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[galaxyproject/galaxy] 128a91: Checks for api_key before checking for header from...
by GitHub 15 Apr '16

15 Apr '16

Branch: refs/heads/release_16.04 Home: https://github.com/galaxyproject/galaxy Commit: 128a9112bb1635c1c49ac7dc1a99b531933ea659 https://github.com/galaxyproject/galaxy/commit/128a9112bb1635c1c49ac7dc1a99… Author: MatthewRalston <mrals89(a)gmail.com> Date: 2016-02-25 (Thu, 25 Feb 2016) Changed paths: M lib/galaxy/web/framework/middleware/remoteuser.py Log Message: ----------- Checks for api_key before checking for header from SSO. Also fixes the NoneType issue discovered in #972. Commit: 4e12c5e782249c3aea1ddbdd5bd2f363111e78b6 https://github.com/galaxyproject/galaxy/commit/4e12c5e782249c3aea1ddbdd5bd2… Author: MatthewRalston <mrals89(a)gmail.com> Date: 2016-02-25 (Thu, 25 Feb 2016) Changed paths: M lib/galaxy/web/framework/middleware/remoteuser.py Log Message: ----------- Fixes NoneType problem in a simpler way. Thanks @nsoranzo. Commit: 6473057f3b63ce615727800babbaf439ed66bb3f https://github.com/galaxyproject/galaxy/commit/6473057f3b63ce615727800babba… Author: Matt Ralston <mrals89(a)gmail.com> Date: 2016-02-26 (Fri, 26 Feb 2016) Changed paths: M lib/galaxy/web/framework/middleware/remoteuser.py Log Message: ----------- Adds whitespace Commit: 774487ddcc9c0e793b6b15b26c971c3df5822644 https://github.com/galaxyproject/galaxy/commit/774487ddcc9c0e793b6b15b26c97… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-03-07 (Mon, 07 Mar 2016) Changed paths: M client/galaxy/scripts/mvc/citation/citation-model.js M static/maps/mvc/citation/citation-model.js.map M static/scripts/mvc/citation/citation-model.js Log Message: ----------- Fix citation-model to fail silently/gracefully when a non-parsable bibtex entry is tried Commit: d225aebc8879b3e96963724d3b5b11aec1d50ed5 https://github.com/galaxyproject/galaxy/commit/d225aebc8879b3e96963724d3b5b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-07 (Mon, 07 Mar 2016) Changed paths: M client/galaxy/scripts/mvc/citation/citation-model.js M static/maps/mvc/citation/citation-model.js.map M static/scripts/mvc/citation/citation-model.js Log Message: ----------- Merge pull request #1884 from carlfeberhard/release_15.10 [15.10] Fix citation-model to fail silently/gracefully Commit: e2a03646fd7c47a0ead962c9842e74f977dab8eb https://github.com/galaxyproject/galaxy/commit/e2a03646fd7c47a0ead962c9842e… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-03-22 (Tue, 22 Mar 2016) Changed paths: M templates/webapps/galaxy/galaxy.panels.mako Log Message: ----------- Fix farbtastic's use of deprecated jquery fns by loading jq-migrate in galaxy.panels.mako Commit: 9cff686d6d94a8d4a47c4c5cdc9d380fe686a8c4 https://github.com/galaxyproject/galaxy/commit/9cff686d6d94a8d4a47c4c5cdc9d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-22 (Tue, 22 Mar 2016) Changed paths: M templates/webapps/galaxy/galaxy.panels.mako Log Message: ----------- Merge pull request #1972 from carlfeberhard/release_15.10 [15.10] Fix farbtastic's use of deprecated jquery fns by loading jq-migrate i… Commit: a2114fdd0e234a3253cec79a02e30899ca081359 https://github.com/galaxyproject/galaxy/commit/a2114fdd0e234a3253cec79a02e3… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-22 (Tue, 22 Mar 2016) Changed paths: M lib/galaxy/web/framework/middleware/remoteuser.py Log Message: ----------- Merge pull request #1801 from MatthewRalston/api_key_patch [15.10] Checks for api_key before checking for header from SSO. Commit: f85aaa4a27a1067a108c05fd1f74fa6060aa4565 https://github.com/galaxyproject/galaxy/commit/f85aaa4a27a1067a108c05fd1f74… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-04-13 (Wed, 13 Apr 2016) Changed paths: M lib/galaxy/webapps/tool_shed/buildapp.py Log Message: ----------- port of middleware fix for TS (#2106) Commit: c0d65092fbbd1ad7380a0b17d3d9a949145d6170 https://github.com/galaxyproject/galaxy/commit/c0d65092fbbd1ad7380a0b17d3d9… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-04-14 (Thu, 14 Apr 2016) Changed paths: M lib/galaxy/webapps/tool_shed/buildapp.py Log Message: ----------- Merge pull request #2154 from martenson/port-middleware-fix [16.01] Port middleware fix Commit: e26bff23ed05eeeb7bac469b95a4ee6509dd537c https://github.com/galaxyproject/galaxy/commit/e26bff23ed05eeeb7bac469b95a4… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-04-14 (Thu, 14 Apr 2016) Changed paths: M client/galaxy/scripts/mvc/citation/citation-model.js M lib/galaxy/web/framework/middleware/remoteuser.py M static/maps/mvc/citation/citation-model.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/citation/citation-model.js M templates/webapps/galaxy/galaxy.panels.mako Log Message: ----------- Merge 'release_15.10' with 'release_16.01' Commit: 570baa5bb6020a2a8b7592dda8e952225ce7beec https://github.com/galaxyproject/galaxy/commit/570baa5bb6020a2a8b7592dda8e9… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-04-14 (Thu, 14 Apr 2016) Changed paths: M lib/galaxy/web/framework/middleware/remoteuser.py Log Message: ----------- Fix bad merge: when HTTP_GX_SECRET is None Commit: 68ce6ce49cc8c3d6f252a52a6bf9ac90f64328a3 https://github.com/galaxyproject/galaxy/commit/68ce6ce49cc8c3d6f252a52a6bf9… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-14 (Thu, 14 Apr 2016) Changed paths: M client/galaxy/scripts/mvc/citation/citation-model.js M lib/galaxy/web/framework/middleware/remoteuser.py M static/maps/mvc/citation/citation-model.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/citation/citation-model.js M templates/webapps/galaxy/galaxy.panels.mako Log Message: ----------- Merge pull request #2169 from carlfeberhard/release_16.01 [16.01] Merge 15.10 with 16.01 Commit: 8b49814859dc4dcc85d5a4b3b8945f3f7e3342f4 https://github.com/galaxyproject/galaxy/commit/8b49814859dc4dcc85d5a4b3b894… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-04-14 (Thu, 14 Apr 2016) Changed paths: M client/galaxy/scripts/mvc/citation/citation-model.js M lib/galaxy/web/framework/middleware/remoteuser.py M static/maps/mvc/citation/citation-model.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/citation/citation-model.js M templates/webapps/galaxy/galaxy.panels.mako Log Message: ----------- Merge 16.01 into 16.04 Compare: https://github.com/galaxyproject/galaxy/compare/f013cf2021ec...8b49814859dc

