June 2015 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/usegalaxy-playbook] dd5a3d: Mutable configs on Test
by GitHub 30 Jun '15

30 Jun '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: dd5a3d875929db5ef6a7bc4e6eec253cec9bc5ae https://github.com/galaxyproject/usegalaxy-playbook/commit/dd5a3d875929db5e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-06-30 (Tue, 30 Jun 2015) Changed paths: 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: ----------- Mutable configs on Test Commit: c541b05c16d4a4cb74bce17a87c6ae3a91b58c1e https://github.com/galaxyproject/usegalaxy-playbook/commit/c541b05c16d4a4cb… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-06-30 (Tue, 30 Jun 2015) Changed paths: M production/group_vars/galaxyservers.yml M stage/group_vars/galaxyservers.yml Log Message: ----------- Decrease max metadata cutoff to 1MB. Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/26e22e0e08e6...…

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[galaxyproject/usegalaxy-playbook] 26e22e: update TTS
by GitHub 25 Jun '15

25 Jun '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 26e22e0e08e63a5da5258fa0a304fe9d455aa665 https://github.com/galaxyproject/usegalaxy-playbook/commit/26e22e0e08e63a5d… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-06-25 (Thu, 25 Jun 2015) Changed paths: M stage/group_vars/toolshedservers.yml Log Message: ----------- update TTS

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[galaxyproject/usegalaxy-playbook] a2b23d: Increase standard deviations for punting tophat jo...
by GitHub 23 Jun '15

23 Jun '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: a2b23df2bd162d25937c8bd654790717100adb8c https://github.com/galaxyproject/usegalaxy-playbook/commit/a2b23df2bd162d25… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-06-23 (Tue, 23 Jun 2015) Changed paths: M files/galaxy/common/dynamic_rules/multi_dynamic_walltime.py Log Message: ----------- Increase standard deviations for punting tophat jobs.

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[galaxyproject/usegalaxy-playbook] 890009: reorder rna structure prediction section on Main a...
by GitHub 22 Jun '15

22 Jun '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 8900091a60d8413494688093397d5fc455cc6059 https://github.com/galaxyproject/usegalaxy-playbook/commit/8900091a60d84134… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-06-22 (Mon, 22 Jun 2015) Changed paths: M files/galaxy/usegalaxy.org/var/integrated_tool_panel.xml Log Message: ----------- reorder rna structure prediction section on Main as requested by nekrut

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[galaxyproject/usegalaxy-playbook] f57e0a: Additional things for PostgreSQL @ TACC, except no...
by GitHub 16 Jun '15

16 Jun '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: f57e0a2f6b8685338827d9582310052afb2b68e7 https://github.com/galaxyproject/usegalaxy-playbook/commit/f57e0a2f6b868533… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-06-16 (Tue, 16 Jun 2015) Changed paths: M common/group_vars/redhat_dbservers.yml M common/host_vars/galaxy-db-01.tacc.utexas.edu.yml M common/host_vars/galaxy01.tacc.utexas.edu.yml M common/host_vars/galaxy05.tacc.utexas.edu.yml M common/inventory M common_infrastructure.yml Log Message: ----------- Additional things for PostgreSQL @ TACC, except none of this actually works at the moment because 9.2 doesn't support include_dir. Note to self: upgrade to 9.4 on Monday.

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[galaxyproject/usegalaxy-playbook] dc73ae: Return 302 from http://galaxyproject.org rather th...
by GitHub 16 Jun '15

