April 2018 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 6ea22b: Exclude only test_grt_export integration test
by GitHub 16 Apr '18

16 Apr '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 6ea22bfe18b60374f9ed6ed49c34f5a6ff4b707f https://github.com/galaxyproject/galaxy/commit/6ea22bfe18b60374f9ed6ed49c34… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-04-16 (Mon, 16 Apr 2018) Changed paths: M test/integration/test_scripts.py Log Message: ----------- Exclude only test_grt_export integration test which takes 35' by itself. Commit: f6b52bafe3866f469da8090ce06bbad659e0a731 https://github.com/galaxyproject/galaxy/commit/f6b52bafe3866f469da8090ce06b… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-04-16 (Mon, 16 Apr 2018) Changed paths: M test/integration/test_scripts.py Log Message: ----------- Merge pull request #5892 from nsoranzo/test_most_scripts Exclude only test_grt_export integration test Compare: https://github.com/galaxyproject/galaxy/compare/2bb388db201f...f6b52bafe386

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[galaxyproject/galaxy] 59002f: Fix update_repository when hg repo has local modif...
by GitHub 16 Apr '18

16 Apr '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 59002f69e6657c1e7f88f8e3095000136f0ffcf0 https://github.com/galaxyproject/galaxy/commit/59002f69e6657c1e7f88f8e30950… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-04-16 (Mon, 16 Apr 2018) Changed paths: M lib/tool_shed/util/hg_util.py Log Message: ----------- Fix update_repository when hg repo has local modifications Fix the following traceback: ``` 149.155.222.206 - - [13/Apr/2018:11:04:46 +0100] "GET /admin_toolshed/update_to_changeset_revision?name=deseq2&latest_ctx_rev=14&tool_shed_url=https%3A%2F%2Ftoolshed.g2.bx.psu.edu%2F&o wner=iuc&changeset_revision=3660c9088494&latest_changeset_revision=d0c39b5e78cf HTTP/1.1" 500 - "https://galaxy.tgac.ac.uk/admin/repositories?__identifer=lhviib0n1kh" "Mozilla/5.0 (X11 ; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/65.0.3325.181 Safari/537.36" Traceback (most recent call last): File "lib/galaxy/web/framework/middleware/batch.py", line 75, in __call__ return self.application(environ, start_response) File "lib/galaxy/web/framework/middleware/request_id.py", line 15, in __call__ return self.app(environ, start_response) File "lib/galaxy/web/framework/middleware/xforwardedhost.py", line 23, in __call__ return self.app(environ, start_response) File "lib/galaxy/web/framework/middleware/translogger.py", line 71, in __call__ return self.application(environ, replacement_start_response) File "lib/galaxy/web/framework/middleware/error.py", line 166, in __call__ response = self.exception_handler(exc_info, environ) File "lib/galaxy/web/framework/middleware/error.py", line 181, in exception_handler get_vars = wsgilib.parse_querystring(environ) File "/opt/galaxy/.venv/lib/python2.7/site-packages/paste/request.py", line 107, in parse_querystring strict_parsing=False) File "/usr/lib64/python2.7/urlparse.py", line 408, in parse_qsl pairs = [s2 for s1 in qs.split('&') for s2 in s1.split(';')] File "lib/galaxy/web/framework/middleware/error.py", line 154, in __call__ app_iter = self.application(environ, sr_checker) File "/opt/galaxy/.venv/lib/python2.7/site-packages/paste/recursive.py", line 85, in __call__ return self.application(environ, start_response) File "/opt/galaxy/.venv/lib/python2.7/site-packages/paste/httpexceptions.py", line 640, in __call__ return self.application(environ, start_response) File "lib/galaxy/web/framework/base.py", line 136, in __call__ return self.handle_request(environ, start_response) File "lib/galaxy/web/framework/base.py", line 