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[galaxyproject/galaxy] 128a91: Checks for api_key before checking for header from...
by GitHub 15 Apr '16

15 Apr '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: 128a9112bb1635c1c49ac7dc1a99b531933ea659 https://github.com/galaxyproject/galaxy/commit/128a9112bb1635c1c49ac7dc1a99… Author: MatthewRalston <mrals89(a)gmail.com> Date: 2016-02-25 (Thu, 25 Feb 2016) Changed paths: M lib/galaxy/web/framework/middleware/remoteuser.py Log Message: ----------- Checks for api_key before checking for header from SSO. Also fixes the NoneType issue discovered in #972. Commit: 4e12c5e782249c3aea1ddbdd5bd2f363111e78b6 https://github.com/galaxyproject/galaxy/commit/4e12c5e782249c3aea1ddbdd5bd2… Author: MatthewRalston <mrals89(a)gmail.com> Date: 2016-02-25 (Thu, 25 Feb 2016) Changed paths: M lib/galaxy/web/framework/middleware/remoteuser.py Log Message: ----------- Fixes NoneType problem in a simpler way. Thanks @nsoranzo. Commit: 6473057f3b63ce615727800babbaf439ed66bb3f https://github.com/galaxyproject/galaxy/commit/6473057f3b63ce615727800babba… Author: Matt Ralston <mrals89(a)gmail.com> Date: 2016-02-26 (Fri, 26 Feb 2016) Changed paths: M lib/galaxy/web/framework/middleware/remoteuser.py Log Message: ----------- Adds whitespace Commit: 774487ddcc9c0e793b6b15b26c971c3df5822644 https://github.com/galaxyproject/galaxy/commit/774487ddcc9c0e793b6b15b26c97… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-03-07 (Mon, 07 Mar 2016) Changed paths: M client/galaxy/scripts/mvc/citation/citation-model.js M static/maps/mvc/citation/citation-model.js.map M static/scripts/mvc/citation/citation-model.js Log Message: ----------- Fix citation-model to fail silently/gracefully when a non-parsable bibtex entry is tried Commit: d225aebc8879b3e96963724d3b5b11aec1d50ed5 https://github.com/galaxyproject/galaxy/commit/d225aebc8879b3e96963724d3b5b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-07 (Mon, 07 Mar 2016) Changed paths: M client/galaxy/scripts/mvc/citation/citation-model.js M static/maps/mvc/citation/citation-model.js.map M static/scripts/mvc/citation/citation-model.js Log Message: ----------- Merge pull request #1884 from carlfeberhard/release_15.10 [15.10] Fix citation-model to fail silently/gracefully Commit: e2a03646fd7c47a0ead962c9842e74f977dab8eb https://github.com/galaxyproject/galaxy/commit/e2a03646fd7c47a0ead962c9842e… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-03-22 (Tue, 22 Mar 2016) Changed paths: M templates/webapps/galaxy/galaxy.panels.mako Log Message: ----------- Fix farbtastic's use of deprecated jquery fns by loading jq-migrate in galaxy.panels.mako Commit: 9cff686d6d94a8d4a47c4c5cdc9d380fe686a8c4 https://github.com/galaxyproject/galaxy/commit/9cff686d6d94a8d4a47c4c5cdc9d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-22 (Tue, 22 Mar 2016) Changed paths: M templates/webapps/galaxy/galaxy.panels.mako Log Message: ----------- Merge pull request #1972 from carlfeberhard/release_15.10 [15.10] Fix farbtastic's use of deprecated jquery fns by loading jq-migrate i… Commit: a2114fdd0e234a3253cec79a02e30899ca081359 https://github.com/galaxyproject/galaxy/commit/a2114fdd0e234a3253cec79a02e3… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-22 (Tue, 22 Mar 2016) Changed paths: M lib/galaxy/web/framework/middleware/remoteuser.py Log Message: ----------- Merge pull request #1801 from MatthewRalston/api_key_patch [15.10] Checks for api_key before checking for header from SSO. Commit: e26bff23ed05eeeb7bac469b95a4ee6509dd537c https://github.com/galaxyproject/galaxy/commit/e26bff23ed05eeeb7bac469b95a4… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-04-14 (Thu, 14 Apr 2016) Changed paths: M client/galaxy/scripts/mvc/citation/citation-model.js M lib/galaxy/web/framework/middleware/remoteuser.py M static/maps/mvc/citation/citation-model.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/citation/citation-model.js M templates/webapps/galaxy/galaxy.panels.mako Log Message: ----------- Merge 'release_15.10' with 'release_16.01' Commit: 570baa5bb6020a2a8b7592dda8e952225ce7beec https://github.com/galaxyproject/galaxy/commit/570baa5bb6020a2a8b7592dda8e9… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-04-14 (Thu, 14 Apr 2016) Changed paths: M lib/galaxy/web/framework/middleware/remoteuser.py Log Message: ----------- Fix bad merge: when HTTP_GX_SECRET is None Commit: 68ce6ce49cc8c3d6f252a52a6bf9ac90f64328a3 https://github.com/galaxyproject/galaxy/commit/68ce6ce49cc8c3d6f252a52a6bf9… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-14 (Thu, 14 Apr 2016) Changed paths: M client/galaxy/scripts/mvc/citation/citation-model.js M lib/galaxy/web/framework/middleware/remoteuser.py M static/maps/mvc/citation/citation-model.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/citation/citation-model.js M templates/webapps/galaxy/galaxy.panels.mako Log Message: ----------- Merge pull request #2169 from carlfeberhard/release_16.01 [16.01] Merge 15.10 with 16.01 Compare: https://github.com/galaxyproject/galaxy/compare/c0d65092fbbd...68ce6ce49cc8

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[galaxyproject/galaxy] b93b62: Place $headers before integrity_check
by GitHub 14 Apr '16

14 Apr '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b93b62ae778905518a5c0d7703cc3e93f2c2ba02 https://github.com/galaxyproject/galaxy/commit/b93b62ae778905518a5c0d7703cc… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-04-13 (Wed, 13 Apr 2016) Changed paths: M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh Log Message: ----------- Place $headers before integrity_check PBS needs the resource selection (which will be filled in using $headers) to appear before anything else (except the shebang), so this changes the order. Commit: e81448c62ab5f78d1519826cc7567aa24b476d82 https://github.com/galaxyproject/galaxy/commit/e81448c62ab5f78d1519826cc756… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-04-14 (Thu, 14 Apr 2016) Changed paths: M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh Log Message: ----------- Merge pull request #2146 from mvdbeek/reorder_job_template Place $headers before integrity_check Compare: https://github.com/galaxyproject/galaxy/compare/a919e98be3ee...e81448c62ab5

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[galaxyproject/usegalaxy-playbook] dce66f: Switch Main to use CVMFS (still needs /galaxy/main...
by GitHub 14 Apr '16

