- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 4b1b15: libraries: provide select all/none options when im...
by GitHub 22 Mar '16

22 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4b1b15aee85c4aed85fe91c72712f2f5086dfd23 https://github.com/galaxyproject/galaxy/commit/4b1b15aee85c4aed85fe91c72712… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-21 (Mon, 21 Mar 2016) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js M client/galaxy/style/less/library.less M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/mvc/library/library-librarytoolbar-view.js.map M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/library/library-librarytoolbar-view.js M static/style/blue/base.css M static/style/blue/library.css Log Message: ----------- libraries: provide select all/none options when importing improve UX by using autofocus in modals fix a bug with selecting all folder items and deleting Commit: 35403f2a91eb33876c973f859fa038f9655dc297 https://github.com/galaxyproject/galaxy/commit/35403f2a91eb33876c973f859fa0… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-22 (Tue, 22 Mar 2016) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js M client/galaxy/style/less/library.less M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/mvc/library/library-librarytoolbar-view.js.map M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/library/library-librarytoolbar-view.js M static/style/blue/base.css M static/style/blue/library.css Log Message: ----------- Merge pull request #1970 from martenson/select-all-from-history libraries: provide select all/none options when importing Compare: https://github.com/galaxyproject/galaxy/compare/c26788a267b9...35403f2a91eb

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[galaxyproject/galaxy] 4e3ca9: Fix nginx-based file upload
by GitHub 22 Mar '16

22 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4e3ca993f213f17568324c98ba05aafe8efe8467 https://github.com/galaxyproject/galaxy/commit/4e3ca993f213f17568324c98ba05… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-03-21 (Mon, 21 Mar 2016) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Fix nginx-based file upload Commit: c26788a267b9caec3bfb28ca752a6a0585535767 https://github.com/galaxyproject/galaxy/commit/c26788a267b9caec3bfb28ca752a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-22 (Tue, 22 Mar 2016) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge pull request #1971 from guerler/fix_nginx_upload_000 Fix nginx-based file upload Compare: https://github.com/galaxyproject/galaxy/compare/35e75d11cea6...c26788a267b9

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[galaxyproject/galaxy] bd0439: Fix tool access rights and forwarding
by GitHub 21 Mar '16

21 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: bd0439d9b724bb72c1fab4c27a4c72814abef0b9 https://github.com/galaxyproject/galaxy/commit/bd0439d9b724bb72c1fab4c27a4c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-03-18 (Fri, 18 Mar 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M lib/galaxy/tools/__init__.py M lib/galaxy/webapps/galaxy/api/tools.py 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 M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tool-form-base.js Log Message: ----------- Fix tool access rights and forwarding Commit: 054fdf76f09faf35662adf0f4a8a6f6428abab4f https://github.com/galaxyproject/galaxy/commit/054fdf76f09faf35662adf0f4a8a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-03-18 (Fri, 18 Mar 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/tools.py Log Message: ----------- Parse user when filtering tools Commit: 566f556b076db164ce73750f33c9824fe0285530 https://github.com/galaxyproject/galaxy/commit/566f556b076db164ce73750f33c9… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-21 (Mon, 21 Mar 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M lib/galaxy/tools/__init__.py M lib/galaxy/webapps/galaxy/api/tools.py 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 M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tool-form-base.js Log Message: ----------- Merge pull request #1952 from guerler/fix_tool_access_000 [16.01] Fix tool access rights and forwarding Commit: 35e75d11cea6e6b0e75fade9eabb1fd96bdd99af https://github.com/galaxyproject/galaxy/commit/35e75d11cea6e6b0e75fade9eabb… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-21 (Mon, 21 Mar 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M lib/galaxy/tools/__init__.py M lib/galaxy/webapps/galaxy/api/tools.py 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 M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tool-form-base.js Log Message: ----------- Merge branch 'release_16.01' into dev. Rebuild client. Compare: https://github.com/galaxyproject/galaxy/compare/c64c6754a84c...35e75d11cea6

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[galaxyproject/galaxy] bd0439: Fix tool access rights and forwarding
by GitHub 21 Mar '16

