July 2017 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/infrastructure-playbook] 5c5b7e: Access list
by GitHub 18 Jul '17

18 Jul '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 5c5b7e5c1f7c832aa3e224a738d0fc73ccc66f51 https://github.com/galaxyproject/infrastructure-playbook/commit/5c5b7e5c1f7… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-07-18 (Tue, 18 Jul 2017) Changed paths: M taccenv/host_vars/galaxy-db-02.tacc.utexas.edu/vault.yml Log Message: ----------- Access list

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[galaxyproject/galaxy] 2f0024: add unipept triple visualization
by GitHub 18 Jul '17

18 Jul '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 2f00242261247ff9f7f7149ae1bad15e3be39c66 https://github.com/galaxyproject/galaxy/commit/2f00242261247ff9f7f7149ae1ba… Author: Caleb <caleb.easterly(a)gmail.com> Date: 2017-07-12 (Wed, 12 Jul 2017) Changed paths: A config/plugins/visualizations/unipept/LICENSE A config/plugins/visualizations/unipept/README.md A config/plugins/visualizations/unipept/config/unipept.xml A config/plugins/visualizations/unipept/static/style.css A config/plugins/visualizations/unipept/static/tooltip.css A config/plugins/visualizations/unipept/static/unipept-visualizations.es5.js A config/plugins/visualizations/unipept/static/unipept-visualizations.es5.js.map A config/plugins/visualizations/unipept/static/unipept-visualizations.js A config/plugins/visualizations/unipept/static/unipept-visualizations.js.map A config/plugins/visualizations/unipept/static/unipept-visualizations.min.js A config/plugins/visualizations/unipept/static/unipept_viz.js A config/plugins/visualizations/unipept/templates/glyphicons-86-repeat.png A config/plugins/visualizations/unipept/templates/unipept.mako Log Message: ----------- add unipept triple visualization Commit: 2a49f1f62a0a536d8a5eca6ab2bc92badecb82cc https://github.com/galaxyproject/galaxy/commit/2a49f1f62a0a536d8a5eca6ab2bc… Author: Caleb <caleb.easterly(a)gmail.com> Date: 2017-07-12 (Wed, 12 Jul 2017) Changed paths: A config/plugins/visualizations/unipept/LICENSE A config/plugins/visualizations/unipept/README.md A config/plugins/visualizations/unipept/config/unipept.xml A config/plugins/visualizations/unipept/static/style.css A config/plugins/visualizations/unipept/static/tooltip.css A config/plugins/visualizations/unipept/static/unipept-visualizations.es5.js A config/plugins/visualizations/unipept/static/unipept-visualizations.es5.js.map A config/plugins/visualizations/unipept/static/unipept-visualizations.js A config/plugins/visualizations/unipept/static/unipept-visualizations.js.map A config/plugins/visualizations/unipept/static/unipept-visualizations.min.js A config/plugins/visualizations/unipept/static/unipept_viz.js A config/plugins/visualizations/unipept/templates/glyphicons-86-repeat.png A config/plugins/visualizations/unipept/templates/unipept.mako Log Message: ----------- add unipept triple visualization Commit: 2044c7fa25e1d9f039f2462a90b86de505127168 https://github.com/galaxyproject/galaxy/commit/2044c7fa25e1d9f039f2462a90b8… Author: Caleb <caleb.easterly(a)gmail.com> Date: 2017-07-12 (Wed, 12 Jul 2017) Log Message: ----------- Merge branch 'dev' of https://github.com/caleb-easterly/galaxy into dev Commit: 2f66a419a442313c952ae8386add6599947d288d https://github.com/galaxyproject/galaxy/commit/2f66a419a442313c952ae8386add… Author: Caleb <caleb.easterly(a)gmail.com> Date: 2017-07-12 (Wed, 12 Jul 2017) Changed paths: A .gitmodules Log Message: ----------- submodules file Commit: 85fc4d11f97facdf8c119f82116acc632c26708e https://github.com/galaxyproject/galaxy/commit/85fc4d11f97facdf8c119f82116a… Author: Caleb <caleb.easterly(a)gmail.com> Date: 2017-07-13 (Thu, 13 Jul 2017) Changed paths: R .gitmodules Log Message: ----------- remove submodule Commit: 2fbf9afc64e4fa41993fe400148527a773226348 https://github.com/galaxyproject/galaxy/commit/2fbf9afc64e4fa41993fe4001485… Author: Caleb <caleb.easterly(a)gmail.com> Date: 2017-07-13 (Thu, 13 Jul 2017) Changed paths: M config/plugins/visualizations/unipept/static/style.css M config/plugins/visualizations/unipept/templates/unipept.mako Log Message: ----------- fix treemap being too wide Commit: c39a82f76c4ab1cc297086d29bb7f4363c6c0aa2 https://github.com/galaxyproject/galaxy/commit/c39a82f76c4ab1cc297086d29bb7… Author: Caleb <caleb.easterly(a)gmail.com> Date: 2017-07-13 (Thu, 13 Jul 2017) Changed paths: R config/plugins/visualizations/unipept/LICENSE Log Message: ----------- remove license Commit: 9445acaa6e8b06dad5602e772a01ceddc5247ef2 https://github.com/galaxyproject/galaxy/commit/9445acaa6e8b06dad5602e772a01… Author: Caleb Easterly <caleb.easterly(a)gmail.com> Date: 2017-07-13 (Thu, 13 Jul 2017) Changed paths: M config/plugins/visualizations/unipept/README.md Log Message: ----------- fix jj's link Commit: 2d13f9b843589e5b33ceaf41762ba759e1e02d98 https://github.com/galaxyproject/galaxy/commit/2d13f9b843589e5b33ceaf41762b… Author: Caleb <caleb.easterly(a)gmail.com> Date: 2017-07-14 (Fri, 14 Jul 2017) Changed paths: M config/plugins/visualizations/unipept/templates/unipept.mako Log Message: ----------- downgrade to unipept-visualizations.es5.js for compatibility with older browsers Commit: b2bb88a41d8e8055faa57658b3a06855f0adebe5 https://github.com/galaxyproject/galaxy/commit/b2bb88a41d8e8055faa57658b3a0… Author: Caleb <caleb.easterly(a)gmail.com> Date: 2017-07-17 (Mon, 17 Jul 2017) Changed paths: R config/plugins/visualizations/unipept/static/unipept-visualizations.js R config/plugins/visualizations/unipept/static/unipept-visualizations.js.map R config/plugins/visualizations/unipept/static/unipept-visualizations.min.js Log Message: ----------- remove extraneous js files Commit: 7351252b21c9364640b264affef199bf1f95d480 https://github.com/galaxyproject/galaxy/commit/7351252b21c9364640b264affef1… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-07-18 (Tue, 18 Jul 2017) Changed paths: A config/plugins/visualizations/unipept/README.md A config/plugins/visualizations/unipept/config/unipept.xml A config/plugins/visualizations/unipept/static/style.css A config/plugins/visualizations/unipept/static/tooltip.css A config/plugins/visualizations/unipept/static/unipept-visualizations.es5.js A config/plugins/visualizations/unipept/static/unipept-visualizations.es5.js.map A config/plugins/visualizations/unipept/static/unipept_viz.js A config/plugins/visualizations/unipept/templates/glyphicons-86-repeat.png A config/plugins/visualizations/unipept/templates/unipept.mako Log Message: ----------- Merge pull request #4310 from caleb-easterly/dev Add Unipept taxonomy viewer plugin Compare: https://github.com/galaxyproject/galaxy/compare/4ba2b9f815e5...7351252b21c9

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[galaxyproject/galaxy] 19a6b4: Swap the deprecated unescape() for decodeURICompon...
by GitHub 17 Jul '17

17 Jul '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 19a6b4f6932706e22a231c5fb156b1857d7aa7dc https://github.com/galaxyproject/galaxy/commit/19a6b4f6932706e22a231c5fb156… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-07-17 (Mon, 17 Jul 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Swap the deprecated unescape() for decodeURIComponent Commit: 4ba2b9f815e5ab2e0789a11ee203ba7e30adff51 https://github.com/galaxyproject/galaxy/commit/4ba2b9f815e5ab2e0789a11ee203… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2017-07-17 (Mon, 17 Jul 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Merge pull request #4321 from dannon/unescape_to_decodeuricomp Swap the deprecated unescape() for decodeURIComponent Compare: https://github.com/galaxyproject/galaxy/compare/9cbcb525ebfc...4ba2b9f815e5

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[galaxyproject/galaxy] c90b94: Instead of setting the tags from a list, workflow ...
by GitHub 17 Jul '17

17 Jul '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c90b94311e5427da95a36a9661c1d0eb19e16fc2 https://github.com/galaxyproject/galaxy/commit/c90b94311e5427da95a36a9661c1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-06-13 (Tue, 13 Jun 2017) Changed paths: M lib/galaxy/jobs/actions/post.py M lib/galaxy/managers/tags.py Log Message: ----------- Instead of setting the tags from a list, workflow PJAs will now append tags, so propagating tags will work alongside this feature. Commit: 01510af8f57508877dda205cb0afdc144bfa73c2 https://github.com/galaxyproject/galaxy/commit/01510af8f57508877dda205cb0af… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-06-13 (Tue, 13 Jun 2017) Changed paths: M lib/galaxy/managers/tags.py Log Message: ----------- Consistent spacing (not a fan of the rule, but consistency is better) Commit: 472ff8ce520a6327179dd54c301db763ea7e979b https://github.com/galaxyproject/galaxy/commit/472ff8ce520a6327179dd54c301d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-06-13 (Tue, 13 Jun 2017) Changed paths: M lib/galaxy/managers/tags.py Log Message: ----------- Fix for when item.tags is undefined Commit: 368be188d0918adaa0d7f752883c24bb79f261ec https://github.com/galaxyproject/galaxy/commit/368be188d0918adaa0d7f752883c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-06-26 (Mon, 26 Jun 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Unescape tool id before parsing to tool form builder Commit: f439fd30eb1f803daf8e1898bc1648c8cee131f8 https://github.com/galaxyproject/galaxy/commit/f439fd30eb1f803daf8e1898bc16… Author: Andrea Bagnacani <andrea.bagnacani(a)uni-rostock.de> Date: 2017-06-26 (Mon, 26 Jun 2017) Changed paths: M client/galaxy/scripts/mvc/tours.js M static/maps/mvc/tool/tool-form-base.js.map M static/maps/mvc/tours.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/tours.js Log Message: ----------- conditional postclick execution onNext Commit: fc613d2d60c126b3b37c9ebe3ddbd9cc58803643 https://github.com/galaxyproject/galaxy/commit/fc613d2d60c126b3b37c9ebe3ddb… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-07-05 (Wed, 05 Jul 2017) Changed paths: M lib/galaxy/jobs/actions/post.py M lib/galaxy/managers/tags.py Log Message: ----------- Merge pull request #4188 from dannon/workflow_pja_add_not_set_tags [17.05] Hashtags w/ workflow-defined tags fix Commit: e58b24db6133720edf442ca85702e4bba050e9c9 https://github.com/galaxyproject/galaxy/commit/e58b24db6133720edf442ca85702… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-07-10 (Mon, 10 Jul 2017) Changed paths: M client/galaxy/scripts/mvc/tours.js M static/maps/mvc/tool/tool-form-base.js.map M static/maps/mvc/tours.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/tours.js Log Message: ----------- Merge pull request #4228 from bagnacan/release_17.05_backport_4062 [17.05] conditional postclick execution onNext Commit: d4d558b27a09f684be8311f3cfb659b16545e167 https://github.com/galaxyproject/galaxy/commit/d4d558b27a09f684be8311f3cfb6… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-07-17 (Mon, 17 Jul 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Merge remote-tracking branch 'guerler/fix_id_encoding' into release_17.05 Includes client rebuild. Commit: 9cbcb525ebfc5368f7cfeade2f1080084ee5f2de https://github.com/galaxyproject/galaxy/commit/9cbcb525ebfc5368f7cfeade2f10… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-07-17 (Mon, 17 Jul 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js M lib/galaxy/jobs/actions/post.py M lib/galaxy/managers/tags.py M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map Log Message: ----------- Merge branch 'release_17.05' into dev Compare: https://github.com/galaxyproject/galaxy/compare/ae2fe8992a87...9cbcb525ebfc