14 Apr '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: dce66f43ebeae399357065686671d4f17d2c7242 https://github.com/galaxyproject/usegalaxy-playbook/commit/dce66f43ebeae399… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-04-14 (Thu, 14 Apr 2016) Changed paths: A files/ssl/usegalaxy.org_cert.pem A files/ssl/wildcard_cert.pem A galaxy.yml M galaxy_configs.yml M galaxy_infrastructure.yml R galaxy_main.yml M galaxy_static.yml R galaxy_test.yml M production/group_vars/all.yml M production/group_vars/galaxyservers.yml M production/group_vars/pulsarservers.yml M production/secret_vars/galaxyservers.yml M roles/galaxyprojectdotorg.nginx/README.md M roles/galaxyprojectdotorg.nginx/defaults/main.yml M roles/galaxyprojectdotorg.nginx/handlers/main.yml A roles/galaxyprojectdotorg.nginx/meta/.galaxy_install_info M roles/galaxyprojectdotorg.nginx/meta/main.yml M roles/galaxyprojectdotorg.nginx/tasks/apt.yml M roles/galaxyprojectdotorg.nginx/tasks/main.yml A roles/galaxyprojectdotorg.nginx/tasks/yum.yml A roles/galaxyprojectdotorg.nginx/templates/epel-nginx.conf.j2 A roles/galaxyprojectdotorg.nginx/templates/supervisord.conf.j2 M stage/group_vars/all.yml M stage/group_vars/galaxyservers.yml M stage/secret_vars/galaxyservers.yml M templates/galaxy/usegalaxy.org/config/job_conf.xml.j2 A templates/nginx/galaxy_bx.j2 A templates/nginx/galaxy_main_installer.j2 A templates/nginx/galaxy_test.j2 A templates/nginx/usegalaxy.j2 A templates/nginx/usegalaxy_rewrites.conf.j2 M templates/supervisor/galaxy_impersonate.j2 Log Message: ----------- Switch Main to use CVMFS (still needs /galaxy/main symlinks for shed_tools, migrated_tools, and deps), and also move all of the nginx handling here from the private playbook. And use the updated nginx role to install "Galaxy nginx", which is basically an updated and recompiled (with Starforge!) version of EPEL nginx.

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[galaxyproject/galaxy] 2ebe94: load options from config, not from options
by GitHub 14 Apr '16

14 Apr '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 2ebe9405106dfc16504e3b6f775425634bb4691f https://github.com/galaxyproject/galaxy/commit/2ebe9405106dfc16504e3b6f7754… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-04-12 (Tue, 12 Apr 2016) Changed paths: M client/galaxy/scripts/layout/page.js M static/maps/layout/page.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/page.js Log Message: ----------- load options from config, not from options Commit: ad952a4b8d7501d0df48e44d7c966ff22f9a63c4 https://github.com/galaxyproject/galaxy/commit/ad952a4b8d7501d0df48e44d7c96… Author: carlfeberhard <carlfeberhard(a)users.noreply.github.com> Date: 2016-04-12 (Tue, 12 Apr 2016) Changed paths: M client/galaxy/scripts/layout/page.js M static/maps/layout/page.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/page.js Log Message: ----------- Merge pull request #2139 from martenson/fix-inactivity [16.01] load options from config, not from options Commit: 1e3b3a15581ecd62e78999f6be9e74d9e7cfbc65 https://github.com/galaxyproject/galaxy/commit/1e3b3a15581ecd62e78999f6be9e… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-04-12 (Tue, 12 Apr 2016) Changed paths: M client/galaxy/scripts/layout/page.js M static/maps/layout/page.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/page.js Log Message: ----------- fix the value passed to Masthead as options were options.config before Commit: 87dbfeeabd03d4b7f7c81b3e9dfadf3890f71b95 https://github.com/galaxyproject/galaxy/commit/87dbfeeabd03d4b7f7c81b3e9dfa… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-04-13 (Wed, 13 Apr 2016) Changed paths: M client/galaxy/scripts/layout/page.js M static/maps/layout/page.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/page.js Log Message: ----------- Merge branch 'release_16.01' into release_16.04 Conflicts: 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 Commit: 4c2bca51171efff42e2852bfa59a91d5acee3e73 https://github.com/galaxyproject/galaxy/commit/4c2bca51171efff42e2852bfa59a… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-04-13 (Wed, 13 Apr 2016) Changed paths: M client/galaxy/scripts/layout/page.js M static/maps/layout/page.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/page.js Log Message: ----------- Merge pull request #2141 from martenson/fix-sideeffect [16.01] fix the value passed to Masthead as options were options.config before Commit: 090e0d33561702b85c82c1bfb228b699c30804ea https://github.com/galaxyproject/galaxy/commit/090e0d33561702b85c82c1bfb228… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-04-13 (Wed, 13 Apr 2016) Log Message: ----------- Merge branch 'release_16.01' into merge01to04 Commit: d5cc3571704d5fe3927d070456f5b934e9f5e1cf https://github.com/galaxyproject/galaxy/commit/d5cc3571704d5fe3927d070456f5… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-13 (Wed, 13 Apr 2016) Changed paths: M client/galaxy/scripts/layout/page.js M static/maps/layout/page.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/page.js Log Message: ----------- Merge pull request #2150 from martenson/merge01to04 [16.04] Merge 16.01 to 16.04 Commit: 82e9ce827c9c76b242e52747b7d2d1a546e683a6 https://github.com/galaxyproject/galaxy/commit/82e9ce827c9c76b242e52747b7d2… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-04-13 (Wed, 13 Apr 2016) Changed paths: M lib/galaxy/tools/parameters/__init__.py Log Message: ----------- Add tool parameters back to parameters Commit: ac141397148c0698a06d7d8d2088d94d00961915 https://github.com/galaxyproject/galaxy/commit/ac141397148c0698a06d7d8d2088… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-04-13 (Wed, 13 Apr 2016) Changed paths: M lib/galaxy/tools/parameters/__init__.py Log Message: ----------- Add blank line Commit: a889e19af7b5a6b87881a4ade1dad4efae168858 https://github.com/galaxyproject/galaxy/commit/a889e19af7b5a6b87881a4ade1da… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-04-14 (Thu, 14 Apr 2016) Changed paths: M lib/galaxy/tools/wrappers.py Log Message: ----------- Fix parameter wrapping Commit: 5be5ba753165da5fa1e2cd7c9c1efbed91f79786 https://github.com/galaxyproject/galaxy/commit/5be5ba753165da5fa1e2cd7c9c1e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-14 (Thu, 14 Apr 2016) Changed paths: M lib/galaxy/tools/wrappers.py Log Message: ----------- Merge pull request #2161 from guerler/fix_wrapper_issue_001 [16.04] Fix wrapper issue, overload __ne__ Commit: 9bb5978d53070363cc83e1f7bf2a1df5f73eaf41 https://github.com/galaxyproject/galaxy/commit/9bb5978d53070363cc83e1f7bf2a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-04-14 (Thu, 14 Apr 2016) Changed paths: M lib/galaxy/tools/parameters/__init__.py Log Message: ----------- Merge pull request #2156 from guerler/fix_data_001 [16.04] Add tool parameters back to parameters and expose for certain tools Commit: 84ef4fd99f602c34ad7de6868864f4d8777ebe23 https://github.com/galaxyproject/galaxy/commit/84ef4fd99f602c34ad7de6868864… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-04-14 (Thu, 14 Apr 2016) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt Log Message: ----------- Update pulsar-galaxy-lib in pinned-requirements.txt (it was already updated in requirements.txt). Commit: f013cf2021ec65893dd16bf193bc30182b945047 https://github.com/galaxyproject/galaxy/commit/f013cf2021ec65893dd16bf193bc… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-04-14 (Thu, 14 Apr 2016) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt Log Message: ----------- Merge pull request #2164 from natefoo/release_16.04 [16.04] Fix missing pulsar-galaxy-lib update Commit: a919e98be3ee7a8e289b66efb35c508441f5e7b8 https://github.com/galaxyproject/galaxy/commit/a919e98be3ee7a8e289b66efb35c… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-04-14 (Thu, 14 Apr 2016) Changed paths: M client/galaxy/scripts/layout/page.js M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/wrappers.py M static/maps/layout/page.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/page.js Log Message: ----------- Merge branch 'release_16.04' into dev Compare: https://github.com/galaxyproject/galaxy/compare/148d4ee88d29...a919e98be3ee