215, in handle_request body = method(trans, **kwargs) File "lib/galaxy/web/framework/decorators.py", line 98, in decorator return func(self, trans, *args, **kwargs) File "lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py", line 1650, in update_to_changeset_revision hg_util.update_repository(repo, latest_ctx_rev) File "lib/tool_shed/util/hg_util.py", line 460, in update_repository commands.update(get_configured_ui(), repo, rev=ctx_rev) File "/opt/galaxy/.venv/lib/python2.7/site-packages/mercurial/commands.py", line 6973, in update ret = hg.update(repo, rev) File "/opt/galaxy/.venv/lib/python2.7/site-packages/mercurial/hg.py", line 680, in update stats = updaterepo(repo, node, False) File "/opt/galaxy/.venv/lib/python2.7/site-packages/mercurial/hg.py", line 676, in updaterepo labels=['working copy', 'destination']) File "/opt/galaxy/.venv/lib/python2.7/site-packages/mercurial/merge.py", line 1532, in update stats = applyupdates(repo, actions, wc, p2, overwrite, labels=labels) File "/opt/galaxy/.venv/lib/python2.7/site-packages/mercurial/merge.py", line 1196, in applyupdates complete, r = ms.preresolve(f, wctx, labels=labels) File "/opt/galaxy/.venv/lib/python2.7/site-packages/mercurial/merge.py", line 502, in preresolve return self._resolve(True, dfile, wctx, labels=labels) File "/opt/galaxy/.venv/lib/python2.7/site-packages/mercurial/merge.py", line 457, in _resolve labels=labels) File "/opt/galaxy/.venv/lib/python2.7/site-packages/mercurial/filemerge.py", line 680, in premerge return _filemerge(True, repo, mynode, orig, fcd, fco, fca, labels=labels) File "/opt/galaxy/.venv/lib/python2.7/site-packages/mercurial/filemerge.py", line 627, in _filemerge r = _premerge(repo, fcd, fco, fca, toolconf, files, labels=labels) File "/opt/galaxy/.venv/lib/python2.7/site-packages/mercurial/filemerge.py", line 324, in _premerge r = simplemerge.simplemerge(ui, a, b, c, quiet=True, label=labels) File "/opt/galaxy/.venv/lib/python2.7/site-packages/mercurial/simplemerge.py", line 397, in simplemerge out = opener(os.path.basename(local), "w", atomictemp=True) File "/opt/galaxy/.venv/lib/python2.7/site-packages/mercurial/scmutil.py", line 530, in __call__ self.audit(path) File "/opt/galaxy/.venv/lib/python2.7/site-packages/mercurial/pathutil.py", line 61, in __call__ or _lowerclean(parts[0]) in ('.hg', '.hg.', '') File "/opt/galaxy/.venv/lib/python2.7/site-packages/mercurial/pathutil.py", line 16, in _lowerclean return encoding.hfsignoreclean(s.lower()) File "/opt/galaxy/.venv/lib/python2.7/site-packages/mercurial/encoding.py", line 35, in hfsignoreclean if "\xe2" in s or "\xef" in s: UnicodeDecodeError: 'ascii' codec can't decode byte 0xe2 in position 0: ordinal not in range(128) ``` Also, use the Mercurial command line interface instead of the internal API, as recommended in https://www.mercurial-scm.org/wiki/MercurialApi . Commit: 3e56c24d0a13f4c0c7bac4deb795de163e214e8c https://github.com/galaxyproject/galaxy/commit/3e56c24d0a13f4c0c7bac4deb795… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-04-16 (Mon, 16 Apr 2018) Changed paths: M lib/tool_shed/util/hg_util.py Log Message: ----------- Merge pull request #5890 from nsoranzo/fix_update_repository [18.01] Fix update_repository when hg repo has local modifications Commit: 2bb388db201fc261afcfe9bb9337ad383f9e2734 https://github.com/galaxyproject/galaxy/commit/2bb388db201fc261afcfe9bb9337… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-04-16 (Mon, 16 Apr 2018) Changed paths: M lib/tool_shed/util/hg_util.py Log Message: ----------- Merge branch 'release_18.01' into dev Compare: https://github.com/galaxyproject/galaxy/compare/a1d76681f6c8...2bb388db201f

