- galaxy-commits - lists.galaxyproject.org

[galaxyproject/usegalaxy-playbook] 0b9825: pylon1 -> pylon5
by GitHub 19 Apr '17

19 Apr '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 0b9825782968350d7b888360a2941fffcadc9793 https://github.com/galaxyproject/usegalaxy-playbook/commit/0b9825782968350d… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-04-18 (Tue, 18 Apr 2017) Changed paths: M production/host_vars/br005.bridges.psc.edu.yml Log Message: ----------- pylon1 -> pylon5

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[galaxyproject/usegalaxy-playbook] bd96bc: Drop the bootstrap script
by GitHub 19 Apr '17

19 Apr '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: bd96bc4406cc67bc067eeffaf5af66f1f52ea11f https://github.com/galaxyproject/usegalaxy-playbook/commit/bd96bc4406cc67bc… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-04-04 (Tue, 04 Apr 2017) Changed paths: R bootstrap-ansible.bash Log Message: ----------- Drop the bootstrap script Commit: 9ae7ebd5030a611879af50da0123089c621c73ad https://github.com/galaxyproject/usegalaxy-playbook/commit/9ae7ebd5030a6118… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-04-18 (Tue, 18 Apr 2017) Changed paths: M production/files/interactive_environments/plugins/bam_iobio/config/bam_iobio.ini.sample M production/files/interactive_environments/plugins/bam_iobio/static/js/bam_iobio.js M production/files/interactive_environments/plugins/bam_iobio/templates/bam_iobio.mako M production/files/interactive_environments/plugins/common/templates/ie.mako R production/files/interactive_environments/plugins/ethercalc/config/allowed_images.yml.sample R production/files/interactive_environments/plugins/ethercalc/config/ethercalc.ini.sample R production/files/interactive_environments/plugins/ethercalc/config/ethercalc.xml R production/files/interactive_environments/plugins/ethercalc/static/js/ethercalc.js R production/files/interactive_environments/plugins/ethercalc/templates/ethercalc.mako M production/files/interactive_environments/plugins/jupyter/config/allowed_images.yml.sample M production/files/interactive_environments/plugins/jupyter/config/jupyter.ini.sample M production/files/interactive_environments/plugins/jupyter/config/jupyter.xml M production/files/interactive_environments/plugins/jupyter/static/js/jupyter.js M production/files/interactive_environments/plugins/jupyter/templates/jupyter.mako M production/files/interactive_environments/plugins/neo/config/neo.ini.sample M production/files/interactive_environments/plugins/neo/static/js/neo.js M production/files/interactive_environments/plugins/neo/templates/neo.mako M production/files/interactive_environments/plugins/phinch/config/phinch.ini.sample M production/files/interactive_environments/plugins/phinch/static/js/phinch.js M production/files/interactive_environments/plugins/phinch/templates/phinch.mako M production/files/interactive_environments/plugins/rstudio/config/rstudio.ini.sample M production/files/interactive_environments/plugins/rstudio/static/js/rstudio.js M production/files/interactive_environments/plugins/rstudio/templates/rstudio.mako M production/files/interactive_environments/proxy/lib/mapper.js M roles/galaxyprojectdotorg.interactive_environments/meta/.galaxy_install_info M roles/galaxyprojectdotorg.interactive_environments/tasks/extract_component.yml M roles/galaxyprojectdotorg.interactive_environments/tasks/synchronize_components.yml M templates/galaxy/usegalaxy.org/config/job_conf.xml.j2 Log Message: ----------- Merge branch 'master' of github.com:/galaxyproject/usegalaxy-playbook Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/ccadc26f89c4...…

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[galaxyproject/usegalaxy-playbook] 1a0914: Upgrade Test
by GitHub 19 Apr '17

19 Apr '17

Branch: refs/heads/reorg Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 1a09141d4a929d05c02cfbf998efc19eee10caea https://github.com/galaxyproject/usegalaxy-playbook/commit/1a09141d4a929d05… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-04-18 (Tue, 18 Apr 2017) Changed paths: M env/test/files/galaxy/galaxy_version.yml M env/test/files/interactive_environments/plugins/.ansible_ie_role_current_version M env/test/files/interactive_environments/proxy/.ansible_ie_role_current_version Log Message: ----------- Upgrade Test Commit: 7b02be926f63742dab881d38cda7492af18d1ba6 https://github.com/galaxyproject/usegalaxy-playbook/commit/7b02be926f63742d… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-04-18 (Tue, 18 Apr 2017) Changed paths: M env/test/host_vars/br005.bridges.psc.edu.yml Log Message: ----------- pylon1 -> pylon5 Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/8dd328d77980...…

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[galaxyproject/usegalaxy-playbook] 8dd328: Fix GIE proxy port
by GitHub 19 Apr '17

19 Apr '17

Branch: refs/heads/reorg Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 8dd328d77980aaff3353f0cc554ebf76fbcb8e7f https://github.com/galaxyproject/usegalaxy-playbook/commit/8dd328d77980aaff… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-04-18 (Tue, 18 Apr 2017) Changed paths: M env/common/templates/supervisor/galaxy_gie_proxy.j2 Log Message: ----------- Fix GIE proxy port

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[galaxyproject/usegalaxy-playbook] 812c4c: Move Test GIEs to Swarm
by GitHub 19 Apr '17

19 Apr '17

Branch: refs/heads/reorg Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 812c4c3451e2174aa07dd1566b0365210c408eee https://github.com/galaxyproject/usegalaxy-playbook/commit/812c4c3451e2174a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-04-18 (Tue, 18 Apr 2017) Changed paths: M env/common/config.yml M env/test/group_vars/galaxyservers/vars.yml Log Message: ----------- Move Test GIEs to Swarm

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[galaxyproject/usegalaxy-playbook] 6cca38: IE fixes
by GitHub 19 Apr '17

