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[galaxyproject/galaxy] abca52: Merge pull request #2118 from jmchilton/version-16...
by GitHub 11 Apr '16

11 Apr '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: abca525bee723fab9027c7fb5554a16b319976ab https://github.com/galaxyproject/galaxy/commit/abca525bee723fab9027c7fb5554… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-04-08 (Fri, 08 Apr 2016) Changed paths: M lib/galaxy/version.py Log Message: ----------- Merge pull request #2118 from jmchilton/version-16.04 [16.04] Update version to 16.04.rc1 Commit: f759961a29eeb28c6140d5d206bfd93fbdbfd379 https://github.com/galaxyproject/galaxy/commit/f759961a29eeb28c6140d5d206bf… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-04-11 (Mon, 11 Apr 2016) Changed paths: M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py Log Message: ----------- mention planemo in the error message for disabled TS pushing rephrase to Norwegian Commit: fe4afefc42a45faca09c7c2aea34a97cad02be76 https://github.com/galaxyproject/galaxy/commit/fe4afefc42a45faca09c7c2aea34… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-04-11 (Mon, 11 Apr 2016) Changed paths: M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py Log Message: ----------- Merge pull request #2114 from martenson/planemo-mention [16.01] mention planemo in the error message for disabled TS pushing Commit: f2bd242a2c28954215fb84d289d19e35a6460c65 https://github.com/galaxyproject/galaxy/commit/f2bd242a2c28954215fb84d289d1… Author: nitesh1989 <nitesh.turaga(a)gmail.com> Date: 2016-04-11 (Mon, 11 Apr 2016) Changed paths: M run_tool_shed.sh Log Message: ----------- change run_tool_shed.py to see the file in the correct lcoation Commit: 5f01cddc4b2a1e0578a2d6dde73b05fe6d95a0a7 https://github.com/galaxyproject/galaxy/commit/5f01cddc4b2a1e0578a2d6dde73b… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-04-11 (Mon, 11 Apr 2016) Changed paths: M run_tool_shed.sh Log Message: ----------- Merge pull request #2131 from nturaga/16.04_toolshed_fix [16.04] change run_tool_shed.py to see the file in the correct lcoation Commit: 6317297cad4e51f25c58a375dedd5d1e3f1f650a https://github.com/galaxyproject/galaxy/commit/6317297cad4e51f25c58a375dedd… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-04-11 (Mon, 11 Apr 2016) Changed paths: M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py Log Message: ----------- Merge branch 'release_16.01' into release_16.04 Commit: baf1bd639f175c6f06fd840a57ec44c8e612841a https://github.com/galaxyproject/galaxy/commit/baf1bd639f175c6f06fd840a57ec… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-04-11 (Mon, 11 Apr 2016) Changed paths: M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py Log Message: ----------- Merge branch 'release_16.04' into dev Compare: https://github.com/galaxyproject/galaxy/compare/03b9f7c372f2...baf1bd639f17

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[galaxyproject/galaxy] f75996: mention planemo in the error message for disabled ...
by GitHub 11 Apr '16

11 Apr '16

Branch: refs/heads/release_16.04 Home: https://github.com/galaxyproject/galaxy Commit: f759961a29eeb28c6140d5d206bfd93fbdbfd379 https://github.com/galaxyproject/galaxy/commit/f759961a29eeb28c6140d5d206bf… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-04-11 (Mon, 11 Apr 2016) Changed paths: M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py Log Message: ----------- mention planemo in the error message for disabled TS pushing rephrase to Norwegian Commit: fe4afefc42a45faca09c7c2aea34a97cad02be76 https://github.com/galaxyproject/galaxy/commit/fe4afefc42a45faca09c7c2aea34… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-04-11 (Mon, 11 Apr 2016) Changed paths: M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py Log Message: ----------- Merge pull request #2114 from martenson/planemo-mention [16.01] mention planemo in the error message for disabled TS pushing Commit: 6317297cad4e51f25c58a375dedd5d1e3f1f650a https://github.com/galaxyproject/galaxy/commit/6317297cad4e51f25c58a375dedd… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-04-11 (Mon, 11 Apr 2016) Changed paths: M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py Log Message: ----------- Merge branch 'release_16.01' into release_16.04 Compare: https://github.com/galaxyproject/galaxy/compare/5f01cddc4b2a...6317297cad4e