21 Mar '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: bd0439d9b724bb72c1fab4c27a4c72814abef0b9 https://github.com/galaxyproject/galaxy/commit/bd0439d9b724bb72c1fab4c27a4c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-03-18 (Fri, 18 Mar 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M lib/galaxy/tools/__init__.py M lib/galaxy/webapps/galaxy/api/tools.py 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 M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tool-form-base.js Log Message: ----------- Fix tool access rights and forwarding Commit: 054fdf76f09faf35662adf0f4a8a6f6428abab4f https://github.com/galaxyproject/galaxy/commit/054fdf76f09faf35662adf0f4a8a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-03-18 (Fri, 18 Mar 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/tools.py Log Message: ----------- Parse user when filtering tools Commit: 566f556b076db164ce73750f33c9824fe0285530 https://github.com/galaxyproject/galaxy/commit/566f556b076db164ce73750f33c9… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-21 (Mon, 21 Mar 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M lib/galaxy/tools/__init__.py M lib/galaxy/webapps/galaxy/api/tools.py 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 M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tool-form-base.js Log Message: ----------- Merge pull request #1952 from guerler/fix_tool_access_000 [16.01] Fix tool access rights and forwarding Compare: https://github.com/galaxyproject/galaxy/compare/377ccbe23b71...566f556b076d

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[galaxyproject/galaxy] 9e9dfd: Fix workflow scheduler log message.
by GitHub 21 Mar '16

21 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 9e9dfdfd55b2b8d2377f8ef4e288a1fa482105b9 https://github.com/galaxyproject/galaxy/commit/9e9dfdfd55b2b8d2377f8ef4e288… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-21 (Mon, 21 Mar 2016) Changed paths: M lib/galaxy/workflow/run.py Log Message: ----------- Fix workflow scheduler log message. Commit: 5f5f0af5cd5e21c64810d29202e149915226c34a https://github.com/galaxyproject/galaxy/commit/5f5f0af5cd5e21c64810d29202e1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-21 (Mon, 21 Mar 2016) Changed paths: M lib/galaxy/workflow/run.py Log Message: ----------- Merge pull request #1955 from jmchilton/fix_wf_log_message [16.01] Fix workflow scheduler log message. Commit: 2efd9c2687d2ca818520249cdb3484e781659069 https://github.com/galaxyproject/galaxy/commit/2efd9c2687d2ca818520249cdb34… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-21 (Mon, 21 Mar 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Fix #1721. TODO: write test... Commit: 377ccbe23b717f9c8cb0d571de9f0d6da08a1ee8 https://github.com/galaxyproject/galaxy/commit/377ccbe23b717f9c8cb0d571de9f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-21 (Mon, 21 Mar 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Merge pull request #1967 from jmchilton/fix_optional_numeric_params [16.01] Fix #1721. Commit: 8d37aeff507b2fa16a1164eeb64a771746d4767d https://github.com/galaxyproject/galaxy/commit/8d37aeff507b2fa16a1164eeb64a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-21 (Mon, 21 Mar 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py M lib/galaxy/workflow/run.py Log Message: ----------- Manual merge to resolve conflict 16.01->dev Commit: c64c6754a84cfb399a9e3f230f08a6a6294406fa https://github.com/galaxyproject/galaxy/commit/c64c6754a84cfb399a9e3f230f08… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-21 (Mon, 21 Mar 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py M lib/galaxy/workflow/run.py Log Message: ----------- Merge pull request #1969 from dannon/dev Merge 16.01->dev Compare: https://github.com/galaxyproject/galaxy/compare/67e6ced2118b...c64c6754a84c

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[galaxyproject/usegalaxy-playbook] 1cef1b: IE version update
by GitHub 21 Mar '16

21 Mar '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 1cef1b4cd90ad8fb46cef0d4605569e692baa97a https://github.com/galaxyproject/usegalaxy-playbook/commit/1cef1b4cd90ad8fb… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-03-21 (Mon, 21 Mar 2016) Changed paths: M stage/files/interactive_environments/plugins/.ansible_ie_role_current_version M stage/files/interactive_environments/proxy/.ansible_ie_role_current_version Log Message: ----------- IE version update Commit: 31c916930b6a264dd7b34f92f2302f507b427a3e https://github.com/galaxyproject/usegalaxy-playbook/commit/31c916930b6a264d… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-03-21 (Mon, 21 Mar 2016) Changed paths: M files/galaxy/test.galaxyproject.org/var/shed_data_manager_conf.xml M files/galaxy/test.galaxyproject.org/var/shed_tool_conf.xml M files/galaxy/test.galaxyproject.org/var/shed_tool_data_table_conf.xml Log Message: ----------- Mutable configs on test Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/19f8ce2bcef0...…

