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

[galaxyproject/usegalaxy-playbook] e457cb: Fix boolean usage in nvc dynamic rule
by GitHub 20 Mar '15

20 Mar '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: e457cb9598045ed3398f0bd6911902d01ce44376 https://github.com/galaxyproject/usegalaxy-playbook/commit/e457cb9598045ed3… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-03-20 (Fri, 20 Mar 2015) Changed paths: M files/galaxy/test.galaxyproject.org/dynamic_rules/nvc_dynamic_memory.py Log Message: ----------- Fix boolean usage in nvc dynamic rule

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[galaxyproject/usegalaxy-playbook] 1dfeee: Put NVC jobs in the normal partition until >16GB i...
by GitHub 19 Mar '15

19 Mar '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 1dfeee4c35ad4e43fe1d71b199e905ed925b63c9 https://github.com/galaxyproject/usegalaxy-playbook/commit/1dfeee4c35ad4e43… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-03-19 (Thu, 19 Mar 2015) Changed paths: M files/galaxy/test.galaxyproject.org/dynamic_rules/nvc_dynamic_memory.py Log Message: ----------- Put NVC jobs in the normal partition until >16GB is required Commit: 2cdb32387197ef7ca691c02b2b6fc332de8b3088 https://github.com/galaxyproject/usegalaxy-playbook/commit/2cdb32387197ef7c… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-03-19 (Thu, 19 Mar 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 Log Message: ----------- Updated mutable configs on Test Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/ffb2e3ac2663...…

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[galaxyproject/usegalaxy-playbook] ffb2e3: Dynamic rule for naive variant caller
by GitHub 19 Mar '15

19 Mar '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: ffb2e3ac266319b708524da4e6e8b3754cb9d3c7 https://github.com/galaxyproject/usegalaxy-playbook/commit/ffb2e3ac266319b7… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-03-19 (Thu, 19 Mar 2015) Changed paths: A files/galaxy/test.galaxyproject.org/dynamic_rules/nvc_dynamic_memory.py M stage/group_vars/galaxyservers.yml M templates/galaxy/test.galaxyproject.org/config/job_conf.xml.j2 Log Message: ----------- Dynamic rule for naive variant caller

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[galaxyproject/usegalaxy-playbook] 776199: Separate playbook that only manages configs, for s...
by GitHub 19 Mar '15

19 Mar '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 7761998fa0b949e741b43d324d0e18322af5dc05 https://github.com/galaxyproject/usegalaxy-playbook/commit/7761998fa0b949e7… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-03-19 (Thu, 19 Mar 2015) Changed paths: M galaxy.yml A galaxy_configs.yml A roles/usegalaxy/defaults Log Message: ----------- Separate playbook that only manages configs, for speed.

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[galaxyproject/usegalaxy-playbook] c748a0: Increase memory for Picard SortSam
by GitHub 19 Mar '15

19 Mar '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: c748a0aa7f6e7d57d1c2d37c93856dbb7c4866e8 https://github.com/galaxyproject/usegalaxy-playbook/commit/c748a0aa7f6e7d57… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-03-19 (Thu, 19 Mar 2015) 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: ----------- Increase memory for Picard SortSam

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[galaxyproject/usegalaxy-playbook] 6e13fe: Additional Blacklight resource selector stuff
by GitHub 19 Mar '15

