- galaxy-commits - lists.galaxyproject.org

[galaxyproject/usegalaxy-playbook] cbbbc2: update MTS and TTS
by GitHub 18 Mar '16

18 Mar '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: cbbbc2025f418bf83dfc21931faa6958339fda3f https://github.com/galaxyproject/usegalaxy-playbook/commit/cbbbc2025f418bf8… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-18 (Fri, 18 Mar 2016) Changed paths: M production/group_vars/toolshedservers.yml M stage/group_vars/toolshedservers.yml Log Message: ----------- update MTS and TTS

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[galaxyproject/usegalaxy-playbook] ec3aba: things that showed up after updating Galaxy's vers...
by GitHub 18 Mar '16

18 Mar '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: ec3abaa9fee94c4a852f3eb14acea2483b0f03ab https://github.com/galaxyproject/usegalaxy-playbook/commit/ec3abaa9fee94c4a… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-18 (Fri, 18 Mar 2016) Changed paths: M production/files/interactive_environments/plugins/.ansible_ie_role_current_version M production/files/interactive_environments/proxy/.ansible_ie_role_current_version Log Message: ----------- things that showed up after updating Galaxy's version

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[galaxyproject/usegalaxy-playbook] c78ef2: install deeptools; update Main to latest 16.01
by GitHub 18 Mar '16

18 Mar '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: c78ef2fec723ea8784b5c2ea9a63c714a1167e63 https://github.com/galaxyproject/usegalaxy-playbook/commit/c78ef2fec723ea87… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-18 (Fri, 18 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: ----------- install deeptools; update Main to latest 16.01 Please enter the commit message for your changes. Lines starting

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[galaxyproject/galaxy] 29c78e: Fix virtualenv broken with #1847.
by GitHub 18 Mar '16

18 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 29c78e984e52ac08b1b36a03e39b65c6edbe6200 https://github.com/galaxyproject/galaxy/commit/29c78e984e52ac08b1b36a03e39b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-08 (Tue, 08 Mar 2016) Changed paths: M run_reports.sh M run_tool_shed.sh Log Message: ----------- Fix virtualenv broken with #1847. Commit: 5824bc04af9270afbebcb2c8f9b6b3bea371b788 https://github.com/galaxyproject/galaxy/commit/5824bc04af9270afbebcb2c8f9b6… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-08 (Tue, 08 Mar 2016) Changed paths: M run_reports.sh M run_tool_shed.sh Log Message: ----------- Fix duplicate print statement reported by @dannon... https://github.com/galaxyproject/galaxy/pull/1890#issuecomment-193873380 Commit: 438661e8945c1bb317f75dabe3db429ea779255d https://github.com/galaxyproject/galaxy/commit/438661e8945c1bb317f75dabe3db… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-10 (Thu, 10 Mar 2016) Changed paths: M run_reports.sh M run_tool_shed.sh Log Message: ----------- Another fix for virtualenv fixes. Commit: 00a7c3af057c0689a53748802740bc2002df375c https://github.com/galaxyproject/galaxy/commit/00a7c3af057c0689a53748802740… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-03-15 (Tue, 15 Mar 2016) Changed paths: M run_reports.sh M run_tool_shed.sh Log Message: ----------- Merge pull request #1890 from jmchilton/fix_virtualenvs [16.01] Fix virtual env handling broken with #1847. Commit: f277f99aed411fede7d1cb91d3177469922a58ae https://github.com/galaxyproject/galaxy/commit/f277f99aed411fede7d1cb91d317… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-17 (Thu, 17 Mar 2016) Changed paths: M lib/galaxy/util/log/fluent_log.py Log Message: ----------- Fix handling of time in fluent logger. Commit: 87bcb5f5a1b6801e948b2cc0f5dc676c7faca682 https://github.com/galaxyproject/galaxy/commit/87bcb5f5a1b6801e948b2cc0f5dc… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-17 (Thu, 17 Mar 2016) Changed paths: M lib/galaxy/util/log/fluent_log.py Log Message: ----------- Fix in a different way not requiring signature change; still not thrilled about overlapping kwarg names w/ stdlib module names. Commit: c8e48bfaccb5d10552df4200e616a9eee49206b0 https://github.com/galaxyproject/galaxy/commit/c8e48bfaccb5d10552df4200e616… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-17 (Thu, 17 Mar 2016) Changed paths: M config/galaxy.ini.sample Log Message: ----------- Add fluentd configuration to galaxy.ini.sample Commit: 98c65dcee08338ea80a7e34251f8fa4ed6bd8dd5 https://github.com/galaxyproject/galaxy/commit/98c65dcee08338ea80a7e34251f8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-17 (Thu, 17 Mar 2016) Changed paths: M lib/galaxy/util/log/fluent_log.py M lib/galaxy/webapps/galaxy/api/metrics.py Log Message: ----------- Swap back to the first fix, update metrics api to use new signature. Commit: 19bf334c7763c2418408083b9a7369386e50ad66 https://github.com/galaxyproject/galaxy/commit/19bf334c7763c2418408083b9a73… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-03-18 (Fri, 18 Mar 2016) Changed paths: M config/galaxy.ini.sample M lib/galaxy/util/log/fluent_log.py M lib/galaxy/webapps/galaxy/api/metrics.py Log Message: ----------- Merge pull request #1945 from dannon/fluent_logging_fix [16.01] Fix handling of time in fluent logger Commit: 53daf30dd284004c7e0b85ce8dbe6daf94622ef1 https://github.com/galaxyproject/galaxy/commit/53daf30dd284004c7e0b85ce8dbe… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-18 (Fri, 18 Mar 2016) Changed paths: M config/galaxy.ini.sample M lib/galaxy/util/log/fluent_log.py M lib/galaxy/webapps/galaxy/api/metrics.py M run_reports.sh M run_tool_shed.sh Log Message: ----------- Merge branch 'release_16.01' into dev Compare: https://github.com/galaxyproject/galaxy/compare/6fff01c01c59...53daf30dd284