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[galaxyproject/usegalaxy-playbook] c8444d: Undo change to Main's version
by GitHub 21 Mar '16

21 Mar '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: c8444d60798041b93fc3b451ef89973ff9039db1 https://github.com/galaxyproject/usegalaxy-playbook/commit/c8444d60798041b9… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-03-21 (Mon, 21 Mar 2016) Changed paths: M production/group_vars/all.yml Log Message: ----------- Undo change to Main's version Commit: 19f8ce2bcef0e7e7a9f108d0bd98112e8733a6fb https://github.com/galaxyproject/usegalaxy-playbook/commit/19f8ce2bcef0e7e7… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-03-21 (Mon, 21 Mar 2016) Changed paths: M templates/galaxy/test.galaxyproject.org/config/job_conf.xml.j2 M templates/galaxy/usegalaxy.org/config/job_conf.xml.j2 Log Message: ----------- Update the location of libdrmaa.so on Test and Main Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/5a4d97470ad4...…

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[galaxyproject/usegalaxy-playbook] 3f3a83: Update main's tools.
by GitHub 21 Mar '16

21 Mar '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 3f3a83376728469a8274d6f2c82e2a5400aed23f https://github.com/galaxyproject/usegalaxy-playbook/commit/3f3a83376728469a… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-03-21 (Mon, 21 Mar 2016) Changed paths: M files/galaxy/usegalaxy.org/var/integrated_tool_panel.xml M files/galaxy/usegalaxy.org/var/shed_tool_conf.xml M files/galaxy/usegalaxy.org/var/shed_tool_data_table_conf.xml M production/group_vars/all.yml Log Message: ----------- Update main's tools. Commit: 3c83d6def60c4352d1c6b61bbd4822853376ee83 https://github.com/galaxyproject/usegalaxy-playbook/commit/3c83d6def60c4352… Author: Dave Bouvier <dabe(a)bx.psu.edu> Date: 2016-03-21 (Mon, 21 Mar 2016) Changed paths: M files/galaxy/usegalaxy.org/var/integrated_tool_panel.xml M files/galaxy/usegalaxy.org/var/shed_data_manager_conf.xml M files/galaxy/usegalaxy.org/var/shed_tool_conf.xml M files/galaxy/usegalaxy.org/var/shed_tool_data_table_conf.xml Log Message: ----------- Update main, adding deeptools and gemini. Commit: 271f965cfd1e61a501d5773d27db29c8b61bdb36 https://github.com/galaxyproject/usegalaxy-playbook/commit/271f965cfd1e61a5… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-03-21 (Mon, 21 Mar 2016) Changed paths: A files/galaxy/common/static/welcome_img/GCC2016OralAbstracts.png A files/galaxy/common/static/welcome_img/GCC2016ScholarshipsInternational.png A files/galaxy/common/static/welcome_img/RDF2GraphGalaxy.png M files/galaxy/test.galaxyproject.org/var/integrated_tool_panel.xml M files/galaxy/test.galaxyproject.org/var/shed_data_manager_conf.xml M files/galaxy/test.galaxyproject.org/var/shed_tool_conf.xml M files/galaxy/test.galaxyproject.org/var/shed_tool_data_table_conf.xml M files/galaxy/usegalaxy.org/var/integrated_tool_panel.xml M files/galaxy/usegalaxy.org/var/shed_data_manager_conf.xml M files/galaxy/usegalaxy.org/var/shed_tool_conf.xml M galaxy.yml M galaxy_configs.yml M production/files/interactive_environments/plugins/.ansible_ie_role_current_version M production/files/interactive_environments/proxy/.ansible_ie_role_current_version M production/group_vars/galaxyservers.yml M production/group_vars/toolshedservers.yml M production/host_vars/galaxy-web-01.tacc.utexas.edu.yml M production/secret_vars/galaxyservers.yml M production/secret_vars/toolshedservers.yml M roles/galaxyprojectdotorg.galaxy/README.md M roles/galaxyprojectdotorg.galaxy/defaults/main.yml M roles/galaxyprojectdotorg.galaxy/meta/.galaxy_install_info M roles/galaxyprojectdotorg.galaxy/tasks/dependencies.yml M roles/galaxyprojectdotorg.galaxy/tasks/main.yml R roles/supervisor/defaults/main.yml R roles/supervisor/handlers/main.yml R roles/supervisor/tasks/main.yml R roles/supervisor/templates/centos.init.j2 R roles/supervisor/templates/debian.init.j2 R roles/supervisor/templates/redhat.init.j2 R roles/supervisor/templates/supervisord.conf.j2 R roles/supervisor/templates/systemd.init.j2 R roles/supervisor/templates/ubuntu.init.j2 M stage/group_vars/all.yml M stage/group_vars/galaxyservers.yml M stage/group_vars/toolshedservers.yml M stage/secret_vars/galaxyservers.yml M stage/secret_vars/toolshedservers.yml M templates/galaxy/common/static/welcome.html.j2 M templates/galaxy/test.galaxyproject.org/config/job_conf.xml.j2 R templates/supervisor/galaxy.conf.j2 A templates/supervisor/galaxy.j2 A templates/supervisor/galaxy_datamanager.j2 R templates/supervisor/galaxy_group.conf.j2 A templates/supervisor/galaxy_group.j2 R templates/supervisor/galaxy_impersonate.conf.j2 A templates/supervisor/galaxy_impersonate.j2 R templates/supervisor/galaxy_installer.conf.j2 A templates/supervisor/galaxy_installer.j2 R templates/supervisor/galaxy_reports.conf.j2 A templates/supervisor/galaxy_reports.j2 R templates/supervisor/testtoolshed.conf.j2 A templates/supervisor/testtoolshed.j2 R templates/supervisor/toolshed.conf.j2 A templates/supervisor/toolshed.j2 Log Message: ----------- Merge remote-tracking branch. Commit: 5a4d97470ad45725e9c2892eac71d63cdf9f1600 https://github.com/galaxyproject/usegalaxy-playbook/commit/5a4d97470ad45725… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-03-21 (Mon, 21 Mar 2016) Changed paths: M files/galaxy/usegalaxy.org/var/integrated_tool_panel.xml M files/galaxy/usegalaxy.org/var/shed_data_manager_conf.xml M files/galaxy/usegalaxy.org/var/shed_tool_conf.xml M files/galaxy/usegalaxy.org/var/shed_tool_data_table_conf.xml M production/group_vars/all.yml Log Message: ----------- Merge pull request #17 from davebx/update_main Update main's tools Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/5b12e0782f98...…