19 Mar '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 6e13fe811edcaffbf1ea6f0c0983584d96653993 https://github.com/galaxyproject/usegalaxy-playbook/commit/6e13fe811edcaffb… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-03-19 (Thu, 19 Mar 2015) Changed paths: M files/galaxy/test.galaxyproject.org/config/job_resource_params_conf.xml M files/galaxy/test.galaxyproject.org/config/tool_conf.xml M files/galaxy/test.galaxyproject.org/dynamic_rules/blacklight_select.py M templates/galaxy/test.galaxyproject.org/config/job_conf.xml.j2 Log Message: ----------- Additional Blacklight resource selector stuff Commit: c397b1a024b0582972e7d34d2a33242941fa1210 https://github.com/galaxyproject/usegalaxy-playbook/commit/c397b1a024b05829… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-03-19 (Thu, 19 Mar 2015) Changed paths: M roles/galaxyprojectdotorg.pulsar/defaults/main.yml M roles/galaxyprojectdotorg.pulsar/templates/server.ini.j2 Log Message: ----------- Allow setup of dependency_resolvers_conf in pulsar role Commit: af5f1e0f674d779707cdcb370fd324d433dbf028 https://github.com/galaxyproject/usegalaxy-playbook/commit/af5f1e0f674d7797… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-03-19 (Thu, 19 Mar 2015) Changed paths: M stage/host_vars/login5.stampede.tacc.utexas.edu.yml M stage/host_vars/tg-login2.blacklight.psc.xsede.org.yml Log Message: ----------- More sensible retry options for pulsar Commit: 596ba8fe8d0001da6f5181071c18f57bc68d5f30 https://github.com/galaxyproject/usegalaxy-playbook/commit/596ba8fe8d0001da… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-03-19 (Thu, 19 Mar 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 Log Message: ----------- Mutable configs on Test (new assembly tools) Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/21a079f166e5...…

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[galaxyproject/usegalaxy-playbook] 21a079: Dropped Beer-lab (sadly!) and GalaxyIsHiring slide...
by GitHub 19 Mar '15

19 Mar '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 21a079f166e521dc17ec606bd92a193bb98719aa https://github.com/galaxyproject/usegalaxy-playbook/commit/21a079f166e521dc… Author: Dave Clements <clements(a)Clements-Galaxy.local> Date: 2015-03-19 (Thu, 19 Mar 2015) Changed paths: A files/galaxy/common/static/welcome_img/GCC2015AbstractsOpen.png A files/galaxy/common/static/welcome_img/WST2015.png M templates/galaxy/common/static/welcome.html.j2 Log Message: ----------- Dropped Beer-lab (sadly!) and GalaxyIsHiring slides, and added Tokyo worshop and GCC2015 Abstract submission.k

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[galaxyproject/usegalaxy-playbook] 8e190f: Forgot to have it actually install the dynamic rul...
by GitHub 19 Mar '15

19 Mar '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 8e190faade7fce536aa0caba45628a9bb3aa1db7 https://github.com/galaxyproject/usegalaxy-playbook/commit/8e190faade7fce53… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-03-19 (Thu, 19 Mar 2015) Changed paths: M stage/group_vars/galaxyservers.yml Log Message: ----------- Forgot to have it actually install the dynamic rule

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[galaxyproject/usegalaxy-playbook] 67ceb4: Resource selector for Blacklight
by GitHub 19 Mar '15

19 Mar '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 67ceb45f5af8791e416dc002ab98ab0c074c85df https://github.com/galaxyproject/usegalaxy-playbook/commit/67ceb45f5af8791e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-03-19 (Thu, 19 Mar 2015) Changed paths: M files/galaxy/test.galaxyproject.org/config/job_resource_params_conf.xml A files/galaxy/test.galaxyproject.org/dynamic_rules/blacklight_select.py M templates/galaxy/test.galaxyproject.org/config/job_conf.xml.j2 Log Message: ----------- Resource selector for Blacklight

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[galaxyproject/usegalaxy-playbook] 372865: Purge the module env prior to running Blacklight j...
by GitHub 19 Mar '15

19 Mar '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 372865d98b9cdf125f6eb2425768f7e33ee7e6c3 https://github.com/galaxyproject/usegalaxy-playbook/commit/372865d98b9cdf12… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-03-19 (Thu, 19 Mar 2015) Changed paths: M files/galaxy/test.galaxyproject.org/var/integrated_tool_panel.xml M templates/galaxy/test.galaxyproject.org/config/job_conf.xml.j2 Log Message: ----------- Purge the module env prior to running Blacklight jobs or else stuff will be output to stderr.

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