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[galaxyproject/galaxy] f2bd24: change run_tool_shed.py to see the file in the cor...
by GitHub 11 Apr '16

11 Apr '16

Branch: refs/heads/release_16.04 Home: https://github.com/galaxyproject/galaxy Commit: f2bd242a2c28954215fb84d289d19e35a6460c65 https://github.com/galaxyproject/galaxy/commit/f2bd242a2c28954215fb84d289d1… Author: nitesh1989 <nitesh.turaga(a)gmail.com> Date: 2016-04-11 (Mon, 11 Apr 2016) Changed paths: M run_tool_shed.sh Log Message: ----------- change run_tool_shed.py to see the file in the correct lcoation Commit: 5f01cddc4b2a1e0578a2d6dde73b05fe6d95a0a7 https://github.com/galaxyproject/galaxy/commit/5f01cddc4b2a1e0578a2d6dde73b… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-04-11 (Mon, 11 Apr 2016) Changed paths: M run_tool_shed.sh Log Message: ----------- Merge pull request #2131 from nturaga/16.04_toolshed_fix [16.04] change run_tool_shed.py to see the file in the correct lcoation Compare: https://github.com/galaxyproject/galaxy/compare/abca525bee72...5f01cddc4b2a

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[galaxyproject/infrastructure-playbook] 8b299c: Install git on controllers
by GitHub 11 Apr '16

11 Apr '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 8b299c5d265ef1ce20e3373e683505e80eaf3eaf https://github.com/galaxyproject/infrastructure-playbook/commit/8b299c5d265… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-04-11 (Mon, 11 Apr 2016) Changed paths: M jetstreamiuenv/group_vars/controllers.yml M jetstreamtaccenv/group_vars/controllers.yml Log Message: ----------- Install git on controllers

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[galaxyproject/infrastructure-playbook] 11a4c7: Jetstream NFS and CVMFS updates for Main
by GitHub 11 Apr '16

11 Apr '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 11a4c763507995bba69c47a38d9db4da78fbc868 https://github.com/galaxyproject/infrastructure-playbook/commit/11a4c763507… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-04-11 (Mon, 11 Apr 2016) Changed paths: M jetstreamiuenv/group_vars/galaxynodes.yml M jetstreamiuenv/inventory M jetstreamtaccenv/group_vars/galaxynodes.yml M jetstreamtaccenv/inventory M roles/cvmfs/defaults/main.yml M roles/jetstream_nfs/tasks/main.yml M taccenv/group_vars/galaxyservers.yml M taccenv/inventory M taccenv/playbook.yml Log Message: ----------- Jetstream NFS and CVMFS updates for Main

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[galaxyproject/infrastructure-playbook] 10e2dd: Export Jetstream NFS to all TACC galaxy VMs
by GitHub 11 Apr '16

11 Apr '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 10e2dd1f4c1a5890cdcf8cb3511fcc402590af15 https://github.com/galaxyproject/infrastructure-playbook/commit/10e2dd1f4c1… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-04-11 (Mon, 11 Apr 2016) Changed paths: M roles/jetstream_nfs/tasks/server.yml Log Message: ----------- Export Jetstream NFS to all TACC galaxy VMs

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[galaxyproject/galaxy] f75996: mention planemo in the error message for disabled ...
by GitHub 11 Apr '16