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[galaxyproject/galaxy] 368be1: Unescape tool id before parsing to tool form build...
by GitHub 17 Jul '17

17 Jul '17

Branch: refs/heads/release_17.05 Home: https://github.com/galaxyproject/galaxy Commit: 368be188d0918adaa0d7f752883c24bb79f261ec https://github.com/galaxyproject/galaxy/commit/368be188d0918adaa0d7f752883c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-06-26 (Mon, 26 Jun 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Unescape tool id before parsing to tool form builder Commit: d4d558b27a09f684be8311f3cfb659b16545e167 https://github.com/galaxyproject/galaxy/commit/d4d558b27a09f684be8311f3cfb6… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-07-17 (Mon, 17 Jul 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Merge remote-tracking branch 'guerler/fix_id_encoding' into release_17.05 Includes client rebuild. Compare: https://github.com/galaxyproject/galaxy/compare/e58b24db6133...d4d558b27a09

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[galaxyproject/galaxy] a69c5b: Fix for loading tools when tool.lineage is None.
by GitHub 17 Jul '17

17 Jul '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a69c5b5c0cd86a493684fbd853f7d09c10de414e https://github.com/galaxyproject/galaxy/commit/a69c5b5c0cd86a493684fbd853f7… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2017-07-14 (Fri, 14 Jul 2017) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Fix for loading tools when tool.lineage is None. Commit: ae2fe8992a878ab92fdcf049dc2398e9cf134da6 https://github.com/galaxyproject/galaxy/commit/ae2fe8992a878ab92fdcf049dc23… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2017-07-17 (Mon, 17 Jul 2017) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Merge pull request #4317 from blankenberg/none-tool-lineage Fix for loading tools when tool.lineage is None. Compare: https://github.com/galaxyproject/galaxy/compare/bded7919b640...ae2fe8992a87

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[galaxyproject/galaxy] cacce9: Fix for the caching of location filenames when the...
by GitHub 17 Jul '17

17 Jul '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: cacce9f1182d10e0d959ff26cde16fecf7db89e4 https://github.com/galaxyproject/galaxy/commit/cacce9f1182d10e0d959ff26cde1… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2017-07-14 (Fri, 14 Jul 2017) Changed paths: M lib/galaxy/tools/data/__init__.py Log Message: ----------- Fix for the caching of location filenames when they are broken symlinks. Commit: bded7919b640d31b839e23e568c80bec5ee025e3 https://github.com/galaxyproject/galaxy/commit/bded7919b640d31b839e23e568c8… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2017-07-17 (Mon, 17 Jul 2017) Changed paths: M lib/galaxy/tools/data/__init__.py Log Message: ----------- Merge pull request #4318 from blankenberg/tool-data-table-broken-symlink Fix for the caching of location filenames when they are broken symlinks. Compare: https://github.com/galaxyproject/galaxy/compare/0f2fe60af44c...bded7919b640

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[galaxyproject/usegalaxy-playbook] ed83ee: Update roles
by GitHub 16 Jul '17