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[galaxyproject/galaxy] 3c97d3: Use "$NCPUS" if defined to set GALAXY_SLOTS
by GitHub 14 Apr '16

14 Apr '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 3c97d30cd6b4f11270fc1e057f236f420542cfea https://github.com/galaxyproject/galaxy/commit/3c97d30cd6b4f11270fc1e057f23… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-04-13 (Wed, 13 Apr 2016) Changed paths: M lib/galaxy/jobs/runners/util/job_script/CLUSTER_SLOTS_STATEMENT.sh Log Message: ----------- Use "$NCPUS" if defined to set GALAXY_SLOTS On our PBS cluster we do not have $PBS_NCPUS, and $PBS_NODEFILE contains the hostname of the nodes the task runs on. But we do have "$NCPUS" with the correct number of CPUS. Commit: 148d4ee88d2982dd5784ec6f1199fa795beaef5d https://github.com/galaxyproject/galaxy/commit/148d4ee88d2982dd5784ec6f1199… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-04-14 (Thu, 14 Apr 2016) Changed paths: M lib/galaxy/jobs/runners/util/job_script/CLUSTER_SLOTS_STATEMENT.sh Log Message: ----------- Merge pull request #2145 from mvdbeek/pbs_ncpu Use "$NCPUS" if defined to set GALAXY_SLOTS Compare: https://github.com/galaxyproject/galaxy/compare/87e2a6cd5753...148d4ee88d29

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[galaxyproject/galaxy] 84ef4f: Update pulsar-galaxy-lib in pinned-requirements.tx...
by GitHub 14 Apr '16

14 Apr '16

Branch: refs/heads/release_16.04 Home: https://github.com/galaxyproject/galaxy Commit: 84ef4fd99f602c34ad7de6868864f4d8777ebe23 https://github.com/galaxyproject/galaxy/commit/84ef4fd99f602c34ad7de6868864… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-04-14 (Thu, 14 Apr 2016) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt Log Message: ----------- Update pulsar-galaxy-lib in pinned-requirements.txt (it was already updated in requirements.txt). Commit: f013cf2021ec65893dd16bf193bc30182b945047 https://github.com/galaxyproject/galaxy/commit/f013cf2021ec65893dd16bf193bc… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-04-14 (Thu, 14 Apr 2016) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt Log Message: ----------- Merge pull request #2164 from natefoo/release_16.04 [16.04] Fix missing pulsar-galaxy-lib update Compare: https://github.com/galaxyproject/galaxy/compare/9bb5978d5307...f013cf2021ec

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[galaxyproject/galaxy] 82e9ce: Add tool parameters back to parameters
by GitHub 14 Apr '16

14 Apr '16

Branch: refs/heads/release_16.04 Home: https://github.com/galaxyproject/galaxy Commit: 82e9ce827c9c76b242e52747b7d2d1a546e683a6 https://github.com/galaxyproject/galaxy/commit/82e9ce827c9c76b242e52747b7d2… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-04-13 (Wed, 13 Apr 2016) Changed paths: M lib/galaxy/tools/parameters/__init__.py Log Message: ----------- Add tool parameters back to parameters Commit: ac141397148c0698a06d7d8d2088d94d00961915 https://github.com/galaxyproject/galaxy/commit/ac141397148c0698a06d7d8d2088… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-04-13 (Wed, 13 Apr 2016) Changed paths: M lib/galaxy/tools/parameters/__init__.py Log Message: ----------- Add blank line Commit: 9bb5978d53070363cc83e1f7bf2a1df5f73eaf41 https://github.com/galaxyproject/galaxy/commit/9bb5978d53070363cc83e1f7bf2a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-04-14 (Thu, 14 Apr 2016) Changed paths: M lib/galaxy/tools/parameters/__init__.py Log Message: ----------- Merge pull request #2156 from guerler/fix_data_001 [16.04] Add tool parameters back to parameters and expose for certain tools Compare: https://github.com/galaxyproject/galaxy/compare/5be5ba753165...9bb5978d5307

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[galaxyproject/galaxy] 024ae7: bail earlier if no SMTP server is configured
by GitHub 14 Apr '16