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[galaxyproject/galaxy] 59002f: Fix update_repository when hg repo has local modif...
by GitHub 16 Apr '18

16 Apr '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: 59002f69e6657c1e7f88f8e3095000136f0ffcf0 https://github.com/galaxyproject/galaxy/commit/59002f69e6657c1e7f88f8e30950… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-04-16 (Mon, 16 Apr 2018) Changed paths: M lib/tool_shed/util/hg_util.py Log Message: ----------- Fix update_repository when hg repo has local modifications Fix the following traceback: ``` 149.155.222.206 - - [13/Apr/2018:11:04:46 +0100] "GET /admin_toolshed/update_to_changeset_revision?name=deseq2&latest_ctx_rev=14&tool_shed_url=https%3A%2F%2Ftoolshed.g2.bx.psu.edu%2F&o wner=iuc&changeset_revision=3660c9088494&latest_changeset_revision=d0c39b5e78cf HTTP/1.1" 500 - "https://galaxy.tgac.ac.uk/admin/repositories?__identifer=lhviib0n1kh" "Mozilla/5.0 (X11 ; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/65.0.3325.181 Safari/537.36" Traceback (most recent call last): File "lib/galaxy/web/framework/middleware/batch.py", line 75, in __call__ return self.application(environ, start_response) File "lib/galaxy/web/framework/middleware/request_id.py", line 15, in __call__ return self.app(environ, start_response) File "lib/galaxy/web/framework/middleware/xforwardedhost.py", line 23, in __call__ return self.app(environ, start_response) File "lib/galaxy/web/framework/middleware/translogger.py", line 71, in __call__ return self.application(environ, replacement_start_response) File "lib/galaxy/web/framework/middleware/error.py", line 166, in __call__ response = self.exception_handler(exc_info, environ) File "lib/galaxy/web/framework/middleware/error.py", line 181, in exception_handler get_vars = wsgilib.parse_querystring(environ) File "/opt/galaxy/.venv/lib/python2.7/site-packages/paste/request.py", line 107, in parse_querystring strict_parsing=False) File "/usr/lib64/python2.7/urlparse.py", line 408, in parse_qsl pairs = [s2 for s1 in qs.split('&') for s2 in s1.split(';')] File "lib/galaxy/web/framework/middleware/error.py", line 154, in __call__ app_iter = self.application(environ, sr_checker) File "/opt/galaxy/.venv/lib/python2.7/site-packages/paste/recursive.py", line 85, in __call__ return self.application(environ, start_response) File "/opt/galaxy/.venv/lib/python2.7/site-packages/paste/httpexceptions.py", line 640, in __call__ return self.application(environ, start_response) File "lib/galaxy/web/framework/base.py", line 136, in __call__ return self.handle_request(environ, start_response) File "lib/galaxy/web/framework/base.py", line 215, in handle_request body = method(trans, **kwargs) File "lib/galaxy/web/framework/decorators.py", line 98, in decorator return func(self, trans, *args, **kwargs) File "lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py", line 1650, in update_to_changeset_revision hg_util.update_repository(repo, latest_ctx_rev) File "lib/tool_shed/util/hg_util.py", line 460, in update_repository commands.update(get_configured_ui(), repo, rev=ctx_rev) File "/opt/galaxy/.venv/lib/python2.7/site-packages/mercurial/commands.py", line 6973, in update ret = hg.update(repo, rev) File "/opt/galaxy/.venv/lib/python2.7/site-packages/mercurial/hg.py", line 680, in update stats = updaterepo(repo, node, False) File "/opt/galaxy/.venv/lib/python2.7/site-packages/mercurial/hg.py", line 676, in updaterepo labels=['working copy', 'destination']) File "/opt/galaxy/.venv/lib/python2.7/site-packages/mercurial/merge.py", line 1532, in update stats = applyupdates(repo, actions, wc, p2, overwrite, labels=labels) File "/opt/galaxy/.venv/lib/python2.7/site-packages/mercurial/merge.py", line 1196, in applyupdates complete, r = ms.preresolve(f, wctx, labels=labels) File "/opt/galaxy/.venv/lib/python2.7/site-packages/mercurial/merge.py", line 502, in preresolve return self._resolve(True, dfile, wctx, labels=labels) File "/opt/galaxy/.venv/lib/python2.7/site-packages/mercurial/merge.py", line 457, in _resolve labels=labels) File "/opt/galaxy/.venv/lib/python2.7/site-packages/mercurial/filemerge.py", line 680, in premerge return _filemerge(True, repo, mynode, orig, fcd, fco, fca, labels=labels) File "/opt/galaxy/.venv/lib/python2.7/site-packages/mercurial/filemerge.py", line 627, in _filemerge r = _premerge(repo, fcd, fco, fca, toolconf, files, labels=labels) File "/opt/galaxy/.venv/lib/python2.7/site-packages/mercurial/filemerge.py", line 324, in _premerge r = simplemerge.simplemerge(ui, a, b, c, quiet=True, label=labels) File "/opt/galaxy/.venv/lib/python2.7/site-packages/mercurial/simplemerge.py", line 397, in simplemerge out = opener(os.path.basename(local), "w", atomictemp=True) File "/opt/galaxy/.venv/lib/python2.7/site-packages/mercurial/scmutil.py", line 530, in __call__ self.audit(path) File "/opt/galaxy/.venv/lib/python2.7/site-packages/mercurial/pathutil.py", line 61, in __call__ or _lowerclean(parts[0]) in ('.hg', '.hg.', '') File "/opt/galaxy/.venv/lib/python2.7/site-packages/mercurial/pathutil.py", line 16, in _lowerclean return encoding.hfsignoreclean(s.lower()) File "/opt/galaxy/.venv/lib/python2.7/site-packages/mercurial/encoding.py", line 35, in hfsignoreclean if "\xe2" in s or "\xef" in s: UnicodeDecodeError: 'ascii' codec can't decode byte 0xe2 in position 0: ordinal not in range(128) ``` Also, use the Mercurial command line interface instead of the internal API, as recommended in https://www.mercurial-scm.org/wiki/MercurialApi . Commit: 3e56c24d0a13f4c0c7bac4deb795de163e214e8c https://github.com/galaxyproject/galaxy/commit/3e56c24d0a13f4c0c7bac4deb795… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-04-16 (Mon, 16 Apr 2018) Changed paths: M lib/tool_shed/util/hg_util.py Log Message: ----------- Merge pull request #5890 from nsoranzo/fix_update_repository [18.01] Fix update_repository when hg repo has local modifications Compare: https://github.com/galaxyproject/galaxy/compare/68b87a07635f...3e56c24d0a13