16 Jul '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook 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 env/common/files/galaxy/dynamic_rules/nvc_dynamic_memory.py A env/common/files/galaxy/dynamic_rules/reserved.py A env/common/files/galaxy/error/413/index.html A env/common/files/galaxy/error/502/index.shtml A env/common/files/galaxy/error/content_bg.png A env/common/files/galaxy/error/error_message_icon.png A env/common/files/galaxy/error/masthead_bg.png A env/common/files/galaxy/static/terms.html A 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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 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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 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: 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 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 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 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 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 Commit: 9ff176d1b0f074e93da2055e29b6decd16b09ead https://github.com/galaxyproject/usegalaxy-playbook/commit/9ff176d1b0f074e9… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-04-24 (Mon, 24 Apr 2017) Changed paths: A env/common/files/pulsar/config/jetstream_dependency_resolvers_conf.xml M env/test/host_vars/jetstream-iu0.galaxyproject.org.yml M env/test/host_vars/jetstream-tacc0.galaxyproject.org.yml Log Message: ----------- Use Conda on Jetstream Commit: 359fee70192fd94fe8c2b505e77e94909f7f7bbf https://github.com/galaxyproject/usegalaxy-playbook/commit/359fee70192fd94f… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-04-24 (Mon, 24 Apr 2017) Changed paths: R env/common/files/pulsar/config/jetstream_dependency_resolvers_conf.xml A env/common/templates/pulsar/config/jetstream_dependency_resolvers_conf.xml.j2 M env/test/host_vars/jetstream-iu0.galaxyproject.org.yml M env/test/host_vars/jetstream-tacc0.galaxyproject.org.yml A env/test/templates/pulsar Log Message: ----------- Install Conda locally on Jetstream Commit: 7684bd4ff0f0222dbb82a16c95cc4b9dc606e9a7 https://github.com/galaxyproject/usegalaxy-playbook/commit/7684bd4ff0f0222d… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-04-28 (Fri, 28 Apr 2017) Changed paths: M env/test/templates/galaxy/config/uwsgi.ini.j2 Log Message: ----------- Increase Test uWSGI buffer-size to hopefully eliminate (104: Connection reset by peer) while reading response header from upstream Commit: d5480a5d067ba3629f8ecf2a008416c4973ec508 https://github.com/galaxyproject/usegalaxy-playbook/commit/d5480a5d067ba362… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-04-28 (Fri, 28 Apr 2017) Changed paths: M env/test/files/galaxy/galaxy_version.yml Log Message: ----------- Update Test Commit: 9f449f0603c50a25c9c6bb697878f6095691bea6 https://github.com/galaxyproject/usegalaxy-playbook/commit/9f449f0603c50a25… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-05-01 (Mon, 01 May 2017) Changed paths: M env/test/group_vars/galaxyservers/vars.yml Log Message: ----------- Fix datamanager server name Commit: dfe930e2290d6cbfb91bd8cb182595b4491fd7cf https://github.com/galaxyproject/usegalaxy-playbook/commit/dfe930e2290d6cbf… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-05-02 (Tue, 02 May 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/plugins/common/templates/ie.mako M env/test/files/interactive_environments/plugins/ethercalc/static/js/ethercalc.js M env/test/files/interactive_environments/plugins/ethercalc/templates/ethercalc.mako M env/test/files/interactive_environments/plugins/jupyter/config/jupyter.ini.sample M env/test/files/interactive_environments/plugins/jupyter/templates/jupyter.mako M env/test/files/interactive_environments/plugins/rstudio/config/allowed_images.yml.sample M env/test/files/interactive_environments/plugins/rstudio/config/rstudio.ini.sample M env/test/files/interactive_environments/plugins/rstudio/static/js/rstudio.js M env/test/files/interactive_environments/plugins/rstudio/templates/rstudio.mako M env/test/files/interactive_environments/proxy/.ansible_ie_role_current_version M env/test/files/interactive_environments/proxy/package.json Log Message: ----------- Update Test Commit: 9fdad33717d819c7370b5d2c8413170f30fba1e7 https://github.com/galaxyproject/usegalaxy-playbook/commit/9fdad33717d819c7… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-05-02 (Tue, 02 May 2017) Changed paths: M env/common/files/galaxy/dynamic_rules/multi_dynamic_walltime.py Log Message: ----------- Override walltime in dynamic rules Commit: 9e45cf23ef9cbc87f398b5d7b302de0bd7c814b1 https://github.com/galaxyproject/usegalaxy-playbook/commit/9e45cf23ef9cbc87… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-05-02 (Tue, 02 May 2017) Changed paths: M env/test/group_vars/galaxyservers/vars.yml Log Message: ----------- Jupyter updates for Test Commit: 49e404c4f6d83c9870f6c666fd9eaeb698920c59 https://github.com/galaxyproject/usegalaxy-playbook/commit/49e404c4f6d83c98… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-05-03 (Wed, 03 May 2017) Changed paths: M env/test/group_vars/dbservers/vault.yml Log Message: ----------- Add grafana Commit: 61b4ab56cf483a5398f3272d992e8106cdccd135 https://github.com/galaxyproject/usegalaxy-playbook/commit/61b4ab56cf483a53… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-05-08 (Mon, 08 May 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/plugins/jupyter/config/allowed_images.yml.sample M env/test/files/interactive_environments/proxy/.ansible_ie_role_current_version M env/test/group_vars/galaxyservers/vars.yml Log Message: ----------- Update Test Commit: c034a067b23940feee7d32f63abfed6e375077a0 https://github.com/galaxyproject/usegalaxy-playbook/commit/c034a067b23940fe… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-05-09 (Tue, 09 May 2017) Changed paths: M env/test/group_vars/ftpservers.yml M env/test/group_vars/galaxyservers/vars.yml M roles/galaxyprojectdotorg.proftpd/tasks/galaxy_auth.yml M roles/galaxyprojectdotorg.proftpd/templates/galaxy_auth.conf.j2 Log Message: ----------- Fix FTP on Test and enable PBKDF2. Commit: 69ea530df07aec1e85d8c40e50479db9f43e1630 https://github.com/galaxyproject/usegalaxy-playbook/commit/69ea530df07aec1e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-05-09 (Tue, 09 May 2017) Changed paths: M env/common/stack.yml R env/test/group_vars/galaxyswarmmanagers/vars.yml R env/test/group_vars/galaxyswarmmanagers/vault.yml A env/test/group_vars/galaxyswarmscaleservers/vars.yml A env/test/group_vars/galaxyswarmscaleservers/vault.yml M env/test/inventory A roles/usegalaxy_swarmscale/files/delete.yml A roles/usegalaxy_swarmscale/files/inc_spawn.yml A roles/usegalaxy_swarmscale/files/instance A roles/usegalaxy_swarmscale/files/inventory.head A roles/usegalaxy_swarmscale/files/inventory.spawn A roles/usegalaxy_swarmscale/files/spawn.yml A roles/usegalaxy_swarmscale/tasks/main.yml A roles/usegalaxy_swarmscale/templates/ssh_config.jetstream.j2 Log Message: ----------- Swarm scale Commit: 385c2a31d7eeb02186330226e50db80919f7b2ff https://github.com/galaxyproject/usegalaxy-playbook/commit/385c2a31d7eeb021… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-05-11 (Thu, 11 May 2017) Changed paths: M env/common/update.yml R env/test/files/interactive_environments/plugins/.ansible_ie_role_current_version R env/test/files/interactive_environments/plugins/bam_iobio/config/bam_iobio.ini.sample R env/test/files/interactive_environments/plugins/bam_iobio/config/bam_iobio.xml R env/test/files/interactive_environments/plugins/bam_iobio/static/js/bam_iobio.js R env/test/files/interactive_environments/plugins/bam_iobio/templates/bam_iobio.mako R env/test/files/interactive_environments/plugins/common/templates/ie.mako R env/test/files/interactive_environments/plugins/ethercalc/config/allowed_images.yml.sample R env/test/files/interactive_environments/plugins/ethercalc/config/ethercalc.ini.sample R env/test/files/interactive_environments/plugins/ethercalc/config/ethercalc.xml R 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env/test/files/interactive_environments/plugins/rstudio/static/js/crypto/rsa.js R env/test/files/interactive_environments/plugins/rstudio/static/js/crypto/rstudio.big.js R env/test/files/interactive_environments/plugins/rstudio/static/js/crypto/rstudio.min.js R env/test/files/interactive_environments/plugins/rstudio/static/js/crypto/rstudio/base64.js R env/test/files/interactive_environments/plugins/rstudio/static/js/crypto/rstudio/jsbn.js R env/test/files/interactive_environments/plugins/rstudio/static/js/crypto/rstudio/prng4.js R env/test/files/interactive_environments/plugins/rstudio/static/js/crypto/rstudio/rng.js R env/test/files/interactive_environments/plugins/rstudio/static/js/crypto/rstudio/rsa.js R env/test/files/interactive_environments/plugins/rstudio/static/js/crypto/wu/base64.js R env/test/files/interactive_environments/plugins/rstudio/static/js/crypto/wu/jsbn.js R env/test/files/interactive_environments/plugins/rstudio/static/js/crypto/wu/prng4.js R env/test/files/interactive_environments/plugins/rstudio/static/js/crypto/wu/rng.js R env/test/files/interactive_environments/plugins/rstudio/static/js/crypto/wu/rsa.js R env/test/files/interactive_environments/plugins/rstudio/static/js/rstudio.js R