19 Apr '17

Branch: refs/heads/reorg Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 6cca389e2fa650cb6479eead5b6866b6f3f0622d https://github.com/galaxyproject/usegalaxy-playbook/commit/6cca389e2fa650cb… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-04-17 (Mon, 17 Apr 2017) Changed paths: M env/common/config.yml M env/common/templates/supervisor/galaxy.j2 M env/common/update.yml M env/test/files/galaxy/var/integrated_tool_panel.xml M env/test/files/interactive_environments/plugins/.ansible_ie_role_current_version A env/test/files/interactive_environments/plugins/ethercalc/config/allowed_images.yml.sample M env/test/files/interactive_environments/plugins/ethercalc/config/ethercalc.ini.sample M env/test/files/interactive_environments/proxy/.ansible_ie_role_current_version M env/test/group_vars/galaxyservers/vars.yml M roles/galaxyprojectdotorg.galaxy/README.md M roles/galaxyprojectdotorg.galaxy/defaults/main.yml M roles/galaxyprojectdotorg.galaxy/meta/.galaxy_install_info M roles/galaxyprojectdotorg.galaxy/tasks/main.yml Log Message: ----------- IE fixes Commit: 86cafa4afe3c594cb25340990388f589cac0d3f6 https://github.com/galaxyproject/usegalaxy-playbook/commit/86cafa4afe3c594c… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-04-18 (Tue, 18 Apr 2017) Changed paths: M env/test/templates/galaxy/config/job_conf.xml.j2 Log Message: ----------- Merge branch 'reorg' of github.com:/galaxyproject/usegalaxy-playbook into reorg Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/b56a94393f25...…

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[galaxyproject/usegalaxy-playbook] ccadc2: pylon1 -> pylon5
by GitHub 19 Apr '17

19 Apr '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: ccadc26f89c4d2cdeaacb9a1dd940cc067bdac7c https://github.com/galaxyproject/usegalaxy-playbook/commit/ccadc26f89c4d2cd… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-04-18 (Tue, 18 Apr 2017) Changed paths: M templates/galaxy/usegalaxy.org/config/job_conf.xml.j2 Log Message: ----------- pylon1 -> pylon5

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[galaxyproject/usegalaxy-playbook] b56a94: pylon1 -> pylon5
by GitHub 19 Apr '17

19 Apr '17

Branch: refs/heads/reorg Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: b56a94393f25cfc03515801c4d83256562da8e68 https://github.com/galaxyproject/usegalaxy-playbook/commit/b56a94393f25cfc0… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-04-18 (Tue, 18 Apr 2017) Changed paths: M env/test/templates/galaxy/config/job_conf.xml.j2 Log Message: ----------- pylon1 -> pylon5

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[galaxyproject/infrastructure-playbook] 4a72e3: Additional Test fixes
by GitHub 17 Apr '17

17 Apr '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 4a72e362611797e43916a0751dd629ad5f53a2d2 https://github.com/galaxyproject/infrastructure-playbook/commit/4a72e362611… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-04-17 (Mon, 17 Apr 2017) Changed paths: A taccenv/group_vars/all.yml M taccenv/group_vars/galaxyservers.yml M taccenv/group_vars/maingalaxyservers.yml M taccenv/group_vars/testgalaxyservers.yml Log Message: ----------- Additional Test fixes Commit: 6d1e7866bbc8a8765b7e4c2946302923b215e432 https://github.com/galaxyproject/infrastructure-playbook/commit/6d1e7866bbc… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-04-17 (Mon, 17 Apr 2017) Changed paths: M jetstreamdockerenv/group_vars/imageinstances.yml M jetstreamdockerenv/inventory M jetstreamdockerenv/snapshot_docker_image.yml Log Message: ----------- Use a single volume for swarm workers Compare: https://github.com/galaxyproject/infrastructure-playbook/compare/33e4f2e997…

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[galaxyproject/galaxy] 77caed: Update text.py Add interaction annotations to Snp...
by GitHub 17 Apr '17

17 Apr '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 77caed9861d3666150c49442df9374b63660c2e5 https://github.com/galaxyproject/galaxy/commit/77caed9861d3666150c49442df93… Author: Jim Johnson <jj(a)umn.edu> Date: 2017-04-17 (Mon, 17 Apr 2017) Changed paths: M lib/galaxy/datatypes/text.py Log Message: ----------- Update text.py Add interaction annotations to SnpEffDb metadata Interaction annotations are now included in SnpEff v4.3 Commit: e9011488f2f5bfe91f542d173a9f7b3132e414ad https://github.com/galaxyproject/galaxy/commit/e9011488f2f5bfe91f542d173a9f… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-04-17 (Mon, 17 Apr 2017) Changed paths: M lib/galaxy/datatypes/text.py Log Message: ----------- Merge pull request #3938 from jj-umn/patch-6 Update text.py Add interaction annotations to SnpEffDb metadata Compare: https://github.com/galaxyproject/galaxy/compare/695293f01563...e9011488f2f5

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[galaxyproject/galaxy] 29331b: Container interface abstraction. Support Docker an...
by GitHub 13 Apr '17

13 Apr '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 29331b36cf4ad350d4919679deeca6f342b1e182 https://github.com/galaxyproject/galaxy/commit/29331b36cf4ad350d4919679deec… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-04-04 (Tue, 04 Apr 2017) Changed paths: M .ci/flake8_docstrings_include_list.txt M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt A config/containers_conf.yml.sample M config/galaxy.ini.sample M lib/galaxy/config.py R lib/galaxy/container/__init__.py R lib/galaxy/container/docker_swarm.py A lib/galaxy/containers/__init__.py A lib/galaxy/containers/docker.py A lib/galaxy/containers/docker_decorators.py A lib/galaxy/containers/docker_model.py A lib/galaxy/containers/docker_swarm.py A lib/galaxy/containers/docker_swarm_manager.py M lib/galaxy/exceptions/__init__.py M lib/galaxy/util/submodules.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/web/proxy/__init__.py M lib/galaxy/webapps/galaxy/controllers/interactive_environments.py Log Message: ----------- Container interface abstraction. Support Docker and Docker Swarm mode (>1.12 SwarmKit). Container interface configuration is performed via the containers_conf.yml config file, for which a documented sample is provided. The GIE launcher has been modified to use the container interface if the `enable_beta_containers_interface` option is set in galaxy.ini. This removes some of the previous GIE-specific swarm mode work that was done. The Galaxy docker swarm manager also uses the container interface now. TODO: The API docker interfaces should be done fairly soon before we have many consumers of the docker model objects, because they'll probably be changed to more closely reflect their API representations. Commit: 695293f01563f56637ee6b63db2c96bfd0204f9f https://github.com/galaxyproject/galaxy/commit/695293f01563f56637ee6b63db2c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-04-13 (Thu, 13 Apr 2017) Changed paths: M .ci/flake8_docstrings_include_list.txt M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt A config/containers_conf.yml.sample M config/galaxy.ini.sample M lib/galaxy/config.py R lib/galaxy/container/__init__.py R lib/galaxy/container/docker_swarm.py A lib/galaxy/containers/__init__.py A lib/galaxy/containers/docker.py A lib/galaxy/containers/docker_decorators.py A lib/galaxy/containers/docker_model.py A lib/galaxy/containers/docker_swarm.py A lib/galaxy/containers/docker_swarm_manager.py M lib/galaxy/exceptions/__init__.py M lib/galaxy/util/submodules.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/web/proxy/__init__.py M lib/galaxy/webapps/galaxy/controllers/interactive_environments.py Log Message: ----------- Merge pull request #3863 from natefoo/containers-abstraction Container interface abstraction Compare: https://github.com/galaxyproject/galaxy/compare/040635d3dcee...695293f01563