14 Apr '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 024ae7a28665950a6d5c194edc0a3b94110684c2 https://github.com/galaxyproject/galaxy/commit/024ae7a28665950a6d5c194edc0a… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-04-12 (Tue, 12 Apr 2016) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- bail earlier if no SMTP server is configured Commit: e9823573e3121bce86740c9ee91d0e049c01820c https://github.com/galaxyproject/galaxy/commit/e9823573e3121bce86740c9ee91d… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-04-13 (Wed, 13 Apr 2016) Changed paths: M lib/galaxy/tools/errors.py M lib/galaxy/util/__init__.py Log Message: ----------- Add HTML Template Commit: c2cff25826e36982b8496e9c50a1c370d427ec81 https://github.com/galaxyproject/galaxy/commit/c2cff25826e36982b8496e9c50a1… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-04-13 (Wed, 13 Apr 2016) Changed paths: M lib/galaxy/tools/errors.py Log Message: ----------- Use CGI for escaping Commit: 5923a67301e966142cd535659ad0e64cf0ada219 https://github.com/galaxyproject/galaxy/commit/5923a67301e966142cd535659ad0… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-04-13 (Wed, 13 Apr 2016) Changed paths: M lib/galaxy/tools/errors.py Log Message: ----------- Fix sanitization completely Commit: a6d95d090981d414d8efc76056ec1d45faf2e0dd https://github.com/galaxyproject/galaxy/commit/a6d95d090981d414d8efc76056ec… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-04-13 (Wed, 13 Apr 2016) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Fix flake8 by reverting a previous commit Commit: df481dabe092ff49e97619138e111d57eafb871b https://github.com/galaxyproject/galaxy/commit/df481dabe092ff49e97619138e11… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-04-13 (Wed, 13 Apr 2016) Changed paths: M lib/galaxy/tools/errors.py Log Message: ----------- Remove unused import Commit: cba10c812b7c9e3979a57bc0b7ece42333e3f364 https://github.com/galaxyproject/galaxy/commit/cba10c812b7c9e3979a57bc0b7ec… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-04-13 (Wed, 13 Apr 2016) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Fix nitpick Commit: a3e925cc1bea692ba76a5efbc38d2a163c80ffea https://github.com/galaxyproject/galaxy/commit/a3e925cc1bea692ba76a5efbc38d… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-04-13 (Wed, 13 Apr 2016) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Fix second nitpick Commit: 4d729ff8906cc371102f711a947af61252e51183 https://github.com/galaxyproject/galaxy/commit/4d729ff8906cc371102f711a947a… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-04-13 (Wed, 13 Apr 2016) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Typo Commit: 6ce9bd82203895226807231158a33b4ec67ff20b https://github.com/galaxyproject/galaxy/commit/6ce9bd82203895226807231158a3… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-04-13 (Wed, 13 Apr 2016) Changed paths: M lib/galaxy/tools/errors.py Log Message: ----------- Minor touch up for consistency Commit: dd05f0ab24b72fd3c387c6294993aceb38f7d441 https://github.com/galaxyproject/galaxy/commit/dd05f0ab24b72fd3c387c6294993… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-04-13 (Wed, 13 Apr 2016) Changed paths: M lib/galaxy/tools/errors.py Log Message: ----------- Escape everything Commit: 3d5663e97f9ec5ddae4e1e50eb2405ed82791b7c https://github.com/galaxyproject/galaxy/commit/3d5663e97f9ec5ddae4e1e50eb24… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-04-13 (Wed, 13 Apr 2016) Changed paths: M lib/galaxy/tools/errors.py Log Message: ----------- Remove double escaping Commit: 87e2a6cd5753adb7f1895e5ad3be94e61e278e04 https://github.com/galaxyproject/galaxy/commit/87e2a6cd5753adb7f1895e5ad3be… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-04-14 (Thu, 14 Apr 2016) Changed paths: M lib/galaxy/tools/errors.py M lib/galaxy/util/__init__.py Log Message: ----------- Merge pull request #2143 from erasche/nicer-emails Nicer bug report emails Compare: https://github.com/galaxyproject/galaxy/compare/d7353d381987...87e2a6cd5753

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[galaxyproject/galaxy] f85aaa: port of middleware fix for TS (#2106)
by GitHub 14 Apr '16

14 Apr '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: f85aaa4a27a1067a108c05fd1f74fa6060aa4565 https://github.com/galaxyproject/galaxy/commit/f85aaa4a27a1067a108c05fd1f74… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-04-13 (Wed, 13 Apr 2016) Changed paths: M lib/galaxy/webapps/tool_shed/buildapp.py Log Message: ----------- port of middleware fix for TS (#2106) Commit: c0d65092fbbd1ad7380a0b17d3d9a949145d6170 https://github.com/galaxyproject/galaxy/commit/c0d65092fbbd1ad7380a0b17d3d9… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-04-14 (Thu, 14 Apr 2016) Changed paths: M lib/galaxy/webapps/tool_shed/buildapp.py Log Message: ----------- Merge pull request #2154 from martenson/port-middleware-fix [16.01] Port middleware fix Compare: https://github.com/galaxyproject/galaxy/compare/4c2bca51171e...c0d65092fbbd

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[galaxyproject/galaxy] 2ebe94: load options from config, not from options
by GitHub 14 Apr '16

14 Apr '16

Branch: refs/heads/release_16.04 Home: https://github.com/galaxyproject/galaxy Commit: 2ebe9405106dfc16504e3b6f775425634bb4691f https://github.com/galaxyproject/galaxy/commit/2ebe9405106dfc16504e3b6f7754… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-04-12 (Tue, 12 Apr 2016) Changed paths: M client/galaxy/scripts/layout/page.js M static/maps/layout/page.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/page.js Log Message: ----------- load options from config, not from options Commit: ad952a4b8d7501d0df48e44d7c966ff22f9a63c4 https://github.com/galaxyproject/galaxy/commit/ad952a4b8d7501d0df48e44d7c96… Author: carlfeberhard <carlfeberhard(a)users.noreply.github.com> Date: 2016-04-12 (Tue, 12 Apr 2016) Changed paths: M client/galaxy/scripts/layout/page.js M static/maps/layout/page.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/page.js Log Message: ----------- Merge pull request #2139 from martenson/fix-inactivity [16.01] load options from config, not from options Commit: 1e3b3a15581ecd62e78999f6be9e74d9e7cfbc65 https://github.com/galaxyproject/galaxy/commit/1e3b3a15581ecd62e78999f6be9e… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-04-12 (Tue, 12 Apr 2016) Changed paths: M client/galaxy/scripts/layout/page.js M static/maps/layout/page.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/page.js Log Message: ----------- fix the value passed to Masthead as options were options.config before Commit: 87dbfeeabd03d4b7f7c81b3e9dfadf3890f71b95 https://github.com/galaxyproject/galaxy/commit/87dbfeeabd03d4b7f7c81b3e9dfa… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-04-13 (Wed, 13 Apr 2016) Changed paths: M client/galaxy/scripts/layout/page.js M static/maps/layout/page.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/page.js Log Message: ----------- Merge branch 'release_16.01' into release_16.04 Conflicts: 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 Commit: 4c2bca51171efff42e2852bfa59a91d5acee3e73 https://github.com/galaxyproject/galaxy/commit/4c2bca51171efff42e2852bfa59a… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-04-13 (Wed, 13 Apr 2016) Changed paths: M client/galaxy/scripts/layout/page.js M static/maps/layout/page.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/page.js Log Message: ----------- Merge pull request #2141 from martenson/fix-sideeffect [16.01] fix the value passed to Masthead as options were options.config before Commit: 090e0d33561702b85c82c1bfb228b699c30804ea https://github.com/galaxyproject/galaxy/commit/090e0d33561702b85c82c1bfb228… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-04-13 (Wed, 13 Apr 2016) Log Message: ----------- Merge branch 'release_16.01' into merge01to04 Commit: d5cc3571704d5fe3927d070456f5b934e9f5e1cf https://github.com/galaxyproject/galaxy/commit/d5cc3571704d5fe3927d070456f5… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-13 (Wed, 13 Apr 2016) Changed paths: M client/galaxy/scripts/layout/page.js M static/maps/layout/page.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/page.js Log Message: ----------- Merge pull request #2150 from martenson/merge01to04 [16.04] Merge 16.01 to 16.04 Compare: https://github.com/galaxyproject/galaxy/compare/f03c0375566a...d5cc3571704d