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[galaxyproject/galaxy] 0ab89c: Implement specification for rules DSL, useful for ...
by GitHub 16 Apr '18

16 Apr '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 0ab89c9c7c46115c542da7f25559695e6e0dec98 https://github.com/galaxyproject/galaxy/commit/0ab89c9c7c46115c542da7f25559… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-04-13 (Fri, 13 Apr 2018) Changed paths: A test/base/data/rules_dsl_spec.yml Log Message: ----------- Implement specification for rules DSL, useful for testing both Python and JS. Commit: 1b90d89814ea7a140d830cf0b499eb35e2a9fea9 https://github.com/galaxyproject/galaxy/commit/1b90d89814ea7a140d830cf0b499… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-04-13 (Fri, 13 Apr 2018) Changed paths: M Makefile A client/galaxy/scripts/mocha/test.js A client/galaxy/scripts/mocha/tests/rules_dsl_spec.yml A client/galaxy/scripts/mocha/tests/rules_tests.js M client/karma.config.js M client/package.json Log Message: ----------- Mocha based client unit testing of rule tests. Commit: a1d76681f6c816ac55ea7fac859822f6d4e908ea https://github.com/galaxyproject/galaxy/commit/a1d76681f6c816ac55ea7fac8598… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-04-16 (Mon, 16 Apr 2018) Changed paths: M Makefile A client/galaxy/scripts/mocha/test.js A client/galaxy/scripts/mocha/tests/rules_dsl_spec.yml A client/galaxy/scripts/mocha/tests/rules_tests.js M client/karma.config.js M client/package.json A test/base/data/rules_dsl_spec.yml Log Message: ----------- Merge pull request #5888 from jmchilton/mocha_tests Mocha/Chai test framework + Rules DSL specification w/tests. Compare: https://github.com/galaxyproject/galaxy/compare/30e3658b8b0e...a1d76681f6c8