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[galaxyproject/galaxy] c4cf41: Allow explicit workflow scheduler handler process ...
by GitHub 13 Apr '17

13 Apr '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c4cf4164b31249457a4cdb92405006136193b1bb https://github.com/galaxyproject/galaxy/commit/c4cf4164b31249457a4cdb924050… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-04-07 (Fri, 07 Apr 2017) Changed paths: M lib/galaxy/jobs/__init__.py A lib/galaxy/util/handlers.py M lib/galaxy/workflow/scheduling_manager.py M test/integration/test_workflow_handler_configuration.py A test/integration/workflow_handler_configuration_workflow_scheduler_conf.xml Log Message: ----------- Allow explicit workflow scheduler handler process configuration. Refactor job handler stuff to allow this with re-use. Commit: fd216163aec719314fb328b87e5bea6f871a3b0a https://github.com/galaxyproject/galaxy/commit/fd216163aec719314fb328b87e5b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-04-07 (Fri, 07 Apr 2017) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/util/handlers.py M lib/galaxy/workflow/scheduling_manager.py Log Message: ----------- Initial workflow scheduling handler fixes caught by :eagle::eyes:. Commit: 040635d3dcee4c13960170010c8a7c10319c4fd5 https://github.com/galaxyproject/galaxy/commit/040635d3dcee4c13960170010c8a… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-04-13 (Thu, 13 Apr 2017) Changed paths: M lib/galaxy/jobs/__init__.py A lib/galaxy/util/handlers.py M lib/galaxy/workflow/scheduling_manager.py M test/integration/test_workflow_handler_configuration.py A test/integration/workflow_handler_configuration_workflow_scheduler_conf.xml Log Message: ----------- Merge pull request #3844 from jmchilton/dev_workflow_conf Allow explicit configuration of handlers for workflow scheduling. Compare: https://github.com/galaxyproject/galaxy/compare/55c4d5245576...040635d3dcee

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[galaxyproject/galaxy] c134da: Identify and handle runtime values when generating...
by GitHub 13 Apr '17

13 Apr '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c134dac9d5f2ec86f0194d114d42c4742f63e6b9 https://github.com/galaxyproject/galaxy/commit/c134dac9d5f2ec86f0194d114d42… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-04-11 (Tue, 11 Apr 2017) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Identify and handle runtime values when generating displayed text Commit: 7439d03bafe6fad42db950e85c0e329a8f0c8bff https://github.com/galaxyproject/galaxy/commit/7439d03bafe6fad42db950e85c0e… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-04-11 (Tue, 11 Apr 2017) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Remove optional app parameter for text conversion caller Commit: 278030638c50e51e18f712d19a2b8e71c2efc4a1 https://github.com/galaxyproject/galaxy/commit/278030638c50e51e18f712d19a2b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-04-11 (Tue, 11 Apr 2017) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Use new runtime value identifier for select field context values Commit: 18b006cb75ba8f8c088e17ebc7adc52a7b0e11f8 https://github.com/galaxyproject/galaxy/commit/18b006cb75ba8f8c088e17ebc7ad… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-04-11 (Tue, 11 Apr 2017) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/wrappers.py Log Message: ----------- Remove app parameter from text conversion caller Commit: 8ef55bca36673a79974f9f2579543ed6cd15ef3d https://github.com/galaxyproject/galaxy/commit/8ef55bca36673a79974f9f257954… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-04-11 (Tue, 11 Apr 2017) Changed paths: M templates/show_params.mako M templates/webapps/galaxy/workflow/display.mako Log Message: ----------- Remove app parameter from callers used in makos Commit: 9c9a7b97c557444e564c2de6669c28c02226f857 https://github.com/galaxyproject/galaxy/commit/9c9a7b97c557444e564c2de6669c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-04-11 (Tue, 11 Apr 2017) Changed paths: M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/parameters/wrapped.py M lib/galaxy/tools/wrappers.py Log Message: ----------- Remove parsing of app parameter from select field wrapper Commit: 7f111eea528b0be4ad6dfd59bb69076c899ce6aa https://github.com/galaxyproject/galaxy/commit/7f111eea528b0be4ad6dfd59bb69… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-04-11 (Tue, 11 Apr 2017) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Add missing spaces Commit: 735e38d1a3c582727476f8223cdd7c4606e5b413 https://github.com/galaxyproject/galaxy/commit/735e38d1a3c582727476f8223cdd… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-04-11 (Tue, 11 Apr 2017) Changed paths: M test/unit/tools/test_wrappers.py Log Message: ----------- Adjust unit test cases Commit: 55c4d52455763f516aed03795b4a6550ae5744c6 https://github.com/galaxyproject/galaxy/commit/55c4d52455763f516aed03795b4a… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-04-13 (Thu, 13 Apr 2017) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/wrapped.py M lib/galaxy/tools/wrappers.py M templates/show_params.mako M templates/webapps/galaxy/workflow/display.mako M test/unit/tools/test_wrappers.py Log Message: ----------- Merge pull request #3920 from guerler/fix_display_to_text_for_runtime_values Identify and handle runtime values when generating displayed text Compare: https://github.com/galaxyproject/galaxy/compare/d21c8dc8f11c...55c4d5245576

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[galaxyproject/galaxy] 33d662: Fix another tool (GeneBed_Maf_Fasta2) requiring th...
by GitHub 13 Apr '17

