- galaxy-commits - lists.galaxyproject.org

[galaxyproject/usegalaxy-playbook] 33423b: Increase Blacklight limits
by GitHub 11 May '15

11 May '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 33423b2892b85ad26a47dc2c8a111de81ec7073c https://github.com/galaxyproject/usegalaxy-playbook/commit/33423b2892b85ad2… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-05-11 (Mon, 11 May 2015) Changed paths: M templates/galaxy/test.galaxyproject.org/config/job_conf.xml.j2 Log Message: ----------- Increase Blacklight limits

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[galaxyproject/usegalaxy-playbook] 90b594: Fix Pulsar staging dir on Blacklight
by GitHub 11 May '15

11 May '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 90b594b528134c302c6b821f8e2c4a411b3a911f https://github.com/galaxyproject/usegalaxy-playbook/commit/90b594b528134c30… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-05-11 (Mon, 11 May 2015) Changed paths: M stage/group_vars/pulsarservers.yml M stage/host_vars/login5.stampede.tacc.utexas.edu.yml M stage/host_vars/tg-login2.blacklight.psc.xsede.org.yml Log Message: ----------- Fix Pulsar staging dir on Blacklight

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[galaxyproject/usegalaxy-playbook] 15eaad: Pulsar and Galaxy updates from last week that I ap...
by GitHub 11 May '15

11 May '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 15eaadf63093a98e53a644b79b544f10ff5c6d1f https://github.com/galaxyproject/usegalaxy-playbook/commit/15eaadf63093a98e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-05-11 (Mon, 11 May 2015) Changed paths: M files/galaxy/test.galaxyproject.org/config/pulsar_stampede_actions.yml M files/galaxy/usegalaxy.org/config/pulsar_stampede_actions.yml M production/group_vars/all.yml M production/group_vars/pulsarservers.yml M stage/group_vars/all.yml M stage/group_vars/pulsarservers.yml Log Message: ----------- Pulsar and Galaxy updates from last week that I apparently forgot to commit.

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[galaxyproject/usegalaxy-playbook] 9937cf: Update Pulsar again due to facepalm.
by GitHub 06 May '15

06 May '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 9937cfa38cef566b743ccf14a3cd48e99a77a43b https://github.com/galaxyproject/usegalaxy-playbook/commit/9937cfa38cef566b… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-05-06 (Wed, 06 May 2015) Changed paths: M production/group_vars/pulsarservers.yml M stage/group_vars/pulsarservers.yml Log Message: ----------- Update Pulsar again due to facepalm.

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[galaxyproject/usegalaxy-playbook] f4c560: Don't stage in tohat_out for resubmit jobs either
by GitHub 06 May '15

06 May '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: f4c56005cfbb9416bc47e8ff84733f80d28aaa1c https://github.com/galaxyproject/usegalaxy-playbook/commit/f4c56005cfbb9416… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-05-06 (Wed, 06 May 2015) Changed paths: M files/galaxy/test.galaxyproject.org/config/pulsar_stampede_actions.yml M files/galaxy/usegalaxy.org/config/pulsar_stampede_actions.yml Log Message: ----------- Don't stage in tohat_out for resubmit jobs either

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[galaxyproject/usegalaxy-playbook] 0c2858: Update Pulsar
by GitHub 06 May '15

06 May '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 0c2858c5dcc2a203da560112302096eefe6aa836 https://github.com/galaxyproject/usegalaxy-playbook/commit/0c2858c5dcc2a203… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-05-06 (Wed, 06 May 2015) Changed paths: M production/group_vars/pulsarservers.yml M stage/group_vars/pulsarservers.yml Log Message: ----------- Update Pulsar

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[galaxyproject/usegalaxy-playbook] 28bdd6: update MTS, enable sentry
by GitHub 06 May '15

06 May '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 28bdd6d4314c90f59332e1d847c842875bf960e5 https://github.com/galaxyproject/usegalaxy-playbook/commit/28bdd6d4314c90f5… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-05-06 (Wed, 06 May 2015) Changed paths: M production/group_vars/toolshedservers.yml Log Message: ----------- update MTS, enable sentry

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[galaxyproject/usegalaxy-playbook] 02483b: update TTS
by GitHub 06 May '15

06 May '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 02483b37f869a92b4eb21c2dac839689372e1081 https://github.com/galaxyproject/usegalaxy-playbook/commit/02483b37f869a92b… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-05-06 (Wed, 06 May 2015) Changed paths: M stage/group_vars/toolshedservers.yml Log Message: ----------- update TTS