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[galaxyproject/infrastructure-playbook] 430f65: Remove some cruft
by GitHub 13 Apr '18

13 Apr '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 430f65ff7e8432de897962705d883ee80f824005 https://github.com/galaxyproject/infrastructure-playbook/commit/430f65ff7e8… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-13 (Fri, 13 Apr 2018) Changed paths: M README.md R play-galaxy Log Message: ----------- Remove some cruft

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[galaxyproject/infrastructure-playbook] 9d8da6: Convert jetstream envs to env/*
by GitHub 13 Apr '18

13 Apr '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 9d8da6c11c47c095c54c5d7f156b23499adc71ff https://github.com/galaxyproject/infrastructure-playbook/commit/9d8da6c11c4… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-13 (Fri, 13 Apr 2018) Changed paths: R common_env M env/common/group_vars/sshservers/vars.yml M env/common/group_vars/sshservers/vault.yml A env/jscommon/files/etc/dhclient.conf A env/jscommon/files/etc/ifcfg-eth1 A env/jscommon/files/slurm/launch A env/jscommon/files/slurm/slurm.conf.elastic A env/jscommon/files/slurm/terminate A env/jscommon/group_vars/controllers.yml A env/jscommon/group_vars/slurmclients/vars.yml A env/jscommon/group_vars/slurmclients/vault.yml A env/jscommon/launch.yml A env/jscommon/playbook.yml A env/jscommon/templates/etc/hosts.j2 A env/jscommon/templates/slurm/slurm.conf.j2 A env/jscommon/templates/supervisor/pulsar.j2 A env/jscommon/terminate.yml A env/jsiu/files A env/jsiu/group_vars/all.yml A env/jsiu/group_vars/controllers.yml A env/jsiu/group_vars/cvmfsclients.yml A env/jsiu/group_vars/galaxynodes.yml A env/jsiu/group_vars/slurmclients.yml A env/jsiu/group_vars/sshservers/common_vars.yml A env/jsiu/group_vars/sshservers/common_vault.yml A env/jsiu/group_vars/sshservers/vars.yml A env/jsiu/instance_inventory A env/jsiu/inventory A env/jsiu/playbook.yml A env/jsiu/templates A env/jstacc/files A env/jstacc/group_vars/all.yml A env/jstacc/group_vars/controllers.yml A env/jstacc/group_vars/cvmfsclients.yml A env/jstacc/group_vars/galaxynodes.yml A env/jstacc/group_vars/slurmclients.yml A env/jstacc/group_vars/sshservers/common_vars.yml A env/jstacc/group_vars/sshservers/common_vault.yml A env/jstacc/group_vars/sshservers/vars.yml A env/jstacc/instance_inventory A env/jstacc/inventory A env/jstacc/playbook.yml A env/jstacc/templates R jetstream_common/files/etc/dhclient.conf R jetstream_common/files/etc/ifcfg-eth1 R jetstream_common/files/slurm/launch R jetstream_common/files/slurm/slurm.conf.elastic R jetstream_common/files/slurm/terminate R jetstream_common/group_vars/baseenv R jetstream_common/launch.yml R jetstream_common/playbook.yml R jetstream_common/secret_group_vars/controllers.yml R jetstream_common/secret_group_vars/slurmclients.yml R jetstream_common/templates/etc/hosts.j2 R jetstream_common/templates/slurm/slurm.conf.j2 R jetstream_common/templates/supervisor/pulsar.j2 R jetstream_common/terminate.yml R jetstreamiuenv/files R jetstreamiuenv/group_vars/all.yml R jetstreamiuenv/group_vars/controllers.yml R jetstreamiuenv/group_vars/cvmfsclients.yml R jetstreamiuenv/group_vars/galaxynodes.yml R jetstreamiuenv/group_vars/slurmclients.yml R jetstreamiuenv/group_vars/sshservers/common_vars.yml R jetstreamiuenv/group_vars/sshservers/common_vault.yml R jetstreamiuenv/group_vars/sshservers/vars.yml R jetstreamiuenv/instance_inventory R jetstreamiuenv/inventory R jetstreamiuenv/playbook.yml R jetstreamiuenv/secret_group_vars R jetstreamiuenv/templates R jetstreamtaccenv/files R jetstreamtaccenv/group_vars/all.yml R jetstreamtaccenv/group_vars/controllers.yml R jetstreamtaccenv/group_vars/cvmfsclients.yml R jetstreamtaccenv/group_vars/galaxynodes.yml R jetstreamtaccenv/group_vars/slurmclients.yml R jetstreamtaccenv/group_vars/sshservers/common_vars.yml R jetstreamtaccenv/group_vars/sshservers/common_vault.yml R jetstreamtaccenv/group_vars/sshservers/vars.yml R jetstreamtaccenv/instance_inventory R jetstreamtaccenv/inventory R jetstreamtaccenv/playbook.yml R jetstreamtaccenv/secret_group_vars R jetstreamtaccenv/templates Log Message: ----------- Convert jetstream envs to env/*