13 Apr '17

Branch: refs/heads/release_17.01 Home: https://github.com/galaxyproject/galaxy Commit: 33d6628dabdf75c27979925cb45b94e7ab59d725 https://github.com/galaxyproject/galaxy/commit/33d6628dabdf75c27979925cb45b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-04-13 (Thu, 13 Apr 2017) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Fix another tool (GeneBed_Maf_Fasta2) requiring the legacy Galaxy environment. Commit: 1fe9c4d066e11b61767e22475a1392e0bbacf196 https://github.com/galaxyproject/galaxy/commit/1fe9c4d066e11b61767e22475a13… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-04-13 (Thu, 13 Apr 2017) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge pull request #3931 from jmchilton/maf_fix_47 [17.01] Fix another tool (GeneBed_Maf_Fasta2) requiring the legacy Galaxy environment. Compare: https://github.com/galaxyproject/galaxy/compare/93b366d75a99...1fe9c4d066e1

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[galaxyproject/galaxy] 676b5c: Fix inability to raise errors if OS in non en_US
by GitHub 13 Apr '17

13 Apr '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 676b5cb2779eda3f87d62d2ee5dd74244aaa8071 https://github.com/galaxyproject/galaxy/commit/676b5cb2779eda3f87d62d2ee5dd… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2017-04-05 (Wed, 05 Apr 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/visualization.py Log Message: ----------- Fix inability to raise errors if OS in non en_US Commit: d6336b712592809aabef507802d7ce8179a9d2d7 https://github.com/galaxyproject/galaxy/commit/d6336b712592809aabef507802d7… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2017-04-13 (Thu, 13 Apr 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/visualization.py Log Message: ----------- Remove unnecessary print Commit: d21c8dc8f11c2d4c40967ab9f532a5ce6364f2ea https://github.com/galaxyproject/galaxy/commit/d21c8dc8f11c2d4c40967ab9f532… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-04-13 (Thu, 13 Apr 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/visualization.py Log Message: ----------- Merge pull request #3881 from erasche/unicode-viz-errors Fix inability for viz to raise loading with non-ascii messages Compare: https://github.com/galaxyproject/galaxy/compare/23895e9ef0a0...d21c8dc8f11c

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[galaxyproject/galaxy] 4f4efe: Fix library parameter style width to avoid second ...
by GitHub 13 Apr '17

13 Apr '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4f4efe6405b866c419760af465500458d8dafdba https://github.com/galaxyproject/galaxy/commit/4f4efe6405b866c419760af46550… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-04-12 (Wed, 12 Apr 2017) Changed paths: M client/galaxy/style/less/ui.less M static/style/blue/base.css Log Message: ----------- Fix library parameter style width to avoid second line Commit: 23895e9ef0a001d4dafdedc8aee4846f8c7505d7 https://github.com/galaxyproject/galaxy/commit/23895e9ef0a001d4dafdedc8aee4… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-04-13 (Thu, 13 Apr 2017) Changed paths: M client/galaxy/style/less/ui.less M static/style/blue/base.css Log Message: ----------- Merge pull request #3926 from guerler/fix_library_parameter_style Fix library parameter style width to avoid second line Compare: https://github.com/galaxyproject/galaxy/compare/3e191c7ff445...23895e9ef0a0

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[galaxyproject/ansible-galaxy]
by GitHub 13 Apr '17

13 Apr '17

Branch: refs/tags/0.7.3 Home: https://github.com/galaxyproject/ansible-galaxy

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[galaxyproject/ansible-galaxy] 317e92: Handle galaxy_manage_errordocs correctly
by GitHub 13 Apr '17

13 Apr '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/ansible-galaxy Commit: 317e925b8dd4901d7da1069dc2b6e0f80da26e85 https://github.com/galaxyproject/ansible-galaxy/commit/317e925b8dd4901d7da1… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-04-13 (Thu, 13 Apr 2017) Changed paths: M defaults/main.yml M tasks/main.yml Log Message: ----------- Handle galaxy_manage_errordocs correctly

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[galaxyproject/ansible-galaxy]
by GitHub 13 Apr '17

13 Apr '17

Branch: refs/tags/0.7.2 Home: https://github.com/galaxyproject/ansible-galaxy

1 0

[galaxyproject/ansible-galaxy] 5fef6e: Need a separate variable for managing errordocs wh...
by GitHub 13 Apr '17

13 Apr '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/ansible-galaxy Commit: 5fef6e20d066750f23b5868900a00338c864ce0b https://github.com/galaxyproject/ansible-galaxy/commit/5fef6e20d066750f23b5… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-04-13 (Thu, 13 Apr 2017) Changed paths: M README.md Log Message: ----------- Need a separate variable for managing errordocs when running a split user config

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[galaxyproject/usegalaxy-playbook] bd96bc: Drop the bootstrap script
by GitHub 12 Apr '17