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[galaxyproject/galaxy] 1e3b3a: fix the value passed to Masthead as options were o...
by GitHub 14 Apr '16

14 Apr '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: 1e3b3a15581ecd62e78999f6be9e74d9e7cfbc65 https://github.com/galaxyproject/galaxy/commit/1e3b3a15581ecd62e78999f6be9e… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-04-12 (Tue, 12 Apr 2016) Changed paths: M client/galaxy/scripts/layout/page.js M static/maps/layout/page.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/page.js Log Message: ----------- fix the value passed to Masthead as options were options.config before Commit: 4c2bca51171efff42e2852bfa59a91d5acee3e73 https://github.com/galaxyproject/galaxy/commit/4c2bca51171efff42e2852bfa59a… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-04-13 (Wed, 13 Apr 2016) Changed paths: M client/galaxy/scripts/layout/page.js M static/maps/layout/page.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/page.js Log Message: ----------- Merge pull request #2141 from martenson/fix-sideeffect [16.01] fix the value passed to Masthead as options were options.config before Compare: https://github.com/galaxyproject/galaxy/compare/ad952a4b8d75...4c2bca51171e

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[galaxyproject/infrastructure-playbook] 6094b4: Connecting all the things.
by GitHub 13 Apr '16

13 Apr '16

Branch: refs/heads/stats_role Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 6094b47bdc5785c8be93c7af38f36741f3d65314 https://github.com/galaxyproject/infrastructure-playbook/commit/6094b47bdc5… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-13 (Wed, 13 Apr 2016) Changed paths: M roles/stats/templates/grafana.conf.j2 M roles/stats/templates/telegraf.conf.j2 Log Message: ----------- Connecting all the things.

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[galaxyproject/galaxy] 295859: This should fix bug #1892 in toolshed
by GitHub 13 Apr '16

13 Apr '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 295859968413f4c01c0f2bb401040bd92f3e833a https://github.com/galaxyproject/galaxy/commit/295859968413f4c01c0f2bb40104… Author: nturaga <nitesh.turaga(a)gmail.com> Date: 2016-04-12 (Tue, 12 Apr 2016) Changed paths: M templates/webapps/tool_shed/repository/view_changeset.mako Log Message: ----------- This should fix bug #1892 in toolshed Commit: 90d21d6353d49bdbda4eed449f8374bd0ea92851 https://github.com/galaxyproject/galaxy/commit/90d21d6353d49bdbda4eed449f83… Author: nturaga <nitesh.turaga(a)gmail.com> Date: 2016-04-13 (Wed, 13 Apr 2016) Changed paths: M client/galaxy/style/less/base.less M static/style/blue/base.css M templates/webapps/tool_shed/repository/view_changeset.mako Log Message: ----------- Added class linewrap base.less file Commit: 2c81a648a767f6b03df12d37182be03a3b02c3eb https://github.com/galaxyproject/galaxy/commit/2c81a648a767f6b03df12d37182b… Author: nturaga <nitesh.turaga(a)gmail.com> Date: 2016-04-13 (Wed, 13 Apr 2016) Changed paths: M client/galaxy/style/less/base.less M static/style/blue/base.css M templates/webapps/tool_shed/repository/view_changeset.mako Log Message: ----------- changed class name Commit: d7353d381987df3c1b2364fd74ded5134d1415fc https://github.com/galaxyproject/galaxy/commit/d7353d381987df3c1b2364fd74de… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-13 (Wed, 13 Apr 2016) Changed paths: M client/galaxy/style/less/base.less M static/style/blue/base.css M templates/webapps/tool_shed/repository/view_changeset.mako Log Message: ----------- Merge pull request #2142 from nturaga/fix_1892_toolshed_commit_linebreaks This should fix bug #1892 in toolshed Compare: https://github.com/galaxyproject/galaxy/compare/4797f811a4ef...d7353d381987

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[galaxyproject/galaxy] e5ce5d: try pushing again when we get unexpected exception...
by GitHub 13 Apr '16

13 Apr '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e5ce5dfe33d8a061ed3013be644a2611da4e0f72 https://github.com/galaxyproject/galaxy/commit/e5ce5dfe33d8a061ed3013be644a… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-04-11 (Mon, 11 Apr 2016) Changed paths: M test/shed_functional/base/twilltestcase.py Log Message: ----------- try pushing again when we get unexpected exception... Commit: cd1e1f5e3ef0ffd600a1ad1f26e4026c7fe809da https://github.com/galaxyproject/galaxy/commit/cd1e1f5e3ef0ffd600a1ad1f26e4… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-04-11 (Mon, 11 Apr 2016) Changed paths: M test/shed_functional/base/twilltestcase.py Log Message: ----------- remove unwanted check Commit: 3dc46809c41b89fa39924427a27f81d3c7e44632 https://github.com/galaxyproject/galaxy/commit/3dc46809c41b89fa39924427a27f… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-04-11 (Mon, 11 Apr 2016) Changed paths: M test/shed_functional/base/twilltestcase.py Log Message: ----------- remove unused import Commit: 26a4c137cecbac357a90ed2811268b55a479c35b https://github.com/galaxyproject/galaxy/commit/26a4c137cecbac357a90ed281126… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-04-12 (Tue, 12 Apr 2016) Changed paths: M test/shed_functional/base/twilltestcase.py Log Message: ----------- improve on refactoring of the test Commit: 4797f811a4ef94c846be8b79334f3b20ccfb8109 https://github.com/galaxyproject/galaxy/commit/4797f811a4ef94c846be8b79334f… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-04-13 (Wed, 13 Apr 2016) Changed paths: M test/shed_functional/base/twilltestcase.py Log Message: ----------- Merge pull request #2130 from martenson/try-fix-pushcheck try pushing again when we get unexpected exception... Compare: https://github.com/galaxyproject/galaxy/compare/408827e251f9...4797f811a4ef

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[galaxyproject/infrastructure-playbook] c978f4: Update nginx confs, remove graphite subdomain. i...
by GitHub 13 Apr '16

13 Apr '16

Branch: refs/heads/stats_role Home: https://github.com/galaxyproject/infrastructure-playbook Commit: c978f4625c72f5b95b898d84d6bf76a71b86a12e https://github.com/galaxyproject/infrastructure-playbook/commit/c978f4625c7… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-13 (Wed, 13 Apr 2016) Changed paths: R taccenv/templates/nginx/graphite.j2 M taccenv/templates/nginx/sentry.j2 M taccenv/templates/nginx/stats.j2 Log Message: ----------- Update nginx confs, remove graphite subdomain. is interesting in nginx, it always returns the first server (which was sentry), and http://stats.galaxyproject.org was redirecting to https://sentry.* before this change.

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[galaxyproject/infrastructure-playbook] d0bf01: Configure default user, add vault.
by GitHub 13 Apr '16

13 Apr '16

Branch: refs/heads/stats_role Home: https://github.com/galaxyproject/infrastructure-playbook Commit: d0bf01aa82c6eedbaadd94720a2ac78ab766cd7d https://github.com/galaxyproject/infrastructure-playbook/commit/d0bf01aa82c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-12 (Tue, 12 Apr 2016) Changed paths: M roles/stats/templates/grafana.conf.j2 M taccenv/playbook.yml A taccenv/secret_group_vars/stats.yml Log Message: ----------- Configure default user, add vault.