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[galaxyproject/usegalaxy-playbook] 65b219: Mutable configs
by GitHub 06 May '15

06 May '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 65b219a203ed2ff472a28e5ed1a36855c8a97cd2 https://github.com/galaxyproject/usegalaxy-playbook/commit/65b219a203ed2ff4… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-05-06 (Wed, 06 May 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_data_table_conf.xml Log Message: ----------- Mutable configs Commit: 0833888e305616865b968c1d984a21cdba4cf1f5 https://github.com/galaxyproject/usegalaxy-playbook/commit/0833888e30561686… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-05-06 (Wed, 06 May 2015) Changed paths: M files/galaxy/test.galaxyproject.org/config/pulsar_stampede_actions.yml M files/galaxy/usegalaxy.org/config/pulsar_stampede_actions.yml Log Message: ----------- Don't stage ref.fai as used by cufflinks, this is a hack until job working directories are cleaned prior to resubmission. Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/ddcb44e2f4bb...…

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[galaxyproject/usegalaxy-playbook] ee3bf0: Add destination for kraken.
by GitHub 06 May '15

06 May '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: ee3bf0febd95b2ecd2a3d284798e9510efa7a5ec https://github.com/galaxyproject/usegalaxy-playbook/commit/ee3bf0febd95b2ec… Author: Dave B. <dave(a)bx.psu.edu> Date: 2015-05-06 (Wed, 06 May 2015) Changed paths: M templates/galaxy/test.galaxyproject.org/config/job_conf.xml.j2 Log Message: ----------- Add destination for kraken. Commit: ddcb44e2f4bba0b064ecb2624cde2b585108b291 https://github.com/galaxyproject/usegalaxy-playbook/commit/ddcb44e2f4bba0b0… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-05-06 (Wed, 06 May 2015) Changed paths: M templates/galaxy/test.galaxyproject.org/config/job_conf.xml.j2 Log Message: ----------- Merge pull request #3 from davebx/slurm_multi_highmem Add destination for kraken. Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/029d714a41a6...…

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[galaxyproject/usegalaxy-playbook] 029d71: Add missing dynamic stampede select destination.
by GitHub 05 May '15

05 May '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 029d714a41a6e2fbcb049419d901b5c79b159184 https://github.com/galaxyproject/usegalaxy-playbook/commit/029d714a41a6e2fb… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-05-05 (Tue, 05 May 2015) Changed paths: M templates/galaxy/usegalaxy.org/config/job_conf.xml.j2 Log Message: ----------- Add missing dynamic stampede select destination.

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[galaxyproject/usegalaxy-playbook] 3e69f8: Update Pulsar
by GitHub 05 May '15

05 May '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 3e69f8f00e70debb72029575abab2684ac9df14d https://github.com/galaxyproject/usegalaxy-playbook/commit/3e69f8f00e70debb… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-05-05 (Tue, 05 May 2015) Changed paths: M production/group_vars/pulsarservers.yml M stage/group_vars/pulsarservers.yml Log Message: ----------- Update Pulsar

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[galaxyproject/usegalaxy-playbook] fddf32: Mutable configs
by GitHub 05 May '15

05 May '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: fddf32f32811ad5d63e6de8b55b1f6b08039cc9f https://github.com/galaxyproject/usegalaxy-playbook/commit/fddf32f32811ad5d… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-05-05 (Tue, 05 May 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/usegalaxy.org/var/integrated_tool_panel.xml Log Message: ----------- Mutable configs Commit: 0516b2c7f399fa3d8daa3573e95ff0378860f837 https://github.com/galaxyproject/usegalaxy-playbook/commit/0516b2c7f399fa3d… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-05-05 (Tue, 05 May 2015) Changed paths: M production/group_vars/pulsarservers.yml M stage/group_vars/pulsarservers.yml M templates/galaxy/test.galaxyproject.org/config/job_conf.xml.j2 M templates/galaxy/usegalaxy.org/config/job_conf.xml.j2 Log Message: ----------- Move Pulsar staging dir to Stampede's /scratch filesystem due to quota on /work (and that's what /scratch is for anyway). Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/6fc059990c68...…

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[galaxyproject/usegalaxy-playbook] 03edc6: Same as the last commit but for Main.
by GitHub 04 May '15

04 May '15

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[galaxyproject/usegalaxy-playbook] 474292: 1. Don't set metadata remotely for nagios jobs on ...
by GitHub 01 May '15