12 Apr '17

Branch: refs/heads/reorg Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: bd96bc4406cc67bc067eeffaf5af66f1f52ea11f https://github.com/galaxyproject/usegalaxy-playbook/commit/bd96bc4406cc67bc… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-04-04 (Tue, 04 Apr 2017) Changed paths: R bootstrap-ansible.bash Log Message: ----------- Drop the bootstrap script Commit: ed83ee9d3c5d3062441fb28cf02cf50fa585f4c0 https://github.com/galaxyproject/usegalaxy-playbook/commit/ed83ee9d3c5d3062… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-04-06 (Thu, 06 Apr 2017) Changed paths: M common_roles M roles/galaxyprojectdotorg.galaxy/README.md M roles/galaxyprojectdotorg.galaxy/defaults/main.yml M roles/galaxyprojectdotorg.galaxy/files/makepyc.py M roles/galaxyprojectdotorg.galaxy/handlers/main.yml M roles/galaxyprojectdotorg.galaxy/meta/.galaxy_install_info M roles/galaxyprojectdotorg.galaxy/tasks/clone.yml M roles/galaxyprojectdotorg.galaxy/tasks/database.yml M roles/galaxyprojectdotorg.galaxy/tasks/dependencies.yml M roles/galaxyprojectdotorg.galaxy/tasks/download.yml M roles/galaxyprojectdotorg.galaxy/tasks/main.yml M roles/galaxyprojectdotorg.galaxy/tasks/mutable_setup.yml M roles/galaxyprojectdotorg.galaxy/tasks/static_setup.yml M roles/galaxyprojectdotorg.galaxy/tasks/virtualenv.yml M roles/galaxyprojectdotorg.nginx/README.md M roles/galaxyprojectdotorg.nginx/meta/.galaxy_install_info M roles/galaxyprojectdotorg.nginx/meta/main.yml M roles/galaxyprojectdotorg.nginx/tasks/main.yml A roles/galaxyprojectdotorg.nginx/tasks/pkgin.yml M roles/galaxyprojectdotorg.nginx/templates/epel-nginx.conf.j2 A roles/galaxyprojectdotorg.nginx/templates/pkgin-nginx.conf.j2 A roles/galaxyprojectdotorg.nginx/vars/pkgin.yml M roles/galaxyprojectdotorg.postgresql/files/get_repo_rpm_release.py M roles/galaxyprojectdotorg.postgresql/meta/.galaxy_install_info M roles/galaxyprojectdotorg.postgresql/tasks/main.yml M roles/galaxyprojectdotorg.postgresql/tasks/redhat.yml M roles/galaxyprojectdotorg.postgresql/templates/archive_wal.sh.j2 M roles/galaxyprojectdotorg.postgresql/templates/backup_working_wal.sh.j2 M roles/galaxyprojectdotorg.postgresql/templates/scheduled_backup.sh.j2 M roles/natefoo.postgresql_objects/README.md M roles/natefoo.postgresql_objects/meta/.galaxy_install_info M roles/natefoo.postgresql_objects/tasks/main.yml Log Message: ----------- Update roles Commit: 60df6e1d5c7879155576d7b98b880c9f74be94e6 https://github.com/galaxyproject/usegalaxy-playbook/commit/60df6e1d5c787915… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-04-07 (Fri, 07 Apr 2017) Changed paths: M production/files/interactive_environments/plugins/bam_iobio/config/bam_iobio.ini.sample M production/files/interactive_environments/plugins/bam_iobio/static/js/bam_iobio.js M production/files/interactive_environments/plugins/bam_iobio/templates/bam_iobio.mako M production/files/interactive_environments/plugins/common/templates/ie.mako R production/files/interactive_environments/plugins/ethercalc/config/allowed_images.yml.sample R production/files/interactive_environments/plugins/ethercalc/config/ethercalc.ini.sample R production/files/interactive_environments/plugins/ethercalc/config/ethercalc.xml R production/files/interactive_environments/plugins/ethercalc/static/js/ethercalc.js R production/files/interactive_environments/plugins/ethercalc/templates/ethercalc.mako M production/files/interactive_environments/plugins/jupyter/config/allowed_images.yml.sample M production/files/interactive_environments/plugins/jupyter/config/jupyter.ini.sample M production/files/interactive_environments/plugins/jupyter/config/jupyter.xml M production/files/interactive_environments/plugins/jupyter/static/js/jupyter.js M production/files/interactive_environments/plugins/jupyter/templates/jupyter.mako M production/files/interactive_environments/plugins/neo/config/neo.ini.sample M production/files/interactive_environments/plugins/neo/static/js/neo.js M production/files/interactive_environments/plugins/neo/templates/neo.mako M production/files/interactive_environments/plugins/phinch/config/phinch.ini.sample M production/files/interactive_environments/plugins/phinch/static/js/phinch.js M production/files/interactive_environments/plugins/phinch/templates/phinch.mako M production/files/interactive_environments/plugins/rstudio/config/rstudio.ini.sample M production/files/interactive_environments/plugins/rstudio/static/js/rstudio.js M production/files/interactive_environments/plugins/rstudio/templates/rstudio.mako M production/files/interactive_environments/proxy/lib/mapper.js M roles/galaxyprojectdotorg.interactive_environments/meta/.galaxy_install_info M roles/galaxyprojectdotorg.interactive_environments/tasks/extract_component.yml M roles/galaxyprojectdotorg.interactive_environments/tasks/synchronize_components.yml Log Message: ----------- Merge branch 'master' of github.com:/galaxyproject/usegalaxy-playbook into reorg Commit: bad32b46a7af10c27f6e6889d10db1c58b8239c1 https://github.com/galaxyproject/usegalaxy-playbook/commit/bad32b46a7af10c2… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-04-12 (Wed, 12 Apr 2017) Changed paths: M README.md M ansible.cfg R common/host_vars/galaxy01.tacc.utexas.edu.yml R common/host_vars/galaxy05.tacc.utexas.edu.yml R common/host_vars/radegast.galaxyproject.org.yml M common/inventory M common_roles A env/common/_inc_restart.yml A env/common/_inc_snapshot.yml A env/common/_inc_static.yml A env/common/config.yml A env/common/files/galaxy/config/disposable_email_blacklist.conf A env/common/files/galaxy/config/pulsar_jetstream_actions.yml A env/common/files/galaxy/dynamic_rules/bridges_select.py A env/common/files/galaxy/dynamic_rules/multi_dynamic_walltime.py A 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env/common/templates/galaxy/config/reports.ini.j2 A env/common/templates/galaxy/static/welcome.html.j2 A env/common/templates/nginx/toolshed.j2 A env/common/templates/supervisor/galaxy.j2 A env/common/templates/supervisor/galaxy_datamanager.j2 A env/common/templates/supervisor/galaxy_gie_proxy.j2 A env/common/templates/supervisor/galaxy_group.j2 A env/common/templates/supervisor/galaxy_handler.j2 A env/common/templates/supervisor/galaxy_impersonate.j2 A env/common/templates/supervisor/galaxy_reports.j2 A env/common/templates/supervisor/toolshed.j2 A env/common/update.yml A env/common/update_shed.yml A env/test/_inc_config_post_tasks.yml A env/test/_inc_restart.yml A env/test/_inc_snapshot.yml A env/test/_inc_static.yml A env/test/config.yml A env/test/files/galaxy/config/builds.txt A env/test/files/galaxy/config/data_manager_conf.xml A env/test/files/galaxy/config/disposable_email_blacklist.conf A env/test/files/galaxy/config/job_metrics_conf.xml A env/test/files/galaxy/config/job_resource_params_conf.xml A env/test/files/galaxy/config/nagios_tool_conf.xml A env/test/files/galaxy/config/object_store_conf.xml A env/test/files/galaxy/config/pulsar_jetstream.yml