env/test/files/interactive_environments/plugins/rstudio/templates/rstudio.mako R env/test/files/interactive_environments/proxy/.ansible_ie_role_current_version R env/test/files/interactive_environments/proxy/Dockerfile R env/test/files/interactive_environments/proxy/README.md R env/test/files/interactive_environments/proxy/lib/main.js R env/test/files/interactive_environments/proxy/lib/mapper.js R env/test/files/interactive_environments/proxy/lib/proxy.js R env/test/files/interactive_environments/proxy/package.json A roles/galaxyproject.interactive_environments/README.md A roles/galaxyproject.interactive_environments/defaults/main.yml A roles/galaxyproject.interactive_environments/handlers/main.yml A roles/galaxyproject.interactive_environments/meta/.galaxy_install_info A roles/galaxyproject.interactive_environments/meta/main.yml A roles/galaxyproject.interactive_environments/tasks/docker_ssl.yml A roles/galaxyproject.interactive_environments/tasks/install_dependencies.yml A roles/galaxyproject.interactive_environments/tasks/main.yml A roles/galaxyproject.interactive_environments/tasks/supervisor.yml A roles/galaxyproject.interactive_environments/tasks/synchronize_components.yml A roles/galaxyproject.interactive_environments/tasks/webserver_conf.yml A roles/galaxyproject.interactive_environments/templates/_prefix.j2 A roles/galaxyproject.interactive_environments/templates/config.ini.j2 A roles/galaxyproject.interactive_environments/templates/generic_apache.conf.j2 A roles/galaxyproject.interactive_environments/templates/generic_nginx.conf.j2 A roles/galaxyproject.interactive_environments/templates/jupyter_apache.conf.j2 A roles/galaxyproject.interactive_environments/templates/jupyter_nginx.conf.j2 A roles/galaxyproject.interactive_environments/templates/proxy_supervisor.conf.j2 R roles/galaxyprojectdotorg.interactive_environments/README.md R roles/galaxyprojectdotorg.interactive_environments/defaults/main.yml R roles/galaxyprojectdotorg.interactive_environments/handlers/main.yml R roles/galaxyprojectdotorg.interactive_environments/meta/.galaxy_install_info R roles/galaxyprojectdotorg.interactive_environments/meta/main.yml R roles/galaxyprojectdotorg.interactive_environments/tasks/docker_ssl.yml R roles/galaxyprojectdotorg.interactive_environments/tasks/extract_component.yml R roles/galaxyprojectdotorg.interactive_environments/tasks/install_dependencies.yml R roles/galaxyprojectdotorg.interactive_environments/tasks/main.yml R roles/galaxyprojectdotorg.interactive_environments/tasks/supervisor.yml R roles/galaxyprojectdotorg.interactive_environments/tasks/synchronize_components.yml R roles/galaxyprojectdotorg.interactive_environments/tasks/webserver_conf.yml R roles/galaxyprojectdotorg.interactive_environments/templates/_prefix.j2 R roles/galaxyprojectdotorg.interactive_environments/templates/config.ini.j2 R roles/galaxyprojectdotorg.interactive_environments/templates/generic_apache.conf.j2 R roles/galaxyprojectdotorg.interactive_environments/templates/generic_nginx.conf.j2 R roles/galaxyprojectdotorg.interactive_environments/templates/jupyter_apache.conf.j2 R roles/galaxyprojectdotorg.interactive_environments/templates/jupyter_nginx.conf.j2 R roles/galaxyprojectdotorg.interactive_environments/templates/proxy_supervisor.conf.j2 Log Message: ----------- Update the interactive_environments role and stop storing a copy of GIEs in the playbook Commit: c318d9a95c079d27c3c8ee72333d12c6dd52c4e2 https://github.com/galaxyproject/usegalaxy-playbook/commit/c318d9a95c079d27… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-05-11 (Thu, 11 May 2017) Changed paths: M env/test/files/galaxy/galaxy_version.yml Log Message: ----------- Update Test Commit: fbd3d5ccb119814c8a42dc6e10d2007ac203da10 https://github.com/galaxyproject/usegalaxy-playbook/commit/fbd3d5ccb119814c… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-05-11 (Thu, 11 May 2017) Changed paths: M env/common/config.yml M env/common/pulsar.yml M env/common/stack.yml M env/common/update.yml A roles/galaxyproject.galaxy/README.md A roles/galaxyproject.galaxy/defaults/main.yml A roles/galaxyproject.galaxy/files/errordocs/content_bg.png A roles/galaxyproject.galaxy/files/errordocs/error_message_icon.png A roles/galaxyproject.galaxy/files/errordocs/masthead_bg.png A roles/galaxyproject.galaxy/files/makepyc.py A roles/galaxyproject.galaxy/handlers/main.yml A roles/galaxyproject.galaxy/meta/.galaxy_install_info A roles/galaxyproject.galaxy/meta/main.yml A roles/galaxyproject.galaxy/tasks/clone.yml A roles/galaxyproject.galaxy/tasks/database.yml A roles/galaxyproject.galaxy/tasks/dependencies.yml A roles/galaxyproject.galaxy/tasks/download.yml A roles/galaxyproject.galaxy/tasks/errordocs.yml A roles/galaxyproject.galaxy/tasks/main.yml A roles/galaxyproject.galaxy/tasks/mutable_setup.yml A roles/galaxyproject.galaxy/tasks/static_setup.yml A roles/galaxyproject.galaxy/tasks/virtualenv.yml A roles/galaxyproject.galaxy/templates/errordocs/413/index.html.j2 A roles/galaxyproject.galaxy/templates/errordocs/502/index.shtml.j2 A roles/galaxyproject.galaxy/templates/galaxy.ini.j2 A roles/galaxyproject.galaxy_toolshed/README.md A roles/galaxyproject.galaxy_toolshed/defaults/main.yml A roles/galaxyproject.galaxy_toolshed/handlers/main.yml A roles/galaxyproject.galaxy_toolshed/meta/.galaxy_install_info A roles/galaxyproject.galaxy_toolshed/meta/main.yml A roles/galaxyproject.galaxy_toolshed/tasks/database.yml A roles/galaxyproject.galaxy_toolshed/tasks/main.yml A roles/galaxyproject.galaxy_toolshed/tasks/static_setup.yml A roles/galaxyproject.galaxy_toolshed/templates/tool_shed.ini.j2 A roles/galaxyproject.galaxy_toolshed/templates/user_info.xml.j2 A roles/galaxyproject.nginx/README.md A roles/galaxyproject.nginx/defaults/main.yml A roles/galaxyproject.nginx/handlers/main.yml A roles/galaxyproject.nginx/meta/.galaxy_install_info A roles/galaxyproject.nginx/meta/main.yml A roles/galaxyproject.nginx/tasks/apt.yml A roles/galaxyproject.nginx/tasks/main.yml A roles/galaxyproject.nginx/tasks/pkgin.yml A roles/galaxyproject.nginx/tasks/yum.yml A roles/galaxyproject.nginx/templates/epel-nginx.conf.j2 A roles/galaxyproject.nginx/templates/http_options.conf.j2 A roles/galaxyproject.nginx/templates/pkgin-nginx.conf.j2 A roles/galaxyproject.nginx/templates/ssl.conf.j2 A roles/galaxyproject.nginx/templates/supervisord.conf.j2 A roles/galaxyproject.nginx/vars/pkgin.yml A roles/galaxyproject.postgresql/.gitignore A roles/galaxyproject.postgresql/README.md A roles/galaxyproject.postgresql/defaults/main.yml A roles/galaxyproject.postgresql/files/get_repo_rpm_release.py A roles/galaxyproject.postgresql/handlers/main.yml A roles/galaxyproject.postgresql/meta/.galaxy_install_info A roles/galaxyproject.postgresql/meta/main.yml A roles/galaxyproject.postgresql/tasks/backup.yml A roles/galaxyproject.postgresql/tasks/debian.yml A roles/galaxyproject.postgresql/tasks/main.yml A roles/galaxyproject.postgresql/tasks/redhat.yml A roles/galaxyproject.postgresql/templates/20ansible_backup.conf.j2 A roles/galaxyproject.postgresql/templates/25ansible_postgresql.conf.j2 A roles/galaxyproject.postgresql/templates/archive_wal.sh.j2 A roles/galaxyproject.postgresql/templates/backup_working_wal.sh.j2 A roles/galaxyproject.postgresql/templates/pg_hba.conf.debian.j2 A roles/galaxyproject.postgresql/templates/pg_hba.conf.redhat.j2 A roles/galaxyproject.postgresql/templates/scheduled_backup.sh.j2 A roles/galaxyproject.postgresql/vars/debian.yml A roles/galaxyproject.postgresql/vars/main.yml A roles/galaxyproject.postgresql/vars/redhat.yml A roles/galaxyproject.proftpd/.travis.yml A roles/galaxyproject.proftpd/README.md A roles/galaxyproject.proftpd/defaults/main.yml A roles/galaxyproject.proftpd/handlers/main.yml A roles/galaxyproject.proftpd/meta/main.yml A roles/galaxyproject.proftpd/tasks/debian.yml A roles/galaxyproject.proftpd/tasks/galaxy_auth.yml A roles/galaxyproject.proftpd/tasks/main.yml A roles/galaxyproject.proftpd/tasks/redhat.yml A roles/galaxyproject.proftpd/tasks/tls.yml A roles/galaxyproject.proftpd/templates/galaxy_auth.conf.j2 A roles/galaxyproject.proftpd/templates/server.conf.j2 A roles/galaxyproject.proftpd/templates/tls.conf.j2 A roles/galaxyproject.proftpd/tests/inventory A roles/galaxyproject.proftpd/tests/test.yml A roles/galaxyproject.proftpd/vars/debian.yml A roles/galaxyproject.proftpd/vars/main.yml A roles/galaxyproject.proftpd/vars/redhat.yml A roles/galaxyproject.pulsar/README.md A roles/galaxyproject.pulsar/defaults/main.yml A roles/galaxyproject.pulsar/meta/.galaxy_install_info A roles/galaxyproject.pulsar/meta/main.yml A roles/galaxyproject.pulsar/tasks/main.yml A roles/galaxyproject.pulsar/templates/app.yml.j2 A roles/galaxyproject.pulsar/templates/job_managers.ini.j2 A roles/galaxyproject.pulsar/templates/job_metrics_conf.xml.j2 A roles/galaxyproject.pulsar/templates/local_env.sh.j2 A roles/galaxyproject.pulsar/templates/server.ini.j2 A roles/galaxyproject.tools/LICENSE A roles/galaxyproject.tools/README.md A roles/galaxyproject.tools/defaults/main.yml A roles/galaxyproject.tools/files/README.md A roles/galaxyproject.tools/files/dbkeys_list.yaml.sample A roles/galaxyproject.tools/files/install_tool_shed_tools.py A roles/galaxyproject.tools/files/tool_list.yaml A roles/galaxyproject.tools/files/tool_list.yaml.sample A roles/galaxyproject.tools/meta/.galaxy_install_info