11 Apr '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: f759961a29eeb28c6140d5d206bfd93fbdbfd379 https://github.com/galaxyproject/galaxy/commit/f759961a29eeb28c6140d5d206bf… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-04-11 (Mon, 11 Apr 2016) Changed paths: M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py Log Message: ----------- mention planemo in the error message for disabled TS pushing rephrase to Norwegian Commit: fe4afefc42a45faca09c7c2aea34a97cad02be76 https://github.com/galaxyproject/galaxy/commit/fe4afefc42a45faca09c7c2aea34… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-04-11 (Mon, 11 Apr 2016) Changed paths: M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py Log Message: ----------- Merge pull request #2114 from martenson/planemo-mention [16.01] mention planemo in the error message for disabled TS pushing Compare: https://github.com/galaxyproject/galaxy/compare/455113d18223...fe4afefc42a4

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[galaxyproject/galaxy] 0ff81d: remove buildbot remnants
by GitHub 11 Apr '16

11 Apr '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 0ff81d3dcb85d82e213b970d48cf948402c40e23 https://github.com/galaxyproject/galaxy/commit/0ff81d3dcb85d82e213b970d48cf… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-04-11 (Mon, 11 Apr 2016) Changed paths: R buildbot_setup.sh M test/casperjs/casperjs_runner.py Log Message: ----------- remove buildbot remnants Commit: 03b9f7c372f288a9a4c4e440d892ca8cbf167b57 https://github.com/galaxyproject/galaxy/commit/03b9f7c372f288a9a4c4e440d892… Author: carlfeberhard <carlfeberhard(a)users.noreply.github.com> Date: 2016-04-11 (Mon, 11 Apr 2016) Changed paths: R buildbot_setup.sh M test/casperjs/casperjs_runner.py Log Message: ----------- Merge pull request #2125 from martenson/remove-buildbot remove buildbot remnants Compare: https://github.com/galaxyproject/galaxy/compare/ebb3c1fcec98...03b9f7c372f2

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[galaxyproject/galaxy] 99c2a6: API: add server_starttime to api/configuration
by GitHub 11 Apr '16

11 Apr '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 99c2a6b623ef063d9b3611d7b5621b737cbe12ab https://github.com/galaxyproject/galaxy/commit/99c2a6b623ef063d9b3611d7b562… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-04-11 (Mon, 11 Apr 2016) Changed paths: M lib/galaxy/managers/configuration.py M lib/galaxy/web/framework/base.py M lib/galaxy/web/framework/helpers/__init__.py Log Message: ----------- API: add server_starttime to api/configuration Adds key server_starttime to the JSON returned from api/configuration. This is the epoch time since the last server restart and may be convenient for use in client-side caching. This moves server_starttime from web/framework/helpers/__init__.py (for use in script cache-busting) to web/framework/base.py. On the client, this should be available to all pages as: Galaxy.config.server_starttime. Commit: ebb3c1fcec988a96f2cd46309096140087ba5aaf https://github.com/galaxyproject/galaxy/commit/ebb3c1fcec988a96f2cd46309096… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-11 (Mon, 11 Apr 2016) Changed paths: M lib/galaxy/managers/configuration.py M lib/galaxy/web/framework/base.py M lib/galaxy/web/framework/helpers/__init__.py Log Message: ----------- Merge pull request #2124 from carlfeberhard/config-restart-time API: add server_starttime to api/configuration Compare: https://github.com/galaxyproject/galaxy/compare/bf83b39e0d30...ebb3c1fcec98

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[galaxyproject/galaxy]
by GitHub 11 Apr '16

11 Apr '16

Branch: refs/heads/iuc_default_conda_channel Home: https://github.com/galaxyproject/galaxy

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[galaxyproject/usegalaxy-playbook] 5d10f5: Updated GCC2016 related slides.
by GitHub 09 Apr '16

09 Apr '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 5d10f5004185bf142fb1cf85d6247a312357c1a7 https://github.com/galaxyproject/usegalaxy-playbook/commit/5d10f5004185bf14… Author: tnabtaf <clements(a)galaxyproject.org> Date: 2016-04-09 (Sat, 09 Apr 2016) Changed paths: A files/galaxy/common/static/welcome_img/GCC2016May20Deadlines.png A files/galaxy/common/static/welcome_img/GCC2016ScholarshipsDomestic.png M templates/galaxy/common/static/welcome.html.j2 Log Message: ----------- Updated GCC2016 related slides.