A env/test/files/galaxy/config/pulsar_jetstream_actions.yml A env/test/files/galaxy/config/pulsar_stampede_actions.yml A env/test/files/galaxy/config/tool_conf.xml A env/test/files/galaxy/config/tool_data_table_conf.xml A env/test/files/galaxy/config/tool_sheds_conf.xml A env/test/files/galaxy/config/ucsc_build_sites.txt A env/test/files/galaxy/dynamic_rules/bridges_select.py A env/test/files/galaxy/dynamic_rules/jetstream.py A env/test/files/galaxy/dynamic_rules/multi_dynamic_walltime.py A env/test/files/galaxy/dynamic_rules/nvc_dynamic_memory.py A env/test/files/galaxy/dynamic_rules/reserved.py A env/test/files/galaxy/dynamic_rules/single_dynamic_memory.py A env/test/files/galaxy/error A env/test/files/galaxy/galaxy_version.yml A env/test/files/galaxy/nagios/echo_test_bridges.xml A env/test/files/galaxy/nagios/echo_test_cluster.xml A env/test/files/galaxy/nagios/echo_test_handler0.xml A env/test/files/galaxy/nagios/echo_test_handler1.xml A env/test/files/galaxy/nagios/echo_test_jetstream_iu.xml A env/test/files/galaxy/nagios/echo_test_jetstream_tacc.xml A env/test/files/galaxy/nagios/echo_test_stampede.xml A env/test/files/galaxy/static A env/test/files/galaxy/tool_list.yaml A env/test/files/galaxy/var/integrated_tool_panel.xml A env/test/files/galaxy/var/migrated_tools_conf.xml A env/test/files/galaxy/var/shed_data_manager_conf.xml A env/test/files/galaxy/var/shed_tool_conf.xml A env/test/files/galaxy/var/shed_tool_data_table_conf.xml A env/test/files/interactive_environments/plugins/.ansible_ie_role_current_version A env/test/files/interactive_environments/plugins/bam_iobio/config/bam_iobio.ini.sample A env/test/files/interactive_environments/plugins/bam_iobio/config/bam_iobio.xml A 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env/test/files/interactive_environments/plugins/jupyter/templates/jupyter.mako A env/test/files/interactive_environments/plugins/neo/config/allowed_images.yml.sample A env/test/files/interactive_environments/plugins/neo/config/neo.ini.sample A env/test/files/interactive_environments/plugins/neo/config/neo.xml A env/test/files/interactive_environments/plugins/neo/static/js/neo.js A env/test/files/interactive_environments/plugins/neo/templates/neo.mako A env/test/files/interactive_environments/plugins/phinch/config/phinch.ini.sample A env/test/files/interactive_environments/plugins/phinch/config/phinch.xml A env/test/files/interactive_environments/plugins/phinch/static/js/phinch.js A env/test/files/interactive_environments/plugins/phinch/templates/phinch.mako A env/test/files/interactive_environments/plugins/rstudio/config/allowed_images.yml.sample A env/test/files/interactive_environments/plugins/rstudio/config/rstudio.ini.sample A 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env/test/files/interactive_environments/proxy/lib/main.js A env/test/files/interactive_environments/proxy/lib/mapper.js A env/test/files/interactive_environments/proxy/lib/proxy.js A env/test/files/interactive_environments/proxy/package.json A env/test/files/pulsar A env/test/files/ssl A env/test/group_vars/all.yml A env/test/group_vars/dbservers/vars.yml A env/test/group_vars/dbservers/vault.yml A env/test/group_vars/ftpservers.yml A env/test/group_vars/galaxyservers/vars.yml A env/test/group_vars/galaxyservers/vault.yml A env/test/group_vars/galaxyswarmmanagers/vars.yml A env/test/group_vars/galaxyswarmmanagers/vault.yml A env/test/group_vars/galaxywebservers.yml A env/test/group_vars/pulsarservers/vars.yml A env/test/group_vars/pulsarservers/vault.yml A env/test/group_vars/sslservers A env/test/group_vars/supervisorservers/vars.yml A env/test/group_vars/supervisorservers/vault.yml A env/test/group_vars/webservers/vars.yml A env/test/group_vars/webservers/vault.yml A env/test/host_vars/br005.bridges.psc.edu.yml A env/test/host_vars/galaxy07.tacc.utexas.edu.yml A env/test/host_vars/jetstream-iu0.galaxyproject.org.yml A env/test/host_vars/jetstream-tacc0.galaxyproject.org.yml A env/test/host_vars/login5.stampede.tacc.utexas.edu.yml A env/test/inventory A env/test/inventory.static A env/test/pulsar.yml A env/test/restart.yml A env/test/snapshot.yml A env/test/stack.yml A env/test/static.yml A env/test/templates/galaxy/config/build_sites.yml.j2 A env/test/templates/galaxy/config/galaxy.ini.j2 A env/test/templates/galaxy/config/job_conf.xml.j2 A env/test/templates/galaxy/config/reports.ini.j2 A env/test/templates/galaxy/config/uwsgi.ini.j2 A env/test/templates/galaxy/static A env/test/templates/nginx/galaxy_test.j2 A env/test/templates/nginx/tacc_protected.j2 A env/test/templates/supervisor A env/test/update.yml A env/testtoolshed/files/ssl A env/testtoolshed/group_vars/sslservers A env/testtoolshed/group_vars/toolsheddbservers.yml A 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files/pulsar/test.galaxyproject.org/config/bridges_dependency_resolvers_con… R files/toolshed/testtoolshed.g2.bx.psu.edu/error R galaxy_configs.yml R galaxy_infrastructure.yml R galaxy_static.yml R pulsar.yml R roles/errordocs/tasks/main.yml M roles/galaxyprojectdotorg.galaxy/README.md M roles/galaxyprojectdotorg.galaxy/defaults/main.yml A roles/galaxyprojectdotorg.galaxy/files/errordocs/content_bg.png A roles/galaxyprojectdotorg.galaxy/files/errordocs/error_message_icon.png A roles/galaxyprojectdotorg.galaxy/files/errordocs/masthead_bg.png M roles/galaxyprojectdotorg.galaxy/meta/.galaxy_install_info A roles/galaxyprojectdotorg.galaxy/tasks/errordocs.yml M roles/galaxyprojectdotorg.galaxy/tasks/main.yml A roles/galaxyprojectdotorg.galaxy/templates/errordocs/413/index.html.j2 A roles/galaxyprojectdotorg.galaxy/templates/errordocs/502/index.shtml.j2 A roles/galaxyprojectdotorg.galaxy_toolshed/README.md M roles/galaxyprojectdotorg.galaxy_toolshed/defaults/main.yml M roles/galaxyprojectdotorg.galaxy_toolshed/handlers/main.yml A roles/galaxyprojectdotorg.galaxy_toolshed/meta/.galaxy_install_info A roles/galaxyprojectdotorg.galaxy_toolshed/meta/main.yml M roles/galaxyprojectdotorg.galaxy_toolshed/tasks/database.yml M roles/galaxyprojectdotorg.galaxy_toolshed/tasks/main.yml M roles/galaxyprojectdotorg.galaxy_toolshed/tasks/static_setup.yml A roles/galaxyprojectdotorg.galaxy_toolshed/templates/user_info.xml.j2 M roles/galaxyprojectdotorg.postgresql/defaults/main.yml M roles/galaxyprojectdotorg.postgresql/meta/.galaxy_install_info M roles/galaxyprojectdotorg.postgresql/templates/archive_wal.sh.j2 A roles/galaxyprojectdotorg.proftpd/.travis.yml A roles/galaxyprojectdotorg.proftpd/README.md A roles/galaxyprojectdotorg.proftpd/defaults/main.yml A roles/galaxyprojectdotorg.proftpd/handlers/main.yml A roles/galaxyprojectdotorg.proftpd/meta/main.yml A roles/galaxyprojectdotorg.proftpd/tasks/debian.yml A roles/galaxyprojectdotorg.proftpd/tasks/galaxy_auth.yml A roles/galaxyprojectdotorg.proftpd/tasks/main.yml A roles/galaxyprojectdotorg.proftpd/tasks/redhat.yml A roles/galaxyprojectdotorg.proftpd/tasks/tls.yml A roles/galaxyprojectdotorg.proftpd/templates/galaxy_auth.conf.j2 