A roles/galaxyproject.tools/meta/main.yml A roles/galaxyproject.tools/tasks/main.yml A roles/galaxyproject.tools/tasks/tools.yml R roles/galaxyprojectdotorg.galaxy/README.md R roles/galaxyprojectdotorg.galaxy/defaults/main.yml R roles/galaxyprojectdotorg.galaxy/files/errordocs/content_bg.png R roles/galaxyprojectdotorg.galaxy/files/errordocs/error_message_icon.png R roles/galaxyprojectdotorg.galaxy/files/errordocs/masthead_bg.png R roles/galaxyprojectdotorg.galaxy/files/makepyc.py R roles/galaxyprojectdotorg.galaxy/handlers/main.yml R roles/galaxyprojectdotorg.galaxy/meta/.galaxy_install_info R roles/galaxyprojectdotorg.galaxy/meta/main.yml R roles/galaxyprojectdotorg.galaxy/tasks/clone.yml R roles/galaxyprojectdotorg.galaxy/tasks/database.yml R roles/galaxyprojectdotorg.galaxy/tasks/dependencies.yml R roles/galaxyprojectdotorg.galaxy/tasks/download.yml R roles/galaxyprojectdotorg.galaxy/tasks/errordocs.yml R roles/galaxyprojectdotorg.galaxy/tasks/main.yml R roles/galaxyprojectdotorg.galaxy/tasks/mutable_setup.yml R roles/galaxyprojectdotorg.galaxy/tasks/static_setup.yml R roles/galaxyprojectdotorg.galaxy/tasks/virtualenv.yml R roles/galaxyprojectdotorg.galaxy/templates/errordocs/413/index.html.j2 R roles/galaxyprojectdotorg.galaxy/templates/errordocs/502/index.shtml.j2 R roles/galaxyprojectdotorg.galaxy/templates/galaxy.ini.j2 R roles/galaxyprojectdotorg.galaxy_toolshed/README.md R roles/galaxyprojectdotorg.galaxy_toolshed/defaults/main.yml R roles/galaxyprojectdotorg.galaxy_toolshed/handlers/main.yml R roles/galaxyprojectdotorg.galaxy_toolshed/meta/.galaxy_install_info R roles/galaxyprojectdotorg.galaxy_toolshed/meta/main.yml R roles/galaxyprojectdotorg.galaxy_toolshed/tasks/database.yml R roles/galaxyprojectdotorg.galaxy_toolshed/tasks/main.yml R roles/galaxyprojectdotorg.galaxy_toolshed/tasks/static_setup.yml R roles/galaxyprojectdotorg.galaxy_toolshed/templates/tool_shed.ini.j2 R roles/galaxyprojectdotorg.galaxy_toolshed/templates/user_info.xml.j2 R roles/galaxyprojectdotorg.nginx/README.md R roles/galaxyprojectdotorg.nginx/defaults/main.yml R roles/galaxyprojectdotorg.nginx/handlers/main.yml R roles/galaxyprojectdotorg.nginx/meta/.galaxy_install_info R roles/galaxyprojectdotorg.nginx/meta/main.yml R roles/galaxyprojectdotorg.nginx/tasks/apt.yml R roles/galaxyprojectdotorg.nginx/tasks/main.yml R roles/galaxyprojectdotorg.nginx/tasks/pkgin.yml R roles/galaxyprojectdotorg.nginx/tasks/yum.yml R roles/galaxyprojectdotorg.nginx/templates/epel-nginx.conf.j2 R roles/galaxyprojectdotorg.nginx/templates/http_options.conf.j2 R roles/galaxyprojectdotorg.nginx/templates/pkgin-nginx.conf.j2 R roles/galaxyprojectdotorg.nginx/templates/ssl.conf.j2 R roles/galaxyprojectdotorg.nginx/templates/supervisord.conf.j2 R roles/galaxyprojectdotorg.nginx/vars/pkgin.yml R roles/galaxyprojectdotorg.postgresql/.gitignore R roles/galaxyprojectdotorg.postgresql/README.md R roles/galaxyprojectdotorg.postgresql/defaults/main.yml R roles/galaxyprojectdotorg.postgresql/files/get_repo_rpm_release.py R roles/galaxyprojectdotorg.postgresql/handlers/main.yml R roles/galaxyprojectdotorg.postgresql/meta/.galaxy_install_info R roles/galaxyprojectdotorg.postgresql/meta/main.yml R roles/galaxyprojectdotorg.postgresql/tasks/backup.yml R roles/galaxyprojectdotorg.postgresql/tasks/debian.yml R roles/galaxyprojectdotorg.postgresql/tasks/main.yml R roles/galaxyprojectdotorg.postgresql/tasks/redhat.yml R roles/galaxyprojectdotorg.postgresql/templates/20ansible_backup.conf.j2 R roles/galaxyprojectdotorg.postgresql/templates/25ansible_postgresql.conf.j2 R roles/galaxyprojectdotorg.postgresql/templates/archive_wal.sh.j2 R roles/galaxyprojectdotorg.postgresql/templates/backup_working_wal.sh.j2 R roles/galaxyprojectdotorg.postgresql/templates/pg_hba.conf.debian.j2 R roles/galaxyprojectdotorg.postgresql/templates/pg_hba.conf.redhat.j2 R roles/galaxyprojectdotorg.postgresql/templates/scheduled_backup.sh.j2 R roles/galaxyprojectdotorg.postgresql/vars/debian.yml R roles/galaxyprojectdotorg.postgresql/vars/main.yml R roles/galaxyprojectdotorg.postgresql/vars/redhat.yml R roles/galaxyprojectdotorg.proftpd/.travis.yml R roles/galaxyprojectdotorg.proftpd/README.md R roles/galaxyprojectdotorg.proftpd/defaults/main.yml R roles/galaxyprojectdotorg.proftpd/handlers/main.yml R roles/galaxyprojectdotorg.proftpd/meta/main.yml R roles/galaxyprojectdotorg.proftpd/tasks/debian.yml R roles/galaxyprojectdotorg.proftpd/tasks/galaxy_auth.yml R roles/galaxyprojectdotorg.proftpd/tasks/main.yml R roles/galaxyprojectdotorg.proftpd/tasks/redhat.yml R roles/galaxyprojectdotorg.proftpd/tasks/tls.yml R roles/galaxyprojectdotorg.proftpd/templates/galaxy_auth.conf.j2 R roles/galaxyprojectdotorg.proftpd/templates/server.conf.j2 R roles/galaxyprojectdotorg.proftpd/templates/tls.conf.j2 R roles/galaxyprojectdotorg.proftpd/tests/inventory R roles/galaxyprojectdotorg.proftpd/tests/test.yml R roles/galaxyprojectdotorg.proftpd/vars/debian.yml R roles/galaxyprojectdotorg.proftpd/vars/main.yml R roles/galaxyprojectdotorg.proftpd/vars/redhat.yml R roles/galaxyprojectdotorg.pulsar/README.md R roles/galaxyprojectdotorg.pulsar/defaults/main.yml R roles/galaxyprojectdotorg.pulsar/meta/.galaxy_install_info R roles/galaxyprojectdotorg.pulsar/meta/main.yml R roles/galaxyprojectdotorg.pulsar/tasks/main.yml R roles/galaxyprojectdotorg.pulsar/templates/app.yml.j2 R roles/galaxyprojectdotorg.pulsar/templates/job_managers.ini.j2 R roles/galaxyprojectdotorg.pulsar/templates/job_metrics_conf.xml.j2 R roles/galaxyprojectdotorg.pulsar/templates/local_env.sh.j2 R roles/galaxyprojectdotorg.pulsar/templates/server.ini.j2 R roles/galaxyprojectdotorg.tools/LICENSE R roles/galaxyprojectdotorg.tools/README.md R roles/galaxyprojectdotorg.tools/defaults/main.yml R roles/galaxyprojectdotorg.tools/files/README.md R roles/galaxyprojectdotorg.tools/files/dbkeys_list.yaml.sample R roles/galaxyprojectdotorg.tools/files/install_tool_shed_tools.py R roles/galaxyprojectdotorg.tools/files/tool_list.yaml R roles/galaxyprojectdotorg.tools/files/tool_list.yaml.sample R roles/galaxyprojectdotorg.tools/meta/.galaxy_install_info R roles/galaxyprojectdotorg.tools/meta/main.yml R roles/galaxyprojectdotorg.tools/tasks/main.yml R roles/galaxyprojectdotorg.tools/tasks/tools.yml Log Message: ----------- Rename roles due to name change in Ansible Galaxy Commit: d812cdd806a7032a981d7f5d8c903c3957846ae7 https://github.com/galaxyproject/usegalaxy-playbook/commit/d812cdd806a7032a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-05-12 (Fri, 12 May 2017) Changed paths: M env/test/group_vars/dbservers/vault.yml Log Message: ----------- Update DB access list Commit: e24a4fee0cb63c1151a583a38bbabf69afdf0e7c https://github.com/galaxyproject/usegalaxy-playbook/commit/e24a4fee0cb63c11… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-05-12 (Fri, 12 May 2017) Changed paths: M README.md R common/docker/galaxy-installer/Dockerfile.main R common/docker/galaxy-installer/Dockerfile.test R common/docker/galaxy-installer/run_main.sh R common/docker/galaxy-installer/run_test.sh R common/docker/galaxy-update/Dockerfile R common/docker/galaxy-update/condarc R common/group_vars/all.yml R common/group_vars/all_debian_based_hosts.yml R common/group_vars/redhat_dbservers.yml R common/group_vars/webservers.yml R common/host_vars/galaxy-db-01.tacc.utexas.edu.yml R common/inventory R common/secret_vars/ssl.yml R common/secret_vars/supervisorusers.yml R common/secret_vars/trellocardcreatorservers.yml R common_infrastructure.yml R ec2.yml A env/common/files/galaxy/dynamic_rules/jetstream.py A env/common/files/galaxy/dynamic_rules/single_dynamic_memory.py A env/common/files/galaxy/static/welcome_img/GCC2017EarlyReg.png A env/common/files/galaxy/static/welcome_img/ISMBECCB2017Tutorial.png M env/common/group_vars/toolshedwebservers.yml M env/common/templates/galaxy/static/welcome.html.j2 A env/common/tools.yml M env/common/update_shed.yml A env/main/_inc_config_post_tasks.yml A env/main/_inc_restart.yml A env/main/_inc_snapshot.yml A env/main/_inc_static.yml A env/main/config.yml A env/main/files/galaxy/config/builds.txt A env/main/files/galaxy/config/data_manager_conf.xml A env/main/files/galaxy/config/disposable_email_blacklist.conf A env/main/files/galaxy/config/job_metrics_conf.xml A env/main/files/galaxy/config/job_resource_params_conf.xml A env/main/files/galaxy/config/nagios_tool_conf.xml A env/main/files/galaxy/config/object_store_conf.xml A env/main/files/galaxy/config/pulsar_jetstream.yml A env/main/files/galaxy/config/pulsar_jetstream_actions.yml A env/main/files/galaxy/config/pulsar_stampede_actions.yml A env/main/files/galaxy/config/tool_conf.xml A env/main/files/galaxy/config/tool_data_table_conf.xml A env/main/files/galaxy/config/tool_sheds_conf.xml A env/main/files/galaxy/config/ucsc_build_sites.txt A env/main/files/galaxy/dynamic_rules/bridges_select.py A env/main/files/galaxy/dynamic_rules/multi_dynamic_walltime.py A env/main/files/galaxy/dynamic_rules/nvc_dynamic_memory.py A env/main/files/galaxy/dynamic_rules/reserved.py A env/main/files/galaxy/error A env/main/files/galaxy/galaxy_version.yml A env/main/files/galaxy/nagios/echo_main_bridges.xml A env/main/files/galaxy/nagios/echo_main_cluster.xml A env/main/files/galaxy/nagios/echo_main_jetstream_iu.xml A env/main/files/galaxy/nagios/echo_main_jetstream_tacc.xml A