01 May '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 4742927e590abae520ced4660e42a107865b8289 https://github.com/galaxyproject/usegalaxy-playbook/commit/4742927e590abae5… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-05-01 (Fri, 01 May 2015) Changed paths: M files/galaxy/test.galaxyproject.org/config/nagios_tool_conf.xml M files/galaxy/test.galaxyproject.org/nagios/echo_test_blacklight.xml A files/galaxy/test.galaxyproject.org/nagios/echo_test_cluster.xml M files/galaxy/test.galaxyproject.org/nagios/echo_test_handler0.xml M files/galaxy/test.galaxyproject.org/nagios/echo_test_handler1.xml M files/galaxy/test.galaxyproject.org/nagios/echo_test_stampede.xml M stage/group_vars/galaxyservers.yml M templates/galaxy/test.galaxyproject.org/config/job_conf.xml.j2 Log Message: ----------- 1. Don't set metadata remotely for nagios jobs on Pulsar servers 2. Only submit 1 job for testing the cluster instead of 1 per handler. Test handlers individually using the local runner.

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[galaxyproject/usegalaxy-playbook] 470050: Mutable config on Test
by GitHub 01 May '15

01 May '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 470050bad9e83f28eae91970bc04a54d0547e563 https://github.com/galaxyproject/usegalaxy-playbook/commit/470050bad9e83f28… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-05-01 (Fri, 01 May 2015) Changed paths: M files/galaxy/test.galaxyproject.org/var/shed_data_manager_conf.xml Log Message: ----------- Mutable config on Test Commit: 27ebbdea4a253e47ee572903e647226ae3fd88aa https://github.com/galaxyproject/usegalaxy-playbook/commit/27ebbdea4a253e47… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-05-01 (Fri, 01 May 2015) Changed paths: M production/group_vars/all.yml Log Message: ----------- Update Main Commit: 28f33e511381d58a1afbd9f3ad6248360602b193 https://github.com/galaxyproject/usegalaxy-playbook/commit/28f33e511381d58a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-05-01 (Fri, 01 May 2015) Changed paths: M files/galaxy/usegalaxy.org/var/integrated_tool_panel.xml M files/galaxy/usegalaxy.org/var/shed_tool_conf.xml Log Message: ----------- Mutable configs on Main Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/5e3f68afc8fa...…

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[galaxyproject/usegalaxy-playbook] 5e3f68: Update Test
by GitHub 01 May '15

01 May '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 5e3f68afc8fa8a91bca48e0bd8c248dfe4fc28eb https://github.com/galaxyproject/usegalaxy-playbook/commit/5e3f68afc8fa8a91… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-05-01 (Fri, 01 May 2015) Changed paths: M stage/group_vars/all.yml Log Message: ----------- Update Test

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[galaxyproject/usegalaxy-playbook] afcf12: Increase Pulsar active job polling interval
by GitHub 01 May '15

01 May '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: afcf12f153af8d39db8151bc85fb92aaaff632e1 https://github.com/galaxyproject/usegalaxy-playbook/commit/afcf12f153af8d39… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-05-01 (Fri, 01 May 2015) Changed paths: M production/host_vars/login5.stampede.tacc.utexas.edu.yml M stage/host_vars/login5.stampede.tacc.utexas.edu.yml M stage/host_vars/tg-login2.blacklight.psc.xsede.org.yml Log Message: ----------- Increase Pulsar active job polling interval

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[galaxyproject/usegalaxy-playbook] e162ff: Updated Main to 15.05 rc1, enabled walltime resubm...
by GitHub 30 Apr '15

30 Apr '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: e162ff44229afc5f01d49d74ef4bf793b32b4f1f https://github.com/galaxyproject/usegalaxy-playbook/commit/e162ff44229afc5f… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-04-30 (Thu, 30 Apr 2015) Changed paths: M files/galaxy/usegalaxy.org/config/job_resource_params_conf.xml R files/galaxy/usegalaxy.org/dynamic_rules/local_stampede_select.py A files/galaxy/usegalaxy.org/dynamic_rules/multi_dynamic_walltime.py M production/group_vars/all.yml M production/group_vars/galaxyservers.yml M templates/galaxy/usegalaxy.org/config/job_conf.xml.j2 Log Message: ----------- Updated Main to 15.05 rc1, enabled walltime resubmission to Stampede.

