a006b01ccd37ad65156be95f5e606dc4ea985 https://github.com/galaxyproject/galaxy/commit/7d5a006b01ccd37ad65156be95f5… Author: Dan Fornika <dfornika(a)gmail.com> Date: 2018-12-07 (Fri, 07 Dec 2018) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Removed extra whitespace to appease linter Commit: 27dc7c42c97db9230657a7db86567ac8b253d6b5 https://github.com/galaxyproject/galaxy/commit/27dc7c42c97db9230657a7db8656… Author: Dan Fornika <dfornika(a)gmail.com> Date: 2018-12-07 (Fri, 07 Dec 2018) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Removed extra whitespace to appease linter Commit: 288453d4d017425f1f6121552e132fe8030624aa https://github.com/galaxyproject/galaxy/commit/288453d4d017425f1f6121552e13… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-12-20 (Thu, 20 Dec 2018) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py Log Message: ----------- Merge pull request #7087 from dfornika/mash-sketch-datatype Add datatype for Mash Sketch files. Compare: https://github.com/galaxyproject/galaxy/compare/7eca9baf5ae5...288453d4d017 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 6f669d: 7132 Updated singleton to address cors issue in to...
by GitHub 20 Dec '18

20 Dec '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 6f669dd79b3ed7ad51658ef4f9b56fad834c2390 https://github.com/galaxyproject/galaxy/commit/6f669dd79b3ed7ad51658ef4f9b5… Author: Mason <nerdinacan(a)gmail.com> Date: 2018-12-19 (Wed, 19 Dec 2018) Changed paths: M client/galaxy/scripts/app/singleton.js M client/galaxy/scripts/layout/panel.js Log Message: ----------- 7132 Updated singleton to address cors issue in toolshed frames Commit: 60146ec89be41aec9a8d6216e96908b9095e6054 https://github.com/galaxyproject/galaxy/commit/60146ec89be41aec9a8d6216e969… Author: Mason <nerdinacan(a)gmail.com> Date: 2018-12-19 (Wed, 19 Dec 2018) Changed paths: M client/galaxy/scripts/layout/panel.js Log Message: ----------- Replaced test code with real code Commit: cf7f1b0745482c5e7cd75fa9d8e91e95124fcfac https://github.com/galaxyproject/galaxy/commit/cf7f1b0745482c5e7cd75fa9d8e9… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-12-20 (Thu, 20 Dec 2018) Changed paths: M client/galaxy/scripts/layout/panel.js Log Message: ----------- Client formatting. Commit: 7eca9baf5ae5c2a43e54d9dd9e76797fe2406568 https://github.com/galaxyproject/galaxy/commit/7eca9baf5ae5c2a43e54d9dd9e76… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-12-20 (Thu, 20 Dec 2018) Changed paths: M client/galaxy/scripts/app/singleton.js M client/galaxy/scripts/layout/panel.js Log Message: ----------- Merge branch '7132_fix_cors_singleton_storage' into dev Compare: https://github.com/galaxyproject/galaxy/compare/6a0a6ec1d1ee...7eca9baf5ae5 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 1edb74: Drop tools without installable dependencies
by GitHub 20 Dec '18

20 Dec '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1edb7489a16775ef2e3810e675c8182762d92540 https://github.com/galaxyproject/galaxy/commit/1edb7489a16775ef2e3810e675c8… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-12-20 (Thu, 20 Dec 2018) Changed paths: M config/tool_conf.xml.sample Log Message: ----------- Drop tools without installable dependencies These seem to be beyond legacy, and since their not installable let's drop them from the default config. I left them in tool_conf.xml.main, since they appear to be installed on main. Commit: 6a0a6ec1d1ee638731eb456da7abdee8b5582853 https://github.com/galaxyproject/galaxy/commit/6a0a6ec1d1ee638731eb456da7ab… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-12-20 (Thu, 20 Dec 2018) Changed paths: M config/tool_conf.xml.sample Log Message: ----------- Merge pull request #7136 from mvdbeek/remove_tools_without_deps Drop tools without installable dependencies Compare: https://github.com/galaxyproject/galaxy/compare/1854c934cb23...6a0a6ec1d1ee **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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