env/main/files/galaxy/nagios/echo_main_stampede.xml A env/main/files/galaxy/nagios/echo_main_w1_handler0.xml A env/main/files/galaxy/nagios/echo_main_w1_handler1.xml A env/main/files/galaxy/nagios/echo_main_w1_handler2.xml A env/main/files/galaxy/nagios/echo_main_w2_handler0.xml A env/main/files/galaxy/nagios/echo_main_w2_handler1.xml A env/main/files/galaxy/nagios/echo_main_w2_handler2.xml A env/main/files/galaxy/static A env/main/files/galaxy/tool_list.yaml A env/main/files/galaxy/var/integrated_tool_panel.xml A env/main/files/galaxy/var/migrated_tools_conf.xml A env/main/files/galaxy/var/shed_data_manager_conf.xml A env/main/files/galaxy/var/shed_tool_conf.xml A env/main/files/galaxy/var/shed_tool_data_table_conf.xml A env/main/files/pulsar A env/main/files/ssl A env/main/group_vars/all.yml A env/main/group_vars/dbservers/vars.yml A env/main/group_vars/dbservers/vault.yml A env/main/group_vars/ftpservers/vars.yml A env/main/group_vars/ftpservers/vault.yml A env/main/group_vars/galaxyjobservers.yml A env/main/group_vars/galaxyservers/vars.yml A env/main/group_vars/galaxyservers/vault.yml A env/main/group_vars/galaxystagingservers.yml A env/main/group_vars/galaxywebservers.yml A env/main/group_vars/pulsarservers/vars.yml A env/main/group_vars/pulsarservers/vault.yml A env/main/group_vars/sslservers A env/main/group_vars/supervisorservers/vars.yml A env/main/group_vars/supervisorservers/vault.yml A env/main/group_vars/webservers.yml A env/main/host_vars/br005.bridges.psc.edu.yml A env/main/host_vars/galaxy-web-03.tacc.utexas.edu.yml A env/main/host_vars/galaxy-web-04.tacc.utexas.edu.yml A env/main/host_vars/galaxy-web-05.tacc.utexas.edu.yml A env/main/host_vars/jetstream-iu0.galaxyproject.org.yml A env/main/host_vars/jetstream-tacc0.galaxyproject.org.yml A env/main/host_vars/login5.stampede.tacc.utexas.edu.yml A env/main/inventory A env/main/pulsar.yml A env/main/restart.yml A env/main/snapshot.yml A env/main/stack.yml A env/main/static.yml A env/main/templates/galaxy/config/build_sites.yml.j2 A env/main/templates/galaxy/config/galaxy.ini.j2 A env/main/templates/galaxy/config/job_conf.xml.j2 A env/main/templates/galaxy/config/reports.ini.j2 A env/main/templates/galaxy/config/uwsgi.ini.j2 A env/main/templates/galaxy/static A env/main/templates/nginx/galaxy_bx.j2 A env/main/templates/nginx/usegalaxy.j2 A env/main/templates/nginx/usegalaxy_rewrites.conf.j2 A env/main/templates/nginx/usegalaxy_staging.j2 A env/main/templates/pulsar A env/main/templates/supervisor A env/main/update.yml R 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R production/group_vars/all.yml R production/group_vars/galaxydbservers.yml R production/group_vars/galaxyjobservers.yml R production/group_vars/galaxyservers.yml R production/group_vars/galaxystagingservers.yml R production/group_vars/galaxywebservers.yml R production/group_vars/pulsarservers.yml R production/group_vars/toolsheddbservers.yml R production/group_vars/toolshedservers.yml R production/host_vars/br005.bridges.psc.edu.yml R production/host_vars/galaxy-web-01.tacc.utexas.edu.yml R production/host_vars/galaxy-web-02.tacc.utexas.edu.yml R production/host_vars/galaxy-web-03.tacc.utexas.edu.yml R production/host_vars/galaxy-web-04.tacc.utexas.edu.yml R production/host_vars/jetstream-iu0.galaxyproject.org.yml R production/host_vars/jetstream-tacc0.galaxyproject.org.yml R production/host_vars/login5.stampede.tacc.utexas.edu.yml R production/host_vars/radegast.galaxyproject.org.yml R production/inventory R production/secret_vars/galaxydbservers.yml R production/secret_vars/galaxyservers.yml R production/secret_vars/pulsarservers.yml R production/secret_vars/toolshedservers.yml R stage/host_vars/radegast.galaxyproject.org.yml R stage/inventory R stage/secret_vars/toolshedservers.yml R templates/galaxy/common/config/reports.ini.j2 R templates/galaxy/common/static/welcome.html.j2 R templates/galaxy/usegalaxy.org/config/build_sites.yml.j2 R templates/galaxy/usegalaxy.org/config/job_conf.xml.j2 R templates/galaxy/usegalaxy.org/config/reports.ini.j2 R templates/galaxy/usegalaxy.org/config/uwsgi.ini.j2 R templates/galaxy/usegalaxy.org/static R templates/nginx/galaxy_bx.j2 R templates/nginx/usegalaxy.j2 R templates/nginx/usegalaxy_rewrites.conf.j2 R templates/nginx/usegalaxy_staging.j2 R templates/supervisor/galaxy.j2 R templates/supervisor/galaxy_group.j2 R templates/supervisor/galaxy_handler.j2 R templates/supervisor/galaxy_impersonate.j2 R templates/supervisor/galaxy_reports.j2 R tools.yml R toolshed_infrastructure.yml Log Message: ----------- Reorganize Main and MTS for new playbook structure. Not deployed yet. Commit: ad99d8528a1b4eaa650edf3783ccd81cfa835e42 https://github.com/galaxyproject/usegalaxy-playbook/commit/ad99d8528a1b4eaa… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-05-16 (Tue, 16 May 2017) Changed paths: M README.md M env/common/tools.yml M env/common/update_shed.yml M env/main/group_vars/galaxyservers/vars.yml M env/main/group_vars/galaxystagingservers.yml M env/main/group_vars/pulsarservers/vars.yml M env/main/group_vars/webservers.yml M env/test/group_vars/galaxyservers/vars.yml M env/test/group_vars/pulsarservers/vars.yml M env/test/group_vars/webservers/vars.yml M env/testtoolshed/group_vars/toolshedservers/vars.yml M env/toolshed/group_vars/toolshedservers/vars.yml M roles/galaxyproject.galaxy/README.md M roles/galaxyproject.galaxy/defaults/main.yml M roles/galaxyproject.galaxy/handlers/main.yml M roles/galaxyproject.galaxy/tasks/main.yml M roles/galaxyproject.galaxy_toolshed/README.md M roles/galaxyproject.galaxy_toolshed/defaults/main.yml M roles/galaxyproject.galaxy_toolshed/handlers/main.yml M roles/galaxyproject.galaxy_toolshed/tasks/main.yml M roles/galaxyproject.interactive_environments/README.md M roles/galaxyproject.interactive_environments/defaults/main.yml M roles/galaxyproject.interactive_environments/handlers/main.yml M roles/galaxyproject.interactive_environments/tasks/main.yml M roles/galaxyproject.nginx/README.md M roles/galaxyproject.nginx/defaults/main.yml M roles/galaxyproject.nginx/handlers/main.yml M roles/galaxyproject.nginx/tasks/main.yml M roles/galaxyproject.proftpd/README.md M roles/galaxyproject.proftpd/defaults/main.yml M roles/galaxyproject.proftpd/handlers/main.yml M roles/galaxyproject.proftpd/tasks/debian.yml M roles/galaxyproject.proftpd/tasks/galaxy_auth.yml M roles/galaxyproject.proftpd/tasks/main.yml M roles/galaxyproject.proftpd/tasks/redhat.yml M roles/galaxyproject.proftpd/tasks/tls.yml M roles/galaxyproject.proftpd/tests/test.yml M roles/galaxyproject.proftpd/vars/main.yml M roles/galaxyproject.pulsar/README.md M roles/galaxyproject.pulsar/defaults/main.yml M roles/galaxyproject.pulsar/tasks/main.yml Log Message: ----------- Finish renaming galaxyprojectdotorg -> galaxyproject Commit: eedfea43fdbb2fe0a0e31d1dd077341f632f6b87 https://github.com/galaxyproject/usegalaxy-playbook/commit/eedfea43fdbb2fe0… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-05-16 (Tue, 16 May 2017) Changed paths: M env/toolshed/group_vars/toolshedservers/vars.yml Log Message: ----------- Update MTS Commit: 890912424aae8cc959f25fe88d70d82a5c0e5102 https://github.com/galaxyproject/usegalaxy-playbook/commit/890912424aae8cc9… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-05-17 (Wed, 17 May 2017) Log Message: ----------- Fixed conda env generation on Jetstream: Manually upgraded galaxy-lib from 16.7.10 to 17.5.9. No committable changes. Commit: 376b8c62fac4419299ec0c85cf2921c8aa47da70 https://github.com/galaxyproject/usegalaxy-playbook/commit/376b8c62fac44192… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-05-17 (Wed, 17 May 2017) Changed paths: M env/testtoolshed/group_vars/toolshedservers/vars.yml Log Message: ----------- Update Test Tool Shed Commit: 19846e3ebdd8597e9e21d9e6a4f3ec0c13b8491c https://github.com/galaxyproject/usegalaxy-playbook/commit/19846e3ebdd8597e… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-05-30 (Tue, 30 May 2017) Changed paths: M env/main/templates/galaxy/config/job_conf.xml.j2 Log Message: ----------- give salmon 16gb and rna_Star 64 Commit: 9c6af8b03364613a7873fb91407893b55ce6fcb0 https://github.com/galaxyproject/usegalaxy-playbook/commit/9c6af8b03364613a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-05-30 (Tue, 30 May 2017) Changed paths: M env/common/files/galaxy/dynamic_rules/multi_dynamic_walltime.py M env/main/files/galaxy/galaxy_version.yml M env/main/files/galaxy/var/integrated_tool_panel.xml M env/main/files/galaxy/var/shed_data_manager_conf.xml M env/main/files/galaxy/var/shed_tool_data_table_conf.xml Log Message: ----------- Fix walltime exception for align families running on local cluster and update Main Conflicts: production/galaxy_version.yml Commit: 622272d426088faad13f230d765b6cb42d2aa2dd https://github.com/galaxyproject/usegalaxy-playbook/commit/622272d426088faa… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-06-01 (Thu, 01 Jun 2017) Changed paths: M env/main/templates/galaxy/config/job_conf.xml.j2 Log Message: ----------- move rna_star to different destination to dynamic_local_stampede_select_dynamic_walltime Commit: ce7d009db5b56e7a31c37b6858418a34d9a0e8c2 https://github.com/galaxyproject/usegalaxy-playbook/commit/ce7d009db5b56e7a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-06-01 (Thu, 01 Jun 2017) Changed paths: M env/main/files/galaxy/galaxy_version.yml