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[galaxyproject/galaxy] 265158: fix blocking issue check;
by GitHub 09 Apr '16

09 Apr '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 2651587e82e42d159372b86190b1cc8c7463a823 https://github.com/galaxyproject/galaxy/commit/2651587e82e42d159372b86190b1… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-04-08 (Fri, 08 Apr 2016) Changed paths: M scripts/bootstrap_history.py Log Message: ----------- fix blocking issue check; it would check the issues created by galaxybot before I think Commit: bf83b39e0d308c2c41d8a18c29bf723c00212019 https://github.com/galaxyproject/galaxy/commit/bf83b39e0d308c2c41d8a18c29bf… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-04-08 (Fri, 08 Apr 2016) Changed paths: M scripts/bootstrap_history.py Log Message: ----------- Merge pull request #2113 from martenson/fix-blocking-issue-check fix blocking issue check Compare: https://github.com/galaxyproject/galaxy/compare/ac789ede75dc...bf83b39e0d30

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[galaxyproject/galaxy] 30f2f5: change run_tool_shed.py to see the file in the cor...
by GitHub 09 Apr '16

09 Apr '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 30f2f5d43056fb679dbc228e0cc8801a2c15ef2f https://github.com/galaxyproject/galaxy/commit/30f2f5d43056fb679dbc228e0cc8… Author: nitesh1989 <nitesh.turaga(a)gmail.com> Date: 2016-04-08 (Fri, 08 Apr 2016) Changed paths: M run_tool_shed.sh Log Message: ----------- change run_tool_shed.py to see the file in the correct lcoation Commit: ac789ede75dcb3435c13889617372a13f085765d https://github.com/galaxyproject/galaxy/commit/ac789ede75dcb3435c1388961737… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-04-08 (Fri, 08 Apr 2016) Changed paths: M run_tool_shed.sh Log Message: ----------- Merge pull request #2121 from nitesh1989/run_tool_shed_fix change run_tool_shed.py to see the file in the correct lcoation Compare: https://github.com/galaxyproject/galaxy/compare/428c30680eb4...ac789ede75dc

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[galaxyproject/galaxy] af4233: Automate and clarify more of the release process.
by GitHub 08 Apr '16

08 Apr '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: af42338ecca940a6d40f356a18fd78e6a8c995af https://github.com/galaxyproject/galaxy/commit/af42338ecca940a6d40f356a18fd… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-04-08 (Fri, 08 Apr 2016) Changed paths: M Makefile M scripts/bootstrap_history.py Log Message: ----------- Automate and clarify more of the release process. upstream is used repeatedly and just assumed to be a remote - this tests for it and adds it if it doesn't exist before using in make commands now. This also automates the previous release to dev merge in the instructions with a new Make command. Additionally, two PRs need to be created to update versions. This prints a reminder to do this and adds it to the release checklist. Ideally, these PRs could be avoided with a direct push or automatically created with hub (https://github.com/github/hub) Commit: 428c30680eb40c6d5456b2b0ce80610642da548f https://github.com/galaxyproject/galaxy/commit/428c30680eb40c6d5456b2b0ce80… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-04-08 (Fri, 08 Apr 2016) Changed paths: M Makefile M scripts/bootstrap_history.py Log Message: ----------- Merge pull request #2117 from jmchilton/release_improve Automate and clarify more of the release process. Compare: https://github.com/galaxyproject/galaxy/compare/aa69d5007d99...428c30680eb4

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[galaxyproject/galaxy] 579846: Update version to 16.04.rc1
by GitHub 08 Apr '16