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[galaxyproject/galaxy] 2efd9c: Fix #1721.
by GitHub 21 Mar '16

21 Mar '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: 2efd9c2687d2ca818520249cdb3484e781659069 https://github.com/galaxyproject/galaxy/commit/2efd9c2687d2ca818520249cdb34… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-21 (Mon, 21 Mar 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Fix #1721. TODO: write test... Commit: 377ccbe23b717f9c8cb0d571de9f0d6da08a1ee8 https://github.com/galaxyproject/galaxy/commit/377ccbe23b717f9c8cb0d571de9f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-21 (Mon, 21 Mar 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Merge pull request #1967 from jmchilton/fix_optional_numeric_params [16.01] Fix #1721. Compare: https://github.com/galaxyproject/galaxy/compare/5f5f0af5cd5e...377ccbe23b71

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[galaxyproject/galaxy] e4e92e: Fix typo: send-->sent
by GitHub 21 Mar '16

21 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e4e92e55ab1df5d0e2847d19e3381cc2cd5db37b https://github.com/galaxyproject/galaxy/commit/e4e92e55ab1df5d0e2847d19e338… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-03-21 (Mon, 21 Mar 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-workflow.js 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/tool/tool-form-workflow.js Log Message: ----------- Fix typo: send-->sent Commit: 67e6ced2118b41627a51d5c9dbd0f4e303e88158 https://github.com/galaxyproject/galaxy/commit/67e6ced2118b41627a51d5c9dbd0… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-21 (Mon, 21 Mar 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-workflow.js 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/tool/tool-form-workflow.js Log Message: ----------- Merge pull request #1965 from blankenberg/typo-dev Fix typo: send-->sent Compare: https://github.com/galaxyproject/galaxy/compare/162f6d49af20...67e6ced2118b

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