Log Message: ----------- Update Main Commit: 8f9080fbb5039af509b30a28a13c9af42f9054e8 https://github.com/galaxyproject/usegalaxy-playbook/commit/8f9080fbb5039af5… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-06-15 (Thu, 15 Jun 2017) Changed paths: M env/test/group_vars/galaxyservers/vars.yml Log Message: ----------- Disable conda copying for per-job envs since all envs are now mulled. always_symlink has also been enabled in _condarc Commit: 1a3bfcec003a4827b75c28cc02a233fe65d952a1 https://github.com/galaxyproject/usegalaxy-playbook/commit/1a3bfcec003a4827… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-06-15 (Thu, 15 Jun 2017) Changed paths: M env/test/group_vars/galaxyservers/vars.yml Log Message: ----------- I forget why these variable names have changed but apparently I didn't finish changing them Commit: 5b00fa5d5c55915aaac7f440b1f074216be6a148 https://github.com/galaxyproject/usegalaxy-playbook/commit/5b00fa5d5c55915a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-06-16 (Fri, 16 Jun 2017) Changed paths: M env/common/templates/supervisor/galaxy_datamanager.j2 M env/test/files/galaxy/var/integrated_tool_panel.xml M env/test/files/galaxy/var/shed_data_manager_conf.xml M env/test/files/galaxy/var/shed_tool_conf.xml M env/test/files/galaxy/var/shed_tool_data_table_conf.xml M env/test/group_vars/galaxyservers/vars.yml M env/test/templates/galaxy/config/job_conf.xml.j2 Log Message: ----------- Fixes for Data Managers, plus allocate 128GB of memory for the RNA STAR DM Commit: 3fbe6d1d53f295cbe7b7a877db72d4a4c706ec4c https://github.com/galaxyproject/usegalaxy-playbook/commit/3fbe6d1d53f295cb… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-06-21 (Wed, 21 Jun 2017) Changed paths: M env/test/templates/galaxy/config/job_conf.xml.j2 Log Message: ----------- Run RNA Star on multi partition on TEst Commit: c06cee0e218843b77ca86bab23007f16cfaa106a https://github.com/galaxyproject/usegalaxy-playbook/commit/c06cee0e218843b7… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-06-22 (Thu, 22 Jun 2017) Changed paths: M env/common/files/galaxy/dynamic_rules/bridges_select.py A env/test/files/galaxy/config/pulsar_bridges_actions.yml M env/test/group_vars/galaxyservers/vars.yml M env/test/templates/galaxy/config/job_conf.xml.j2 Log Message: ----------- Run RNA Star on Bridges on Test, configure data path rewrites. Commit: 5f46d03b2050f4bdb89ca8364c3ea4a72314cd9c https://github.com/galaxyproject/usegalaxy-playbook/commit/5f46d03b2050f4bd… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-06-22 (Thu, 22 Jun 2017) Log Message: ----------- Manually upgraded Test galaxy-lib on Jetstream from 16.7.7 to 17.9.1. No committable changes. Commit: 49a63ad338ca092dd8739bc1d650d645e00bc6fd https://github.com/galaxyproject/usegalaxy-playbook/commit/49a63ad338ca092d… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-06-22 (Thu, 22 Jun 2017) Changed paths: M env/common/files/galaxy/dynamic_rules/multi_dynamic_walltime.py M env/test/files/galaxy/config/job_resource_params_conf.xml M env/test/templates/galaxy/config/job_conf.xml.j2 Log Message: ----------- Hack RNA STAR into the terrible One Dynamic Rule To Rule Them All Commit: bdcfa1009eb413827f509c6c1787a6418f6cb9f3 https://github.com/galaxyproject/usegalaxy-playbook/commit/bdcfa1009eb41382… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-07-12 (Wed, 12 Jul 2017) Changed paths: M env/test/files/galaxy/var/integrated_tool_panel.xml M env/test/files/galaxy/var/shed_tool_conf.xml M env/test/group_vars/galaxyservers/vars.yml M roles/usegalaxy_swarmscale/files/instance M roles/usegalaxy_swarmscale/files/inventory.spawn Log Message: ----------- Get swarm scale / swarm manager working for Test, update Test to new GIE images (Jupyter 17.05.1) Commit: 4dd07fe64f3d15501701f84950ea46ca82f43b03 https://github.com/galaxyproject/usegalaxy-playbook/commit/4dd07fe64f3d1550… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-07-12 (Wed, 12 Jul 2017) Changed paths: M env/test/group_vars/galaxyservers/vars.yml Log Message: ----------- Update Jupyter version in Galaxy config for Test Commit: 437643a11e6b5dfc33099a6fdf8864fa620b3326 https://github.com/galaxyproject/usegalaxy-playbook/commit/437643a11e6b5dfc… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-07-12 (Wed, 12 Jul 2017) Changed paths: M roles/usegalaxy_swarmscale/files/instance Log Message: ----------- Return node names on swarm scale destruction Commit: 001e2190f319f928f6858f540072bc264d0f849c https://github.com/galaxyproject/usegalaxy-playbook/commit/001e2190f319f928… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-07-13 (Thu, 13 Jul 2017) Changed paths: M env/test/group_vars/galaxyservers/vars.yml M roles/usegalaxy_swarmscale/files/inc_spawn.yml M roles/usegalaxy_swarmscale/files/inventory.spawn Log Message: ----------- Swarm GIE fixes Commit: 6d6da7427592691795bc94efed9441f278369338 https://github.com/galaxyproject/usegalaxy-playbook/commit/6d6da74275926917… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-07-16 (Sun, 16 Jul 2017) Changed paths: M common_roles M env/common/templates/supervisor/galaxy_group.j2 M env/main/group_vars/dbservers/vault.yml M env/main/group_vars/ftpservers/vars.yml M env/main/group_vars/galaxyservers/vars.yml M env/main/group_vars/galaxywebservers.yml M env/main/inventory M env/test/group_vars/galaxyservers/vars.yml Log Message: ----------- Supervisor and GIE path fixes Commit: 4c72ad524957ea08ac8157f977ef0bb8c967278b https://github.com/galaxyproject/usegalaxy-playbook/commit/4c72ad524957ea08… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-07-16 (Sun, 16 Jul 2017) Changed paths: M env/common/files/galaxy/dynamic_rules/multi_dynamic_walltime.py M env/main/files/galaxy/config/job_resource_params_conf.xml A env/main/files/galaxy/config/pulsar_bridges_actions.yml M env/main/files/galaxy/config/tool_data_table_conf.xml M env/main/files/galaxy/var/integrated_tool_panel.xml M env/main/files/galaxy/var/shed_tool_data_table_conf.xml M env/main/group_vars/dbservers/vault.yml M env/main/group_vars/galaxyservers/vars.yml M env/main/group_vars/galaxywebservers.yml M env/main/templates/galaxy/config/job_conf.xml.j2 M env/test/group_vars/galaxyservers/vars.yml Log Message: ----------- Merge branch 'master' into reorg Conflicts: common/host_vars/galaxy-db-01.tacc.utexas.edu.yml env/common/files/galaxy/dynamic_rules/multi_dynamic_walltime.py env/main/files/galaxy/galaxy_version.yml env/main/files/galaxy/var/integrated_tool_panel.xml env/main/files/galaxy/var/shed_tool_data_table_conf.xml env/main/group_vars/galaxyservers/vars.yml env/main/host_vars/jetstream-iu0.galaxyproject.org.yml env/main/host_vars/jetstream-tacc0.galaxyproject.org.yml env/main/templates/galaxy/config/job_conf.xml.j2 env/main/templates/nginx/usegalaxy.j2 env/test/host_vars/br005.bridges.psc.edu.yml env/testtoolshed/group_vars/toolshedservers/vars.yml files/galaxy/usegalaxy.org/var/shed_data_manager_conf.xml production/files/interactive_environments/plugins/.ansible_ie_role_current_version production/files/interactive_environments/plugins/bam_iobio/config/bam_iobio.ini.sample production/files/interactive_environments/plugins/bam_iobio/static/js/bam_iobio.js production/files/interactive_environments/plugins/bam_iobio/templates/bam_iobio.mako production/files/interactive_environments/plugins/common/templates/ie.mako production/files/interactive_environments/plugins/jupyter/config/allowed_images.yml.sample production/files/interactive_environments/plugins/jupyter/config/jupyter.ini.sample production/files/interactive_environments/plugins/jupyter/config/jupyter.xml production/files/interactive_environments/plugins/jupyter/static/js/jupyter.js production/files/interactive_environments/plugins/jupyter/templates/jupyter.mako production/files/interactive_environments/plugins/neo/config/neo.ini.sample production/files/interactive_environments/plugins/neo/static/js/neo.js production/files/interactive_environments/plugins/neo/templates/neo.mako production/files/interactive_environments/plugins/phinch/config/phinch.ini.sample production/files/interactive_environments/plugins/phinch/static/js/phinch.js production/files/interactive_environments/plugins/phinch/templates/phinch.mako production/files/interactive_environments/plugins/rstudio/config/allowed_images.yml.sample production/files/interactive_environments/plugins/rstudio/config/rstudio.ini.sample production/files/interactive_environments/plugins/rstudio/static/js/rstudio.js production/files/interactive_environments/plugins/rstudio/templates/rstudio.mako production/files/interactive_environments/proxy/.ansible_ie_role_current_version production/files/interactive_environments/proxy/lib/mapper.js production/files/interactive_environments/proxy/package.json production/galaxy_version.yml production/group_vars/all.yml production/group_vars/galaxydbservers.yml production/group_vars/galaxywebservers.yml production/secret_vars/galaxydbservers.yml stage/inventory Commit: 00d29581d31378bb0c56277950aeef63641316b6 https://github.com/galaxyproject/usegalaxy-playbook/commit/00d29581d31378bb… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-07-16 (Sun, 16 Jul 2017) Changed paths: M env/test/group_vars/galaxyservers/vars.yml Log Message: ----------- Remove duplicate definition Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/0638aacc35f6...…