08 Apr '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 579846fdfbbb6ca2363d9b79e0ec308f96af120a https://github.com/galaxyproject/galaxy/commit/579846fdfbbb6ca2363d9b79e0ec… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-04-08 (Fri, 08 Apr 2016) Changed paths: M lib/galaxy/version.py Log Message: ----------- Update version to 16.04.rc1 Commit: 5739f25003981b22aac3bc055166390a84e07072 https://github.com/galaxyproject/galaxy/commit/5739f25003981b22aac3bc055166… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-04-08 (Fri, 08 Apr 2016) Changed paths: M lib/galaxy/version.py Log Message: ----------- Update version to 16.07.dev Commit: 986ea22ed770e1876953e5aee780427d71fe698f https://github.com/galaxyproject/galaxy/commit/986ea22ed770e1876953e5aee780… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-04-08 (Fri, 08 Apr 2016) Log Message: ----------- Merge branch 'version-16.04' into version-16.07.dev Commit: aa69d5007d99c94fedced2646ca8a0e9f18eba54 https://github.com/galaxyproject/galaxy/commit/aa69d5007d99c94fedced2646ca8… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-04-08 (Fri, 08 Apr 2016) Changed paths: M lib/galaxy/version.py Log Message: ----------- Merge pull request #2119 from jmchilton/version-16.07.dev Version 16.07.dev Compare: https://github.com/galaxyproject/galaxy/compare/f377d069e2aa...aa69d5007d99

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[galaxyproject/galaxy] 579846: Update version to 16.04.rc1
by GitHub 08 Apr '16

08 Apr '16

Branch: refs/heads/release_16.04 Home: https://github.com/galaxyproject/galaxy Commit: 579846fdfbbb6ca2363d9b79e0ec308f96af120a https://github.com/galaxyproject/galaxy/commit/579846fdfbbb6ca2363d9b79e0ec… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-04-08 (Fri, 08 Apr 2016) Changed paths: M lib/galaxy/version.py Log Message: ----------- Update version to 16.04.rc1 Commit: abca525bee723fab9027c7fb5554a16b319976ab https://github.com/galaxyproject/galaxy/commit/abca525bee723fab9027c7fb5554… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-04-08 (Fri, 08 Apr 2016) Changed paths: M lib/galaxy/version.py Log Message: ----------- Merge pull request #2118 from jmchilton/version-16.04 [16.04] Update version to 16.04.rc1 Compare: https://github.com/galaxyproject/galaxy/compare/f377d069e2aa...abca525bee72

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[galaxyproject/usegalaxy-playbook] e1cab2: Pulsar stuff for Jetstream @ TACC and IU
by GitHub 08 Apr '16

08 Apr '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: e1cab2530d7cfa772da483e442a3d40b381b91d8 https://github.com/galaxyproject/usegalaxy-playbook/commit/e1cab2530d7cfa77… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-04-08 (Fri, 08 Apr 2016) Changed paths: A files/galaxy/test.galaxyproject.org/config/pulsar_jetstream_actions.yml R files/galaxy/test.galaxyproject.org/config/pulsar_jetstream_iu_actions.yml A files/galaxy/test.galaxyproject.org/config/pulsar_jetstream_tacc.yml A files/galaxy/test.galaxyproject.org/dynamic_rules/jetstream.py M stage/group_vars/all.yml M stage/group_vars/galaxyservers.yml M templates/galaxy/test.galaxyproject.org/config/job_conf.xml.j2 Log Message: ----------- Pulsar stuff for Jetstream @ TACC and IU

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[galaxyproject/infrastructure-playbook] f35e16: Fix Jetstream node mount points
by GitHub 08 Apr '16

08 Apr '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: f35e1659581e8fe4bc433accb393b2e862b0f73a https://github.com/galaxyproject/infrastructure-playbook/commit/f35e1659581… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-04-08 (Fri, 08 Apr 2016) Changed paths: M jetstreamiuenv/group_vars/galaxynodes.yml M jetstreamtaccenv/group_vars/galaxynodes.yml M roles/jetstream_nfs/tasks/main.yml Log Message: ----------- Fix Jetstream node mount points