16 Jun '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: dc73ae97ee71dc1b4b0951f10c06d4e54bf2172f https://github.com/galaxyproject/usegalaxy-playbook/commit/dc73ae97ee71dc1b… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-06-16 (Tue, 16 Jun 2015) Changed paths: M templates/nginx/galaxyproject.j2 Log Message: ----------- Return 302 from http://galaxyproject.org rather than 307. Commit: 187e641178bff364fc439e6bb90b87841c338acd https://github.com/galaxyproject/usegalaxy-playbook/commit/187e641178bff364… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-06-16 (Tue, 16 Jun 2015) Changed paths: A common/group_vars/redhat_dbservers.yml A common/host_vars/galaxy-db-01.tacc.utexas.edu.yml A common/host_vars/galaxy01.tacc.utexas.edu.yml A common/host_vars/galaxy05.tacc.utexas.edu.yml M common/host_vars/radegast.galaxyproject.org.yml M common_infrastructure.yml A roles/cron/defaults/main.yml A roles/cron/tasks/main.yml M roles/galaxyprojectdotorg.postgresql/defaults/main.yml M roles/galaxyprojectdotorg.postgresql/templates/archive_wal.sh.j2 M roles/galaxyprojectdotorg.postgresql/templates/scheduled_backup.sh.j2 Log Message: ----------- 1. Update the postgresql role 2. Disable PostgreSQL backup rotation on radegast (using snapshots) 3. Move Galaxy/TACC db server configs to this playbook 4. Add a generic "cron" role for scheduling cron jobs 5. Schedule Test/Main toolshed data backups to westvleteren See https://github.com/natefoo/smf-smartos/tree/westvleteren for the snapshotting side of the backup process. Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/350a6e56969c...…

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[galaxyproject/usegalaxy-playbook] 350a6e: update TTS
by GitHub 16 Jun '15

16 Jun '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 350a6e56969ca7f4a22da3c2aaaf9c616db8e9c2 https://github.com/galaxyproject/usegalaxy-playbook/commit/350a6e56969ca7f4… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-06-16 (Tue, 16 Jun 2015) Changed paths: M stage/group_vars/toolshedservers.yml Log Message: ----------- update TTS

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[galaxyproject/usegalaxy-playbook] 157e12: Update Main and enable metadata truncation.
by GitHub 16 Jun '15

16 Jun '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 157e12cc2cdcca5f94fdc701032ef4e2c901f865 https://github.com/galaxyproject/usegalaxy-playbook/commit/157e12cc2cdcca5f… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-06-16 (Tue, 16 Jun 2015) Changed paths: M production/group_vars/all.yml M production/group_vars/galaxyservers.yml Log Message: ----------- Update Main and enable metadata truncation.

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[galaxyproject/usegalaxy-playbook] e5c555: Update Test
by GitHub 16 Jun '15

16 Jun '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: e5c55593055ac2df7d02bac5f382c4fd95094f39 https://github.com/galaxyproject/usegalaxy-playbook/commit/e5c55593055ac2df… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-06-16 (Tue, 16 Jun 2015) Changed paths: 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 M stage/group_vars/all.yml M stage/group_vars/galaxyservers.yml Log Message: ----------- Update Test

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[galaxyproject/usegalaxy-playbook] 2c8739: Switch Test to uWSGI Pasteless mode.
by GitHub 10 Jun '15

10 Jun '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 2c8739a8aff5f72584b16a76ba657e7390f0b640 https://github.com/galaxyproject/usegalaxy-playbook/commit/2c8739a8aff5f725… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-06-10 (Wed, 10 Jun 2015) Changed paths: M stage/group_vars/all.yml M stage/group_vars/galaxyservers.yml A templates/galaxy/test.galaxyproject.org/config/uwsgi.ini.j2 M templates/supervisor/galaxy.conf.j2 Log Message: ----------- Switch Test to uWSGI Pasteless mode. Commit: 041d017dc795df86ebad15bb4d11dc1ec2fad641 https://github.com/galaxyproject/usegalaxy-playbook/commit/041d017dc795df86… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-06-10 (Wed, 10 Jun 2015) Changed paths: 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 Log Message: ----------- Mutable configs on Test (+GATK) Commit: d73fa75178e3a9f794cc25c27f67ddf2660a351e https://github.com/galaxyproject/usegalaxy-playbook/commit/d73fa75178e3a9f7… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-06-10 (Wed, 10 Jun 2015) Changed paths: M files/galaxy/common/dynamic_rules/multi_dynamic_walltime.py M files/galaxy/common/dynamic_rules/reserved.py Log Message: ----------- Handle when user_email is None (anon jobs) in dynamic rules. Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/664d38a60d87...…

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