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[galaxyproject/infrastructure-playbook] abab64: Bump Jupyter image to latest
by GitHub 16 Jul '17

16 Jul '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: abab646b5ada9b7ab9a9ff603fd3e3d987ed47bd https://github.com/galaxyproject/infrastructure-playbook/commit/abab646b5ad… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-07-16 (Sun, 16 Jul 2017) Changed paths: M jetstreamdockerenv/group_vars/imageinstances.yml Log Message: ----------- Bump Jupyter image to latest

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[galaxyproject/usegalaxy-playbook] ccadc2: pylon1 -> pylon5
by GitHub 16 Jul '17

16 Jul '17

Branch: refs/heads/reorg 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 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 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 Commit: 89fb31b48a37fd54891c99eb4117dbcf8d2d3dbe https://github.com/galaxyproject/usegalaxy-playbook/commit/89fb31b48a37fd54… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-04-19 (Wed, 19 Apr 2017) Changed paths: M files/galaxy/usegalaxy.org/var/integrated_tool_panel.xml M files/galaxy/usegalaxy.org/var/shed_tool_data_table_conf.xml Log Message: ----------- Main mutable config updates Commit: 448253e6cd22b4ac0bba5266aec3d4a376374810 https://github.com/galaxyproject/usegalaxy-playbook/commit/448253e6cd22b4ac… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-04-24 (Mon, 24 Apr 2017) Changed paths: A files/pulsar/usegalaxy.org/config/jetstream_dependency_resolvers_conf.xml M production/host_vars/jetstream-iu0.galaxyproject.org.yml M production/host_vars/jetstream-tacc0.galaxyproject.org.yml Log Message: ----------- Enable Conda on Main Jetstream Commit: f5c0310b009c6bf2f94335486d753c1a2bc6aa33 https://github.com/galaxyproject/usegalaxy-playbook/commit/f5c0310b009c6bf2… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-04-24 (Mon, 24 Apr 2017) Changed paths: M production/group_vars/pulsarservers.yml Log Message: ----------- Upgrade Main Pulsar Commit: 9c8d4734f98ae8731096cbe9bf96f5b379fcc15f https://github.com/galaxyproject/usegalaxy-playbook/commit/9c8d4734f98ae873… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-04-24 (Mon, 24 Apr 2017) Changed paths: R files/pulsar/usegalaxy.org/config/jetstream_dependency_resolvers_conf.xml M production/host_vars/jetstream-iu0.galaxyproject.org.yml M production/host_vars/jetstream-tacc0.galaxyproject.org.yml A templates/pulsar/usegalaxy.org/config/jetstream_dependency_resolvers_conf.x… Log Message: ----------- Install Conda locally on Jetstream Commit: 55280cc37e5906cc0f2cb74caca0c293fe5d2bd6 https://github.com/galaxyproject/usegalaxy-playbook/commit/55280cc37e5906cc… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-04-28 (Fri, 28 Apr 2017) Changed paths: M files/galaxy/usegalaxy.org/var/integrated_tool_panel.xml M files/galaxy/usegalaxy.org/var/shed_tool_data_table_conf.xml Log Message: ----------- Main mutable configs Commit: dc487e2a2f585554dc5140660c2536e505eedca9 https://github.com/galaxyproject/usegalaxy-playbook/commit/dc487e2a2f585554… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-04-28 (Fri, 28 Apr 2017) Changed paths: M templates/galaxy/usegalaxy.org/config/uwsgi.ini.j2 Log Message: ----------- Increase Main uWSGI buffer-size to hopefully eliminate (104: Connection reset by peer) while reading response header from upstream Commit: 3dcc0653c2816126d10fbdbcf518c192eb20c279 https://github.com/galaxyproject/usegalaxy-playbook/commit/3dcc0653c2816126… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-04-30 (Sun, 30 Apr 2017) Changed paths: M stage/group_vars/toolshedservers.yml Log Message: ----------- update TTS Commit: e765f7f020a92885a9fb74cc125bd9ddf53cdc23 https://github.com/galaxyproject/usegalaxy-playbook/commit/e765f7f020a92885… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-05-02 (Tue, 02 May 2017) Changed paths: M files/galaxy/common/dynamic_rules/multi_dynamic_walltime.py Log Message: ----------- Allow overriding the walltime on a per-tool basis Commit: ccd062f81075a8399f2b0a1be627dc69bf2d0be6 https://github.com/galaxyproject/usegalaxy-playbook/commit/ccd062f81075a839… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-05-03 (Wed, 03 May 2017) Changed paths: M common/host_vars/galaxy-db-01.tacc.utexas.edu.yml M production/group_vars/galaxydbservers.yml M production/secret_vars/galaxydbservers.yml Log Message: ----------- Add grafana for Main Commit: d32bb89ae9efc13ae94a2ab9b4cba90d62f574eb https://github.com/galaxyproject/usegalaxy-playbook/commit/d32bb89ae9efc13a… Author: tnabtaf <clements(a)galaxyproject.org> Date: 2017-05-04 (Thu, 04 May 2017) Changed paths: A files/galaxy/common/static/welcome_img/GCC2017EarlyReg.png A files/galaxy/common/static/welcome_img/ISMBECCB2017Tutorial.png M templates/galaxy/common/static/welcome.html.j2 Log Message: ----------- Updated slide show on landing page. Commit: 2c06456c007e38670d343967f1d601bb28923db6 https://github.com/galaxyproject/usegalaxy-playbook/commit/2c06456c007e3867… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-05-08 (Mon, 08 May 2017) Changed paths: M production/files/interactive_environments/plugins/.ansible_ie_role_current_version 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 A production/files/interactive_environments/plugins/ethercalc/config/allowed_images.yml.sample A production/files/interactive_environments/plugins/ethercalc/config/ethercalc.ini.sample A production/files/interactive_environments/plugins/ethercalc/config/ethercalc.xml A production/files/interactive_environments/plugins/ethercalc/static/js/ethercalc.js A 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production/files/interactive_environments/plugins/rstudio/config/allowed_images.yml.sample 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/.ansible_ie_role_current_version M production/files/interactive_environments/proxy/lib/mapper.js M production/files/interactive_environments/proxy/package.json M production/galaxy_version.yml M production/group_vars/all.yml Log Message: ----------- Update Main to 17.05 Commit: dd1df620bf43bfa0cb0c83258f93bd20eea621ba https://github.com/galaxyproject/usegalaxy-playbook/commit/dd1df620bf43bfa0… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-05-09 (Tue, 09 May 2017) Changed paths: M files/galaxy/usegalaxy.org/var/integrated_tool_panel.xml M templates/galaxy/usegalaxy.org/config/job_conf.xml.j2 Log Message: ----------- Increase extract maf blocks to 16GB Commit: 10512706c236c3dcacbbd14c5ea96c4ed357c591 https://github.com/galaxyproject/usegalaxy-playbook/commit/10512706c236c3dc… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-05-09 (Tue, 09 May 2017) Changed paths: M production/group_vars/galaxywebservers.yml M templates/nginx/usegalaxy.j2 Log Message: ----------- 17.05 fixes for Jupyter on Main Commit: d982b0e86e073930f362ef28f0660d69d5ccac22 https://github.com/galaxyproject/usegalaxy-playbook/commit/d982b0e86e073930… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-05-09 (Tue, 09 May 2017) Changed paths: M production/group_vars/galaxyservers.yml Log Message: ----------- Message for Main Commit: 00ff306a13bd25f59670a51a432a1b8711b3dfc4 https://github.com/galaxyproject/usegalaxy-playbook/commit/00ff306a13bd25f5… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-05-10 (Wed, 10 May 2017) Changed paths: M files/galaxy/usegalaxy.org/var/integrated_tool_panel.xml M production/group_vars/galaxyservers.yml Log Message: ----------- Remove message Commit: ee705bc05e7db9bf730bc94fbbad9dbbf4f92dbf https://github.com/galaxyproject/usegalaxy-playbook/commit/ee705bc05e7db9bf… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-05-11 (Thu, 11 May 2017) Changed paths: M production/files/interactive_environments/plugins/.ansible_ie_role_current_version M production/files/interactive_environments/proxy/.ansible_ie_role_current_version M production/galaxy_version.yml Log Message: ----------- Update Main Commit: 07c13f0094d292a15b5c8a930304bc9914fd2062 https://github.com/galaxyproject/usegalaxy-playbook/commit/07c13f0094d292a1… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-05-25 (Thu, 25 May 2017) Changed paths: A env/main/files/galaxy/galaxy_version.yml Log Message: ----------- Update Main Commit: 1283e77813b20b31ee19271f289e01a149dc94cd https://github.com/galaxyproject/usegalaxy-playbook/commit/1283e77813b20b31… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-05-25 (Thu, 25 May 2017) Changed paths: M templates/galaxy/usegalaxy.org/config/job_conf.xml.j2 Log Message: ----------- give salmon 16gb and rna_Star 64 Commit: 4de1718bc260a36bc13be6d3c049a83231077e75 https://github.com/galaxyproject/usegalaxy-playbook/commit/4de1718bc260a36b… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-05-30 (Tue, 30 May 2017) Changed paths: M templates/galaxy/usegalaxy.org/config/job_conf.xml.j2 Log Message: ----------- Merge pull request #28 from galaxyproject/martenson-patch-1 give salmon 16gb and rna_Star 64 Commit: dc7efc2de746b58812b8e318ed6bad54c175e515 https://github.com/galaxyproject/usegalaxy-playbook/commit/dc7efc2de746b588… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-05-30 (Tue, 30 May 2017) Changed paths: M files/galaxy/common/dynamic_rules/multi_dynamic_walltime.py M files/galaxy/usegalaxy.org/var/integrated_tool_panel.xml M files/galaxy/usegalaxy.org/var/shed_data_manager_conf.xml M files/galaxy/usegalaxy.org/var/shed_tool_data_table_conf.xml M production/galaxy_version.yml Log Message: ----------- Fix walltime exception for align families running on local cluster and update Main Commit: 9b34d3babc373b9324722a4647fd3dd2d821a2f4 https://github.com/galaxyproject/usegalaxy-playbook/commit/9b34d3babc373b93… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-06-01 (Thu, 01 Jun 2017) Changed paths: M templates/galaxy/usegalaxy.org/config/job_conf.xml.j2 Log Message: ----------- move rna_star to different destination to dynamic_local_stampede_select_dynamic_walltime Commit: 5d772ebe86f5c12dcd2947f9105e857af9b07a0f https://github.com/galaxyproject/usegalaxy-playbook/commit/5d772ebe86f5c12d… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-06-01 (Thu, 01 Jun 2017) Changed paths: M production/files/interactive_environments/plugins/.ansible_ie_role_current_version M production/files/interactive_environments/proxy/.ansible_ie_role_current_version Log Message: ----------- IE version update missed w/ last Main update commit Commit: b19102b88cc335eacb6d45368d605c9af614334c https://github.com/galaxyproject/usegalaxy-playbook/commit/b19102b88cc335ea… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-06-01 (Thu, 01 Jun 2017) Changed paths: M stage/inventory Log Message: ----------- Prevent accidental attempts to run the playbook on Test/TTS Commit: 2fd3b1fc1cb22a423496f2ddf34b95911eed5a6f https://github.com/galaxyproject/usegalaxy-playbook/commit/2fd3b1fc1cb22a42… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-06-01 (Thu, 01 Jun 2017) Changed paths: M production/files/interactive_environments/plugins/.ansible_ie_role_current_version M production/files/interactive_environments/proxy/.ansible_ie_role_current_version M production/galaxy_version.yml Log Message: ----------- Update Main Commit: 8ae4c0768d9e012e329cc71bd0d64eadba174a8b https://github.com/galaxyproject/usegalaxy-playbook/commit/8ae4c0768d9e012e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-06-22 (Thu, 22 Jun 2017) Changed paths: A files/galaxy/usegalaxy.org/config/pulsar_bridges_actions.yml M files/galaxy/usegalaxy.org/var/integrated_tool_panel.xml M files/galaxy/usegalaxy.org/var/shed_tool_data_table_conf.xml M production/group_vars/galaxyservers.yml Log Message: ----------- Data rewrites for Bridges on Main Commit: c3f315583d3449bd6269f0d6edbdd64300ca0efb https://github.com/galaxyproject/usegalaxy-playbook/commit/c3f315583d3449bd… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-06-23 (Fri, 23 Jun 2017) Changed paths: M files/galaxy/common/dynamic_rules/multi_dynamic_walltime.py M files/galaxy/usegalaxy.org/config/job_resource_params_conf.xml M templates/galaxy/usegalaxy.org/config/job_conf.xml.j2 Log Message: ----------- Quick and dirty dynamic rule changes for RNA STAR Commit: d3d2a4733f1fe844089a077bf029a703e159ec67 https://github.com/galaxyproject/usegalaxy-playbook/commit/d3d2a4733f1fe844… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-06-23 (Fri, 23 Jun 2017) Changed paths: M files/galaxy/usegalaxy.org/var/integrated_tool_panel.xml M files/galaxy/usegalaxy.org/var/shed_tool_data_table_conf.xml Log Message: ----------- Main mutable configs Commit: 067433f547f67b848f2e4597274a379f06da04b2 https://github.com/galaxyproject/usegalaxy-playbook/commit/067433f547f67b84… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-06-27 (Tue, 27 Jun 2017) Changed paths: M files/galaxy/usegalaxy.org/config/tool_data_table_conf.xml Log Message: ----------- Add missing twobit data table to by-hand tool_data_table_conf.xml for Main Commit: cedb92eef64b06c061ee831e3686f0e09a45e592 https://github.com/galaxyproject/usegalaxy-playbook/commit/cedb92eef64b06c0… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-07-12 (Wed, 12 Jul 2017) Changed paths: M production/group_vars/galaxywebservers.yml Log Message: ----------- Switch Main to Jupyter 17.05.1 image Commit: 33366949a7e2a5eae219a108899a305670dab73d 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env/main/files/galaxy/config/pulsar_bridges_actions.yml M env/main/files/galaxy/config/tool_data_table_conf.xml M env/main/files/galaxy/var/integrated_tool_panel.xml M env/main/files/galaxy/var/shed_tool_data_table_conf.xml M env/main/group_vars/dbservers/vault.yml M env/main/group_vars/galaxyservers/vars.yml M env/main/group_vars/galaxywebservers.yml M env/main/templates/galaxy/config/job_conf.xml.j2 M env/test/group_vars/galaxyservers/vars.yml Log Message: ----------- Merge branch 'master' into reorg Conflicts: common/host_vars/galaxy-db-01.tacc.utexas.edu.yml env/common/files/galaxy/dynamic_rules/multi_dynamic_walltime.py env/main/files/galaxy/galaxy_version.yml env/main/files/galaxy/var/integrated_tool_panel.xml env/main/files/galaxy/var/shed_tool_data_table_conf.xml env/main/group_vars/galaxyservers/vars.yml env/main/host_vars/jetstream-iu0.galaxyproject.org.yml env/main/host_vars/jetstream-tacc0.galaxyproject.org.yml env/main/templates/galaxy/config/job_conf.xml.j2 env/main/templates/nginx/usegalaxy.j2 env/test/host_vars/br005.bridges.psc.edu.yml env/testtoolshed/group_vars/toolshedservers/vars.yml files/galaxy/usegalaxy.org/var/shed_data_manager_conf.xml production/files/interactive_environments/plugins/.ansible_ie_role_current_version production/files/interactive_environments/plugins/bam_iobio/config/bam_iobio.ini.sample production/files/interactive_environments/plugins/bam_iobio/static/js/bam_iobio.js production/files/interactive_environments/plugins/bam_iobio/templates/bam_iobio.mako production/files/interactive_environments/plugins/common/templates/ie.mako production/files/interactive_environments/plugins/jupyter/config/allowed_images.yml.sample production/files/interactive_environments/plugins/jupyter/config/jupyter.ini.sample production/files/interactive_environments/plugins/jupyter/config/jupyter.xml production/files/interactive_environments/plugins/jupyter/static/js/jupyter.js production/files/interactive_environments/plugins/jupyter/templates/jupyter.mako production/files/interactive_environments/plugins/neo/config/neo.ini.sample production/files/interactive_environments/plugins/neo/static/js/neo.js production/files/interactive_environments/plugins/neo/templates/neo.mako production/files/interactive_environments/plugins/phinch/config/phinch.ini.sample production/files/interactive_environments/plugins/phinch/static/js/phinch.js production/files/interactive_environments/plugins/phinch/templates/phinch.mako production/files/interactive_environments/plugins/rstudio/config/allowed_images.yml.sample production/files/interactive_environments/plugins/rstudio/config/rstudio.ini.sample production/files/interactive_environments/plugins/rstudio/static/js/rstudio.js production/files/interactive_environments/plugins/rstudio/templates/rstudio.mako production/files/interactive_environments/proxy/.ansible_ie_role_current_version production/files/interactive_environments/proxy/lib/mapper.js production/files/interactive_environments/proxy/package.json production/galaxy_version.yml production/group_vars/all.yml production/group_vars/galaxydbservers.yml production/group_vars/galaxywebservers.yml production/secret_vars/galaxydbservers.yml stage/inventory Commit: 00d29581d31378bb0c56277950aeef63641316b6 https://github.com/galaxyproject/usegalaxy-playbook/commit/00d29581d31378bb… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-07-16 (Sun, 16 Jul 2017) Changed paths: M env/test/group_vars/galaxyservers/vars.yml Log Message: ----------- Remove duplicate definition Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/6d6da7427592...…

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