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[galaxyproject/infrastructure-playbook] ed50d1: Add TACC Jetstream stuff
by GitHub 08 Apr '16

08 Apr '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: ed50d1a2f94f9874a30dd17fd9dea9c5235ef822 https://github.com/galaxyproject/infrastructure-playbook/commit/ed50d1a2f94… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-04-08 (Fri, 08 Apr 2016) Changed paths: A galaxyenv/host_vars/cvmfs1-tacc0.galaxyproject.org.yml A jetstreamiuenv/group_vars/controllers.yml M jetstreamiuenv/group_vars/galaxynodes.yml A jetstreamtaccenv/group_vars/all.yml A jetstreamtaccenv/group_vars/controllers.yml A jetstreamtaccenv/group_vars/cvmfsclients.yml A jetstreamtaccenv/group_vars/galaxynodes.yml A jetstreamtaccenv/group_vars/slurmclients.yml A jetstreamtaccenv/instance_inventory A jetstreamtaccenv/inventory A jetstreamtaccenv/playbook.yml A jetstreamtaccenv/secret_group_vars/slurmclients.yml A jetstreamtaccenv/templates/slurm/slurm.conf.j2 R roles/jetstream_nfs/vars/main.yml Log Message: ----------- Add TACC Jetstream stuff

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[galaxyproject/galaxy]
by GitHub 08 Apr '16

08 Apr '16

Branch: refs/heads/release_16.04 Home: https://github.com/galaxyproject/galaxy

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[galaxyproject/galaxy] 90b95d: Merge pull request #2043 from martenson/update_mer...
by GitHub 08 Apr '16