A roles/galaxyprojectdotorg.proftpd/templates/server.conf.j2 A roles/galaxyprojectdotorg.proftpd/templates/tls.conf.j2 A roles/galaxyprojectdotorg.proftpd/tests/inventory A roles/galaxyprojectdotorg.proftpd/tests/test.yml A roles/galaxyprojectdotorg.proftpd/vars/debian.yml A roles/galaxyprojectdotorg.proftpd/vars/main.yml A roles/galaxyprojectdotorg.proftpd/vars/redhat.yml M roles/usegalaxy/tasks/main.yml A roles/usegalaxy/templates/galaxyctl.j2 A roles/usegalaxy/templates/supervisorctl.j2 A roles/usegalaxy/templates/supervisord.conf.j2 M roles/usegalaxy_admin/tasks/main.yml A roles/usegalaxy_cvmfs/tasks/main.yml A roles/usegalaxy_cvmfs/tasks/snapshot.yml A roles/usegalaxy_cvmfs/tasks/update.yml A roles/usegalaxy_cvmfs/tasks/wipecache.yml M roles/usegalaxy_privileged/tasks/main.yml M roles/usegalaxy_static/tasks/main.yml R stage/files/interactive_environments/plugins/.ansible_ie_role_current_version R stage/files/interactive_environments/plugins/bam_iobio/config/bam_iobio.ini.sample R stage/files/interactive_environments/plugins/bam_iobio/config/bam_iobio.xml R stage/files/interactive_environments/plugins/bam_iobio/static/js/bam_iobio.js R stage/files/interactive_environments/plugins/bam_iobio/templates/bam_iobio.mako R stage/files/interactive_environments/plugins/common/templates/ie.mako R stage/files/interactive_environments/plugins/ethercalc/config/ethercalc.ini.sample R stage/files/interactive_environments/plugins/ethercalc/config/ethercalc.xml R stage/files/interactive_environments/plugins/ethercalc/static/js/ethercalc.js R stage/files/interactive_environments/plugins/ethercalc/templates/ethercalc.mako R stage/files/interactive_environments/plugins/interactive_environments.dtd R stage/files/interactive_environments/plugins/jupyter/config/allowed_images.yml.sample R stage/files/interactive_environments/plugins/jupyter/config/jupyter.ini.sample R stage/files/interactive_environments/plugins/jupyter/config/jupyter.xml R stage/files/interactive_environments/plugins/jupyter/static/js/jupyter.js R stage/files/interactive_environments/plugins/jupyter/templates/jupyter.mako R stage/files/interactive_environments/plugins/neo/config/allowed_images.yml.sample R stage/files/interactive_environments/plugins/neo/config/neo.ini.sample R stage/files/interactive_environments/plugins/neo/config/neo.xml R stage/files/interactive_environments/plugins/neo/static/js/neo.js R stage/files/interactive_environments/plugins/neo/templates/neo.mako R stage/files/interactive_environments/plugins/phinch/config/phinch.ini.sample R stage/files/interactive_environments/plugins/phinch/config/phinch.xml R stage/files/interactive_environments/plugins/phinch/static/js/phinch.js R stage/files/interactive_environments/plugins/phinch/templates/phinch.mako R stage/files/interactive_environments/plugins/rstudio/config/allowed_images.yml.sample R stage/files/interactive_environments/plugins/rstudio/config/rstudio.ini.sample R stage/files/interactive_environments/plugins/rstudio/config/rstudio.xml R stage/files/interactive_environments/plugins/rstudio/static/js/crypto/base64.js R stage/files/interactive_environments/plugins/rstudio/static/js/crypto/jsbn.js R stage/files/interactive_environments/plugins/rstudio/static/js/crypto/prng4.js R stage/files/interactive_environments/plugins/rstudio/static/js/crypto/rng.js R stage/files/interactive_environments/plugins/rstudio/static/js/crypto/rsa.js R stage/files/interactive_environments/plugins/rstudio/static/js/crypto/rstudio.big.js R stage/files/interactive_environments/plugins/rstudio/static/js/crypto/rstudio.min.js R stage/files/interactive_environments/plugins/rstudio/static/js/crypto/rstudio/base64.js R stage/files/interactive_environments/plugins/rstudio/static/js/crypto/rstudio/jsbn.js R stage/files/interactive_environments/plugins/rstudio/static/js/crypto/rstudio/prng4.js R stage/files/interactive_environments/plugins/rstudio/static/js/crypto/rstudio/rng.js R stage/files/interactive_environments/plugins/rstudio/static/js/crypto/rstudio/rsa.js R stage/files/interactive_environments/plugins/rstudio/static/js/crypto/wu/base64.js R stage/files/interactive_environments/plugins/rstudio/static/js/crypto/wu/jsbn.js R stage/files/interactive_environments/plugins/rstudio/static/js/crypto/wu/prng4.js R stage/files/interactive_environments/plugins/rstudio/static/js/crypto/wu/rng.js R stage/files/interactive_environments/plugins/rstudio/static/js/crypto/wu/rsa.js R stage/files/interactive_environments/plugins/rstudio/static/js/rstudio.js R stage/files/interactive_environments/plugins/rstudio/templates/rstudio.mako R stage/files/interactive_environments/proxy/.ansible_ie_role_current_version R stage/files/interactive_environments/proxy/Dockerfile R stage/files/interactive_environments/proxy/README.md R stage/files/interactive_environments/proxy/lib/main.js R stage/files/interactive_environments/proxy/lib/mapper.js R stage/files/interactive_environments/proxy/lib/proxy.js R stage/files/interactive_environments/proxy/package.json R stage/galaxy_version.yml R stage/group_vars/all.yml R stage/group_vars/galaxydbservers.yml R stage/group_vars/galaxyservers.yml R stage/group_vars/pulsarservers.yml R stage/group_vars/toolsheddbservers.yml R stage/group_vars/toolshedservers.yml R stage/host_vars/br005.bridges.psc.edu.yml R stage/host_vars/galaxy01.tacc.utexas.edu.yml R stage/host_vars/jetstream-iu0.galaxyproject.org.yml R stage/host_vars/jetstream-tacc0.galaxyproject.org.yml R stage/host_vars/login5.stampede.tacc.utexas.edu.yml R stage/secret_vars/galaxydbservers.yml R stage/secret_vars/galaxyservers.yml R stage/secret_vars/pulsarservers.yml R templates/galaxy/test.galaxyproject.org/config/build_sites.yml.j2 R templates/galaxy/test.galaxyproject.org/config/job_conf.xml.j2 R templates/galaxy/test.galaxyproject.org/config/reports.ini.j2 R templates/galaxy/test.galaxyproject.org/config/uwsgi.ini.j2 R templates/galaxy/test.galaxyproject.org/static R templates/nginx/galaxy_main_installer.j2 R templates/nginx/galaxy_test.j2 R templates/nginx/tacc_protected.j2 R templates/nginx/testtoolshed.j2 R templates/nginx/toolshed.j2 R templates/supervisor/galaxy_datamanager.j2 R templates/supervisor/galaxy_installer.j2 R templates/supervisor/testtoolshed.j2 R templates/supervisor/toolshed.j2 R toolshed.yml Log Message: ----------- Reorganize and update playbook for complete redeployment of Test on to a new VM. The new VM was deployed entirely with infrastructure-playbook and this playbook. The Test Tool Shed was also reorganized due to the removal of `stage`. Coming soon: Main Commit: be93b172eb3ea3a4aa41e8a16b7027799a5d8533 https://github.com/galaxyproject/usegalaxy-playbook/commit/be93b172eb3ea3a4… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-04-12 (Wed, 12 Apr 2017) Changed paths: M env/test/files/galaxy/galaxy_version.yml Log Message: ----------- Update Test Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/bd96bc4406cc^..…