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[galaxyproject/galaxy]
by GitHub 12 Apr '16

12 Apr '16

Branch: refs/heads/revert-2139-fix-inactivity Home: https://github.com/galaxyproject/galaxy

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[galaxyproject/galaxy] b0ac29: Revert "[16.01] load options from config, not from...
by GitHub 12 Apr '16

12 Apr '16

Branch: refs/heads/revert-2139-fix-inactivity Home: https://github.com/galaxyproject/galaxy Commit: b0ac297536681545637bf5c7a0084a0af907a40b https://github.com/galaxyproject/galaxy/commit/b0ac297536681545637bf5c7a008… Author: carlfeberhard <carlfeberhard(a)users.noreply.github.com> Date: 2016-04-12 (Tue, 12 Apr 2016) Changed paths: M client/galaxy/scripts/layout/page.js M static/maps/layout/page.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/page.js Log Message: ----------- Revert "[16.01] load options from config, not from options"

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[galaxyproject/galaxy] 2ebe94: load options from config, not from options
by GitHub 12 Apr '16

12 Apr '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: 2ebe9405106dfc16504e3b6f775425634bb4691f https://github.com/galaxyproject/galaxy/commit/2ebe9405106dfc16504e3b6f7754… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-04-12 (Tue, 12 Apr 2016) Changed paths: M client/galaxy/scripts/layout/page.js M static/maps/layout/page.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/page.js Log Message: ----------- load options from config, not from options Commit: ad952a4b8d7501d0df48e44d7c966ff22f9a63c4 https://github.com/galaxyproject/galaxy/commit/ad952a4b8d7501d0df48e44d7c96… Author: carlfeberhard <carlfeberhard(a)users.noreply.github.com> Date: 2016-04-12 (Tue, 12 Apr 2016) Changed paths: M client/galaxy/scripts/layout/page.js M static/maps/layout/page.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/page.js Log Message: ----------- Merge pull request #2139 from martenson/fix-inactivity [16.01] load options from config, not from options Compare: https://github.com/galaxyproject/galaxy/compare/fe4afefc42a4...ad952a4b8d75

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[galaxyproject/infrastructure-playbook] d8006e: Basic nginx config for stats.galaxyproject.org
by GitHub 12 Apr '16

12 Apr '16

Branch: refs/heads/stats_role Home: https://github.com/galaxyproject/infrastructure-playbook Commit: d8006eecfab6822ea881bcd5d2d20018e7593992 https://github.com/galaxyproject/infrastructure-playbook/commit/d8006eecfab… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-12 (Tue, 12 Apr 2016) Changed paths: M taccenv/host_vars/galaxy06.tacc.utexas.edu.yml A taccenv/templates/nginx/stats.j2 Log Message: ----------- Basic nginx config for stats.galaxyproject.org

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[galaxyproject/infrastructure-playbook] a98bdd: Influx stack packages.
by GitHub 12 Apr '16

12 Apr '16

Branch: refs/heads/stats_role Home: https://github.com/galaxyproject/infrastructure-playbook Commit: a98bdd24183c8185424265cfa4358dc39880bfd1 https://github.com/galaxyproject/infrastructure-playbook/commit/a98bdd24183… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-12 (Tue, 12 Apr 2016) Changed paths: A roles/stats/defaults/main.yml A roles/stats/tasks/main.yml M taccenv/host_vars/galaxy06.tacc.utexas.edu.yml M taccenv/playbook.yml Log Message: ----------- Influx stack packages. Commit: 4cb6510b3e5278c55278e72f770e0a95256f9c7e https://github.com/galaxyproject/infrastructure-playbook/commit/4cb6510b3e5… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-12 (Tue, 12 Apr 2016) Changed paths: M roles/stats/tasks/main.yml A roles/stats/templates/influxdb.conf.j2 A roles/stats/templates/telegraf.conf.j2 Log Message: ----------- Add stats configs, defaults for now. Commit: 52c4b7f3ac2a14367e6e21bfe4a925651ceb3202 https://github.com/galaxyproject/infrastructure-playbook/commit/52c4b7f3ac2… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-12 (Tue, 12 Apr 2016) Changed paths: M roles/stats/tasks/main.yml A roles/stats/templates/grafana.conf.j2 M taccenv/group_vars/statsservers.yml A taccenv/templates/supervisor/stats.j2 Log Message: ----------- Supervisor configs and more for stats role. Commit: 4bc99b4dfb69263e7895729dbaa3c0a69b46e2c4 https://github.com/galaxyproject/infrastructure-playbook/commit/4bc99b4dfb6… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-12 (Tue, 12 Apr 2016) Changed paths: M roles/stats/tasks/main.yml M roles/stats/templates/grafana.conf.j2 M roles/stats/templates/influxdb.conf.j2 M taccenv/templates/supervisor/stats.j2 Log Message: ----------- Stats startup fixes. Compare: https://github.com/galaxyproject/infrastructure-playbook/compare/a98bdd2418…

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[galaxyproject/galaxy] 84ad9c: Rev Pulsar to 0.7.0.dev3.
by GitHub 12 Apr '16