08 Apr '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 90b95dc665bd736a21bd16d2852caf5c23bb83c4 https://github.com/galaxyproject/galaxy/commit/90b95dc665bd736a21bd16d2852c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-31 (Thu, 31 Mar 2016) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt Log Message: ----------- Merge pull request #2043 from martenson/update_mercurial_wheel [16.01] upgrade mercurial wheel to latest (fixing CVE issues) Commit: 20f61e6a2f36967e16a92cbcf8ad7f81ca76fb29 https://github.com/galaxyproject/galaxy/commit/20f61e6a2f36967e16a92cbcf8ad… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-04-04 (Mon, 04 Apr 2016) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- workaround for error message in case original toolshed had been disabled Commit: 65a7ebee23364a89d72e528bfcde6b1f6b3c5cd9 https://github.com/galaxyproject/galaxy/commit/65a7ebee23364a89d72e528bfcde… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-04-04 (Mon, 04 Apr 2016) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Merge pull request #2072 from mvdbeek/backport_1738 [16.01] backport #1738 Commit: 2a53be67ad4ac99b6e9fe5fb803bfa44442dbd3c https://github.com/galaxyproject/galaxy/commit/2a53be67ad4ac99b6e9fe5fb803b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-04-05 (Tue, 05 Apr 2016) Changed paths: M templates/webapps/galaxy/workflow/run.mako Log Message: ----------- Show sections in workflow run Commit: 3002e404ef17cd7db9b817085b2f3ed5a82bd109 https://github.com/galaxyproject/galaxy/commit/3002e404ef17cd7db9b817085b2f… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-04-05 (Tue, 05 Apr 2016) Changed paths: M templates/webapps/galaxy/workflow/run.mako Log Message: ----------- Patch in visual separation of section parameters Commit: 040410b1d3f0ea01374f183ee0b9447e0fc3cefb https://github.com/galaxyproject/galaxy/commit/040410b1d3f0ea01374f183ee0b9… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-04-05 (Tue, 05 Apr 2016) Changed paths: M templates/webapps/galaxy/workflow/run.mako Log Message: ----------- Merge pull request #2092 from erasche/workflow-section-backport [16.01] Workflow section fix backport Commit: 9ecf99c227466a586a6299e37555655f5ff79a25 https://github.com/galaxyproject/galaxy/commit/9ecf99c227466a586a6299e37555… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-04-06 (Wed, 06 Apr 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/tool_shed/util/shed_util_common.py Log Message: ----------- make dependencies browsable again it would be denied previously as the dependency folder is outside of the repository (symlink protection) Commit: 0882b4d8fb31752f1fa8c963c3f260f975c918f7 https://github.com/galaxyproject/galaxy/commit/0882b4d8fb31752f1fa8c963c3f2… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-04-06 (Wed, 06 Apr 2016) Changed paths: M lib/galaxy/webapps/tool_shed/controllers/repository.py Log Message: ----------- use proper method for detecting admin Commit: 50268cb8ca4a5f812346a71cc640141781f22a3d https://github.com/galaxyproject/galaxy/commit/50268cb8ca4a5f812346a71cc640… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-04-07 (Thu, 07 Apr 2016) Changed paths: M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/tool_shed/util/shed_util_common.py Log Message: ----------- fix missing call; add docs and refactor a bit Commit: 455113d182236a0fec880db296b746a413a8edc4 https://github.com/galaxyproject/galaxy/commit/455113d182236a0fec880db296b7… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-04-08 (Fri, 08 Apr 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/tool_shed/util/shed_util_common.py Log Message: ----------- Merge pull request #2101 from martenson/fix-browsing-dependencies [16.01] make dependencies browsable again Commit: 094580909964c5fad91b1068917832bedaddf579 https://github.com/galaxyproject/galaxy/commit/094580909964c5fad91b10689178… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-04-08 (Fri, 08 Apr 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/tool_shed/util/shed_util_common.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_16.01' into dev Commit: f377d069e2aa02434742b3061b2b300c50d6dd86 https://github.com/galaxyproject/galaxy/commit/f377d069e2aa02434742b3061b2b… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-04-08 (Fri, 08 Apr 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/tool_shed/util/shed_util_common.py Log Message: ----------- Merge pull request #2115 from jmchilton/dev-merge Merge release into latest dev. Compare: https://github.com/galaxyproject/galaxy/compare/ce278630860e...f377d069e2aa

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[galaxyproject/galaxy] 4df7e4: Consolidate duplicated method.
by GitHub 08 Apr '16

08 Apr '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4df7e45f61f505d94b854c312d970a4a363bc50f https://github.com/galaxyproject/galaxy/commit/4df7e45f61f505d94b854c312d97… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-04-06 (Wed, 06 Apr 2016) Changed paths: M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/model/__init__.py Log Message: ----------- Consolidate duplicated method. Commit: 4b8b7b46476d0ec9d56b2710759e963938e53bd0 https://github.com/galaxyproject/galaxy/commit/4b8b7b46476d0ec9d56b2710759e… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-04-07 (Thu, 07 Apr 2016) Changed paths: M lib/galaxy/webapps/tool_shed/api/repositories.py Log Message: ----------- Update which method is used in API. Commit: ce278630860e38e0e103c71fdae7674e2e40f56b https://github.com/galaxyproject/galaxy/commit/ce278630860e38e0e103c71fdae7… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-04-08 (Fri, 08 Apr 2016) Changed paths: M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/model/__init__.py Log Message: ----------- Merge pull request #2099 from davebx/shed_model_trim Consolidate duplicated method in tool_shed/model. Compare: https://github.com/galaxyproject/galaxy/compare/0d616af28a17...ce278630860e

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[galaxyproject/galaxy] b4e768: Workaround for the toolshed's hgweb.
by GitHub 08 Apr '16