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[galaxyproject/usegalaxy-playbook] 467a9c: Mutable configs on Test
by GitHub 29 Apr '15

29 Apr '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 467a9cc9728e806c28212e09f893fd2487be3406 https://github.com/galaxyproject/usegalaxy-playbook/commit/467a9cc9728e806c… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-04-29 (Wed, 29 Apr 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 Commit: c137320bcd555903d0849dd3ee76cf2ddb00aecb https://github.com/galaxyproject/usegalaxy-playbook/commit/c137320bcd555903… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-04-29 (Wed, 29 Apr 2015) Changed paths: M stage/group_vars/all.yml Log Message: ----------- Update Test Commit: 09e42f45651eae8be6c7175ad3e652ed5d6b1d7b https://github.com/galaxyproject/usegalaxy-playbook/commit/09e42f45651eae8b… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-04-29 (Wed, 29 Apr 2015) Changed paths: A files/galaxy/common/dynamic_rules/multi_dynamic_walltime.py A files/galaxy/common/dynamic_rules/reserved.py M files/galaxy/test.galaxyproject.org/config/job_resource_params_conf.xml M files/galaxy/test.galaxyproject.org/dynamic_rules/blacklight_select.py M files/galaxy/test.galaxyproject.org/dynamic_rules/multi_dynamic_walltime.py M files/galaxy/test.galaxyproject.org/dynamic_rules/nvc_dynamic_memory.py M files/galaxy/test.galaxyproject.org/dynamic_rules/reserved.py R files/galaxy/test.galaxyproject.org/dynamic_rules/stampede_select.py M files/galaxy/usegalaxy.org/dynamic_rules/reserved.py M stage/group_vars/galaxyservers.yml M templates/galaxy/test.galaxyproject.org/config/job_conf.xml.j2 Log Message: ----------- Combine the Stampede selector rule with the dynamic walltime rule, make Test's destinations and dynamic job rules match Main's. Changes for Main pending. Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/d804047d9369...…

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[galaxyproject/usegalaxy-playbook] d80404: Test mutable configs
by GitHub 28 Apr '15

28 Apr '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: d804047d9369e3703f09916eae9948cf6b7149f8 https://github.com/galaxyproject/usegalaxy-playbook/commit/d804047d9369e370… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-04-28 (Tue, 28 Apr 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: ----------- Test mutable configs

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[galaxyproject/usegalaxy-playbook] 8e1145: Update Test
by GitHub 28 Apr '15

28 Apr '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 8e1145e622f3ba43800fbbac6586a770e294f812 https://github.com/galaxyproject/usegalaxy-playbook/commit/8e1145e622f3ba43… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-04-28 (Tue, 28 Apr 2015) Changed paths: M stage/group_vars/all.yml Log Message: ----------- Update Test

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[galaxyproject/usegalaxy-playbook] 97ca21: Dropped Galaxy Japan Workshop slide; added GCC2015...
by GitHub 28 Apr '15

28 Apr '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 97ca219e7fc4a4a63985fbb7c6721b6acf68ebec https://github.com/galaxyproject/usegalaxy-playbook/commit/97ca219e7fc4a4a6… Author: tnabtaf <clements(a)galaxyproject.org> Date: 2015-04-28 (Tue, 28 Apr 2015) Changed paths: A files/galaxy/common/static/welcome_img/GCC2015EarlyReg.png M templates/galaxy/common/static/welcome.html.j2 Log Message: ----------- Dropped Galaxy Japan Workshop slide; added GCC2015 early registration slide

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[galaxyproject/usegalaxy-playbook] 1cc4ec: Updated Test mutable configs.
by GitHub 27 Apr '15

27 Apr '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 1cc4ecc7caf9e0ac987e5ed4a2e944c03ca10a44 https://github.com/galaxyproject/usegalaxy-playbook/commit/1cc4ecc7caf9e0ac… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-04-27 (Mon, 27 Apr 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 Log Message: ----------- Updated Test mutable configs.

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[galaxyproject/usegalaxy-playbook] 1666f6: Update Test and Main, fetch/distribute mutable con...
by GitHub 27 Apr '15

27 Apr '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 1666f64955a84eb2c89b49d96034a0b54606b641 https://github.com/galaxyproject/usegalaxy-playbook/commit/1666f64955a84eb2… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-04-27 (Mon, 27 Apr 2015) Changed paths: M files/galaxy/test.galaxyproject.org/var/integrated_tool_panel.xml M files/galaxy/usegalaxy.org/var/integrated_tool_panel.xml M files/galaxy/usegalaxy.org/var/shed_tool_conf.xml M production/group_vars/all.yml M stage/group_vars/all.yml Log Message: ----------- Update Test and Main, fetch/distribute mutable configs

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