12 Apr '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 84ad9c2ee2c5cf0420f837405dfbd1893f1d0ed2 https://github.com/galaxyproject/galaxy/commit/84ad9c2ee2c5cf0420f837405dfb… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-04-10 (Sun, 10 Apr 2016) Changed paths: M config/job_conf.xml.sample_advanced M lib/galaxy/dependencies/requirements.txt M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/runners/pulsar.py M test/unit/jobs/test_command_factory.py Log Message: ----------- Rev Pulsar to 0.7.0.dev3. - Fixes numerous problems mostly notably fixes external metadata generation and job metrics collection for recent Pulsar. This was broken when tools were given clean working directory. - Produce a new message if an older Pulsar version is targetted via REST of library (should help with upgrading to Galaxy 16.04). - Newer pulsar lib allows more flexible configuration of managers - update documntation to reflect this. Commit: 27f418c52d685d41646fa6cf932e8144fef63bb5 https://github.com/galaxyproject/galaxy/commit/27f418c52d685d41646fa6cf932e… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-04-11 (Mon, 11 Apr 2016) Changed paths: R install_and_test_tool_shed_repositories.sh R scripts/tool_shed/check_repositories_for_functional_tests.py R scripts/tool_shed/check_tool_dependency_definition_repositories.py Log Message: ----------- Remove scripts which depend on install_and_test_tool_shed_repositories. Commit: a9d675f5e854de8634789fca54bb88c6a9f5de2c https://github.com/galaxyproject/galaxy/commit/a9d675f5e854de8634789fca54bb… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-04-11 (Mon, 11 Apr 2016) Changed paths: M scripts/tool_shed/check_filesystem_for_empty_tool_dependency_installation_paths.py M scripts/tool_shed/check_s3_for_empty_tool_dependency_installation_paths.py M scripts/tool_shed/deprecate_repositories_without_metadata.py M scripts/tool_shed/show_tool_dependency_installation_dir_contents.py Log Message: ----------- Fix sys.path.insert() after #2093. Commit: ceeb01d84e7f510fab39626dec7f7d537a66f2fd https://github.com/galaxyproject/galaxy/commit/ceeb01d84e7f510fab39626dec7f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-04-11 (Mon, 11 Apr 2016) Changed paths: R install_and_test_tool_shed_repositories.sh M scripts/tool_shed/check_filesystem_for_empty_tool_dependency_installation_paths.py R scripts/tool_shed/check_repositories_for_functional_tests.py M scripts/tool_shed/check_s3_for_empty_tool_dependency_installation_paths.py R scripts/tool_shed/check_tool_dependency_definition_repositories.py M scripts/tool_shed/deprecate_repositories_without_metadata.py M scripts/tool_shed/show_tool_dependency_installation_dir_contents.py Log Message: ----------- Merge pull request #2133 from nsoranzo/release_16.04_fix_for_2093 [16.04] Fixes due to #2093 and #2018 Commit: f03c0375566a835b9e75135ba9462ddad1dfeb70 https://github.com/galaxyproject/galaxy/commit/f03c0375566a835b9e75135ba946… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-04-12 (Tue, 12 Apr 2016) Changed paths: M config/job_conf.xml.sample_advanced M lib/galaxy/dependencies/requirements.txt M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/runners/pulsar.py M test/unit/jobs/test_command_factory.py Log Message: ----------- Merge pull request #2122 from jmchilton/pulsar_metadata [16.04] Rev Pulsar to 0.7.0.dev3. Commit: 408827e251f92cdc5b6c794272a6ba2dc1473780 https://github.com/galaxyproject/galaxy/commit/408827e251f92cdc5b6c794272a6… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-04-12 (Tue, 12 Apr 2016) Changed paths: M config/job_conf.xml.sample_advanced R install_and_test_tool_shed_repositories.sh M lib/galaxy/dependencies/requirements.txt M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/runners/pulsar.py M scripts/tool_shed/check_filesystem_for_empty_tool_dependency_installation_paths.py R scripts/tool_shed/check_repositories_for_functional_tests.py M scripts/tool_shed/check_s3_for_empty_tool_dependency_installation_paths.py R scripts/tool_shed/check_tool_dependency_definition_repositories.py M scripts/tool_shed/deprecate_repositories_without_metadata.py M scripts/tool_shed/show_tool_dependency_installation_dir_contents.py M test/unit/jobs/test_command_factory.py Log Message: ----------- Merge branch 'release_16.04' into dev Compare: https://github.com/galaxyproject/galaxy/compare/baf1bd639f17...408827e251f9

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[galaxyproject/galaxy] 84ad9c: Rev Pulsar to 0.7.0.dev3.
by GitHub 12 Apr '16

12 Apr '16

Branch: refs/heads/release_16.04 Home: https://github.com/galaxyproject/galaxy Commit: 84ad9c2ee2c5cf0420f837405dfbd1893f1d0ed2 https://github.com/galaxyproject/galaxy/commit/84ad9c2ee2c5cf0420f837405dfb… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-04-10 (Sun, 10 Apr 2016) Changed paths: M config/job_conf.xml.sample_advanced M lib/galaxy/dependencies/requirements.txt M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/runners/pulsar.py M test/unit/jobs/test_command_factory.py Log Message: ----------- Rev Pulsar to 0.7.0.dev3. - Fixes numerous problems mostly notably fixes external metadata generation and job metrics collection for recent Pulsar. This was broken when tools were given clean working directory. - Produce a new message if an older Pulsar version is targetted via REST of library (should help with upgrading to Galaxy 16.04). - Newer pulsar lib allows more flexible configuration of managers - update documntation to reflect this. Commit: f03c0375566a835b9e75135ba9462ddad1dfeb70 https://github.com/galaxyproject/galaxy/commit/f03c0375566a835b9e75135ba946… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-04-12 (Tue, 12 Apr 2016) Changed paths: M config/job_conf.xml.sample_advanced M lib/galaxy/dependencies/requirements.txt M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/runners/pulsar.py M test/unit/jobs/test_command_factory.py Log Message: ----------- Merge pull request #2122 from jmchilton/pulsar_metadata [16.04] Rev Pulsar to 0.7.0.dev3. Compare: https://github.com/galaxyproject/galaxy/compare/ceeb01d84e7f...f03c0375566a

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[galaxyproject/galaxy] 27f418: Remove scripts which depend on install_and_test_to...
by GitHub 12 Apr '16

12 Apr '16

Branch: refs/heads/release_16.04 Home: https://github.com/galaxyproject/galaxy Commit: 27f418c52d685d41646fa6cf932e8144fef63bb5 https://github.com/galaxyproject/galaxy/commit/27f418c52d685d41646fa6cf932e… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-04-11 (Mon, 11 Apr 2016) Changed paths: R install_and_test_tool_shed_repositories.sh R scripts/tool_shed/check_repositories_for_functional_tests.py R scripts/tool_shed/check_tool_dependency_definition_repositories.py Log Message: ----------- Remove scripts which depend on install_and_test_tool_shed_repositories. Commit: a9d675f5e854de8634789fca54bb88c6a9f5de2c https://github.com/galaxyproject/galaxy/commit/a9d675f5e854de8634789fca54bb… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-04-11 (Mon, 11 Apr 2016) Changed paths: M scripts/tool_shed/check_filesystem_for_empty_tool_dependency_installation_paths.py M scripts/tool_shed/check_s3_for_empty_tool_dependency_installation_paths.py M scripts/tool_shed/deprecate_repositories_without_metadata.py M scripts/tool_shed/show_tool_dependency_installation_dir_contents.py Log Message: ----------- Fix sys.path.insert() after #2093. Commit: ceeb01d84e7f510fab39626dec7f7d537a66f2fd https://github.com/galaxyproject/galaxy/commit/ceeb01d84e7f510fab39626dec7f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-04-11 (Mon, 11 Apr 2016) Changed paths: R install_and_test_tool_shed_repositories.sh M scripts/tool_shed/check_filesystem_for_empty_tool_dependency_installation_paths.py R scripts/tool_shed/check_repositories_for_functional_tests.py M scripts/tool_shed/check_s3_for_empty_tool_dependency_installation_paths.py R scripts/tool_shed/check_tool_dependency_definition_repositories.py M scripts/tool_shed/deprecate_repositories_without_metadata.py M scripts/tool_shed/show_tool_dependency_installation_dir_contents.py Log Message: ----------- Merge pull request #2133 from nsoranzo/release_16.04_fix_for_2093 [16.04] Fixes due to #2093 and #2018 Compare: https://github.com/galaxyproject/galaxy/compare/6317297cad4e...ceeb01d84e7f

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