08 Apr '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b4e768b82804c54d107c8cf866e3814135867211 https://github.com/galaxyproject/galaxy/commit/b4e768b82804c54d107c8cf866e3… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-04-07 (Thu, 07 Apr 2016) Changed paths: M lib/galaxy/webapps/tool_shed/buildapp.py M lib/galaxy/webapps/tool_shed/controllers/hg.py Log Message: ----------- Workaround for the toolshed's hgweb. Commit: 2a76eb19c1d8d442859ea33b19100689ca6bf1fb https://github.com/galaxyproject/galaxy/commit/2a76eb19c1d8d442859ea33b1910… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-04-07 (Thu, 07 Apr 2016) Changed paths: M lib/galaxy/webapps/tool_shed/controllers/hg.py Log Message: ----------- Remove unused import, restore used import. Commit: 5ead1c089f2f2a3f06ee55ac77be1d9f89a377ae https://github.com/galaxyproject/galaxy/commit/5ead1c089f2f2a3f06ee55ac77be… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-04-08 (Fri, 08 Apr 2016) Changed paths: M lib/galaxy/webapps/tool_shed/buildapp.py M lib/galaxy/webapps/tool_shed/controllers/hg.py Log Message: ----------- Remove refactoring that belongs in a different PR. Commit: 0d616af28a175bae8e193f429a18f97cd8b274ec https://github.com/galaxyproject/galaxy/commit/0d616af28a175bae8e193f429a18… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-04-08 (Fri, 08 Apr 2016) Changed paths: M lib/galaxy/webapps/tool_shed/buildapp.py Log Message: ----------- Merge pull request #2106 from davebx/hg_middleware Workaround for the toolshed's hgweb. Compare: https://github.com/galaxyproject/galaxy/compare/6f6554ea8c7e...0d616af28a17

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[galaxyproject/galaxy] c720c0: Updated to Dependency change in b167a741a444c39884...
by GitHub 08 Apr '16

08 Apr '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c720c0fde89174445a6bbb96436d781bbbdc0941 https://github.com/galaxyproject/galaxy/commit/c720c0fde89174445a6bbb96436d… Author: Christian-B <github(a)brenn.co.uk> Date: 2016-04-07 (Thu, 07 Apr 2016) Changed paths: M lib/galaxy/tools/deps/resolvers/unlinked_tool_shed_packages.py Log Message: ----------- Updated to Dependency change in b167a741a444c3988447b0d63a1ba3dc5e4e62f5 Commit: 6f6554ea8c7e8f6511db0899ce5c8050056d802c https://github.com/galaxyproject/galaxy/commit/6f6554ea8c7e8f6511db0899ce5c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-04-08 (Fri, 08 Apr 2016) Changed paths: M lib/galaxy/tools/deps/resolvers/unlinked_tool_shed_packages.py Log Message: ----------- Merge pull request #2104 from Christian-B/unlinked_depenency_resolver_update_to_new_dependency Updated to Dependency change in b167a741a444c3988447b0d63a1ba3dc5e4e62f5 Compare: https://github.com/galaxyproject/galaxy/compare/f0272e02f7eb...6f6554ea8c7e

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[galaxyproject/galaxy] d6a7ac: Update debian init script
by GitHub 08 Apr '16

08 Apr '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d6a7acab996b7a157ce7de07117b523ae4e0fa46 https://github.com/galaxyproject/galaxy/commit/d6a7acab996b7a157ce7de07117b… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-04-08 (Fri, 08 Apr 2016) Changed paths: M contrib/galaxy.debian-init Log Message: ----------- Update debian init script to include instructions for starting galaxy >= 16.01. Commit: f0272e02f7eb9b433c31eecaa5ce2986b2e728dd https://github.com/galaxyproject/galaxy/commit/f0272e02f7eb9b433c31eecaa5ce… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-04-08 (Fri, 08 Apr 2016) Changed paths: M contrib/galaxy.debian-init Log Message: ----------- Merge pull request #2109 from mvdbeek/fix_debian_init_script Update debian init script Compare: https://github.com/galaxyproject/galaxy/compare/4c7f187b353d...f0272e02f7eb

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