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[galaxyproject/ansible-galaxy]
by GitHub 12 Apr '17

12 Apr '17

Branch: refs/tags/0.7.1 Home: https://github.com/galaxyproject/ansible-galaxy

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[galaxyproject/ansible-galaxy] 1bff19: Add error documents for nginx
by GitHub 12 Apr '17

12 Apr '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/ansible-galaxy Commit: 1bff199822c7c8456a6d2ff802ec98732c57a4d0 https://github.com/galaxyproject/ansible-galaxy/commit/1bff199822c7c8456a6d… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-04-12 (Wed, 12 Apr 2017) Changed paths: M README.md M defaults/main.yml A files/errordocs/content_bg.png A files/errordocs/error_message_icon.png A files/errordocs/masthead_bg.png A tasks/errordocs.yml M tasks/main.yml A templates/errordocs/413/index.html.j2 A templates/errordocs/502/index.shtml.j2 Log Message: ----------- Add error documents for nginx

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[galaxyproject/galaxy] 9aa023: Fix for direct message routing using a 'real' exch...
by GitHub 12 Apr '17

12 Apr '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 9aa02339e730988cc1174103e3091690f3c8a42d https://github.com/galaxyproject/galaxy/commit/9aa02339e730988cc1174103e309… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-29 (Wed, 29 Mar 2017) Changed paths: M lib/galaxy/queue_worker.py M lib/galaxy/queues.py Log Message: ----------- Fix for direct message routing using a 'real' exchange like rabbitmq -- this worked with local/database connections already, if accidentally. I want to do more refactoring of how these are configured, but am deferring that for now as it's not a priority. Commit: cda2b32ebeb9a02c44377ded8b1727d3bd2a394d https://github.com/galaxyproject/galaxy/commit/cda2b32ebeb9a02c44377ded8b17… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-04-08 (Sat, 08 Apr 2017) Changed paths: M lib/galaxy/queue_worker.py Log Message: ----------- Fix Instance is not bound to a Session by refreshing the tool_version_cache, just like we do when we reload the toolbox. Commit: 2396befa02df1083da56357b9210e9d62fdb4266 https://github.com/galaxyproject/galaxy/commit/2396befa02df1083da56357b9210… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-04-09 (Sun, 09 Apr 2017) Changed paths: M lib/galaxy/queue_worker.py M lib/galaxy/queues.py Log Message: ----------- Merge pull request #3846 from dannon/mq_routing_fix [17.01] Fix for direct message routing using a 'real' exchange like rabbitmq Commit: 93b366d75a99b3335a92be792c89443487bfd49d https://github.com/galaxyproject/galaxy/commit/93b366d75a99b3335a92be792c89… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-04-09 (Sun, 09 Apr 2017) Changed paths: M lib/galaxy/queue_worker.py Log Message: ----------- Merge pull request #3904 from mvdbeek/fix_instance_not_bound [17.01] Fix Instance is not bound to a Session Commit: 3e191c7ff4457ce4723c914d3ae9ad8157beecb5 https://github.com/galaxyproject/galaxy/commit/3e191c7ff4457ce4723c914d3ae9… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-04-12 (Wed, 12 Apr 2017) Changed paths: M lib/galaxy/queue_worker.py M lib/galaxy/queues.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_17.01' into dev Compare: https://github.com/galaxyproject/galaxy/compare/e7a4ae5c154e...3e191c7ff445

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[galaxyproject/usegalaxy-playbook] 5f58c1: Swap sanitize_whitelist to use mutable config dir
by GitHub 11 Apr '17

11 Apr '17

Branch: refs/heads/mutable_config_for_whitelist Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 5f58c100f70ef653802c750b01d5ee7f5f0748da https://github.com/galaxyproject/usegalaxy-playbook/commit/5f58c100f70ef653… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-04-11 (Tue, 11 Apr 2017) Changed paths: M production/group_vars/galaxyservers.yml Log Message: ----------- Swap sanitize_whitelist to use mutable config dir

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