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[galaxyproject/infrastructure-playbook] b55fdb: Add celery beat for sentry, should be the last pie...
by GitHub 18 Mar '16

18 Mar '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: b55fdbafe09e758a51466cf633f016ebab820039 https://github.com/galaxyproject/infrastructure-playbook/commit/b55fdbafe09… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-18 (Fri, 18 Mar 2016) Changed paths: M taccenv/templates/supervisor/sentry.j2 Log Message: ----------- Add celery beat for sentry, should be the last piece of the puzzle.

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[galaxyproject/usegalaxy-playbook] b3de5c: update Test mutable configs and common_roles subre...
by GitHub 18 Mar '16

18 Mar '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: b3de5c2b03848640a2cbf3210faf165be774a720 https://github.com/galaxyproject/usegalaxy-playbook/commit/b3de5c2b03848640… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-18 (Fri, 18 Mar 2016) Changed paths: M common_roles M files/galaxy/test.galaxyproject.org/var/integrated_tool_panel.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: ----------- update Test mutable configs and common_roles subrepo that has not been committed

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[galaxyproject/usegalaxy-playbook] 3daa3e: Update sentry DSNs for main/test/shed/testshed
by GitHub 18 Mar '16

18 Mar '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 3daa3eca9dd8f7c5917273c499be973bfa344ba6 https://github.com/galaxyproject/usegalaxy-playbook/commit/3daa3eca9dd8f7c5… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-18 (Fri, 18 Mar 2016) Changed paths: M production/secret_vars/galaxyservers.yml M production/secret_vars/toolshedservers.yml M stage/secret_vars/galaxyservers.yml M stage/secret_vars/toolshedservers.yml Log Message: ----------- Update sentry DSNs for main/test/shed/testshed

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[galaxyproject/infrastructure-playbook] 96fd80: Add sentry_memcached to sentry group.
by GitHub 18 Mar '16

18 Mar '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 96fd80d84b739176bd6888aaffb55f8dc084b183 https://github.com/galaxyproject/infrastructure-playbook/commit/96fd80d84b7… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-18 (Fri, 18 Mar 2016) Changed paths: M taccenv/templates/supervisor/sentry.j2 Log Message: ----------- Add sentry_memcached to sentry group.

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[galaxyproject/infrastructure-playbook] 0f91b8: Enable and start memcached on statsservers
by GitHub 18 Mar '16

18 Mar '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 0f91b8b9e33a229423252d6aed2ea6cd692afc85 https://github.com/galaxyproject/infrastructure-playbook/commit/0f91b8b9e33… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-18 (Fri, 18 Mar 2016) Changed paths: M roles/sentry/tasks/main.yml Log Message: ----------- Enable and start memcached on statsservers Commit: dede2824ad219409ab4210d6ab32390754549171 https://github.com/galaxyproject/infrastructure-playbook/commit/dede2824ad2… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-18 (Fri, 18 Mar 2016) Changed paths: M roles/sentry/tasks/main.yml M taccenv/templates/supervisor/sentry.j2 Log Message: ----------- Use supervisor instead of systemd Compare: https://github.com/galaxyproject/infrastructure-playbook/compare/51f6f60c38…

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[galaxyproject/galaxy] 89e6a3: Add IUC as a new default bioconda channel
by GitHub 18 Mar '16

18 Mar '16

Branch: refs/heads/iuc_default_conda_channel Home: https://github.com/galaxyproject/galaxy Commit: 89e6a37d43d85ffd46a786e689e5b2fdc6a6c4ae https://github.com/galaxyproject/galaxy/commit/89e6a37d43d85ffd46a786e689e5… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-03-18 (Fri, 18 Mar 2016) Changed paths: M config/galaxy.ini.sample Log Message: ----------- Add IUC as a new default bioconda channel

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