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[galaxyproject/infrastructure-playbook] fe919a: Relocate galaxyenv to env/galaxy
by GitHub 13 Apr '18

13 Apr '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: fe919ae973e1c6a2b9c777624ff4b44a2ddef969 https://github.com/galaxyproject/infrastructure-playbook/commit/fe919ae973e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-26 (Thu, 26 Oct 2017) Changed paths: A env/galaxy/files/apache/galaxy-installers.conf A env/galaxy/files/jenkins/jenkins_server_user_ssh_config A env/galaxy/files/jenkins/jenkins_slave_user_ssh_config A env/galaxy/files/orval/rsyncd.xml A env/galaxy/files/ssl/athena.galaxyproject.org_cert.pem A env/galaxy/files/ssl/wildcard_cert.pem A env/galaxy/group_vars/all.yml A env/galaxy/group_vars/baseenv.yml A env/galaxy/group_vars/cvmfsstratum0servers.yml A env/galaxy/group_vars/cvmfsstratum1servers.yml A env/galaxy/group_vars/ec2hosts.yml A env/galaxy/group_vars/jenkinsservers.yml A env/galaxy/group_vars/jenkinsslaves.yml A env/galaxy/group_vars/listservers.yml A env/galaxy/group_vars/liteenv.yml A env/galaxy/group_vars/mailservers.yml A env/galaxy/group_vars/starforgebuilders.yml A env/galaxy/host_vars/athena.galaxyproject.org.yml A env/galaxy/host_vars/chouffe.galaxyproject.org.yml A env/galaxy/host_vars/cvmfs0-psu0.galaxyproject.org.yml A env/galaxy/host_vars/cvmfs0-tacc0.galaxyproject.org.yml A env/galaxy/host_vars/cvmfs1-iu0.galaxyproject.org.yml A env/galaxy/host_vars/cvmfs1-psu0.galaxyproject.org.yml A env/galaxy/host_vars/cvmfs1-tacc0.galaxyproject.org.yml A env/galaxy/host_vars/delirium.galaxyproject.org.yml A env/galaxy/host_vars/duvel.galaxyproject.org.yml A env/galaxy/host_vars/jetstream-iu0.galaxyproject.org.yml A env/galaxy/host_vars/jetstream-tacc0.galaxyproject.org.yml A env/galaxy/host_vars/leeroy.galaxyproject.org.yml A env/galaxy/host_vars/n4.galaxyproject.org.yml A env/galaxy/host_vars/n6.galaxyproject.org.yml A env/galaxy/host_vars/orval.galaxyproject.org.yml A env/galaxy/host_vars/westvleteren.galaxyproject.org.yml A env/galaxy/inventory A env/galaxy/library/README A env/galaxy/library/cron.py A env/galaxy/playbook.yml A env/galaxy/secret_group_vars/all.yml A env/galaxy/secret_group_vars/dockersslservers.yml A env/galaxy/secret_group_vars/dockerswarmmanagers.yml A env/galaxy/secret_group_vars/jenkinsslaves.yml A env/galaxy/secret_group_vars/sslwebservers.yml A env/galaxy/secret_host_vars/athena.galaxyproject.org.yml A env/galaxy/secret_host_vars/biostar.usegalaxy.org.yml A env/galaxy/secret_host_vars/chouffe.galaxyproject.org.yml A env/galaxy/secret_host_vars/cvmfs0-psu0.galaxyproject.org.yml A env/galaxy/secret_host_vars/cvmfs0-tacc0.galaxyproject.org.yml A env/galaxy/secret_host_vars/cvmfs1-iu0.galaxyproject.org.yml A env/galaxy/secret_host_vars/cvmfs1-psu0.galaxyproject.org.yml A env/galaxy/secret_host_vars/cvmfs1-tacc0.galaxyproject.org.yml A env/galaxy/secret_host_vars/default.yml A env/galaxy/secret_host_vars/delirium.galaxyproject.org.yml A env/galaxy/secret_host_vars/leeroy.galaxyproject.org.yml A env/galaxy/secret_host_vars/mjolnir0.galaxyproject.org.yml A env/galaxy/secret_host_vars/orval.galaxyproject.org.yml A env/galaxy/secret_host_vars/radegast.galaxyproject.org.yml A env/galaxy/secret_host_vars/westvleteren.galaxyproject.org.yml A env/galaxy/templates/nginx/bioarchive.j2 A env/galaxy/templates/nginx/cloudlaunch.j2 A env/galaxy/templates/nginx/depot.j2 A env/galaxy/templates/nginx/docs.j2 A env/galaxy/templates/nginx/duvel.j2 A env/galaxy/templates/nginx/eggs.j2 A env/galaxy/templates/nginx/galaxy.tools.j2 A env/galaxy/templates/nginx/galaxydomains.j2 A env/galaxy/templates/nginx/galaxyproject.j2 A env/galaxy/templates/nginx/images-proxy.j2 A env/galaxy/templates/nginx/images.j2 A env/galaxy/templates/nginx/intron.j2 A env/galaxy/templates/nginx/jenkins.j2 A env/galaxy/templates/nginx/lists.j2 A env/galaxy/templates/nginx/moin.j2 A env/galaxy/templates/nginx/new.j2 A env/galaxy/templates/nginx/orval.j2 A env/galaxy/templates/nginx/sample-data.j2 A env/galaxy/templates/nginx/screencast.j2 A env/galaxy/templates/nginx/snpeff-data.j2 A env/galaxy/templates/nginx/toolshed.tools.j2 A env/galaxy/templates/nginx/training.j2 A env/galaxy/templates/nginx/wheels.j2 A env/galaxy/templates/nginx/wiki.j2 A env/galaxy/templates/nginx/wiki_hub_rewrites.conf.j2 A env/galaxy/templates/supervisor/pypiserver.j2 R galaxyenv/files/apache/galaxy-installers.conf R galaxyenv/files/jenkins/jenkins_server_user_ssh_config R galaxyenv/files/jenkins/jenkins_slave_user_ssh_config R galaxyenv/files/orval/rsyncd.xml R galaxyenv/files/ssl/athena.galaxyproject.org_cert.pem R galaxyenv/files/ssl/wildcard_cert.pem R galaxyenv/group_vars/all.yml R galaxyenv/group_vars/baseenv.yml R galaxyenv/group_vars/cvmfsstratum0servers.yml R galaxyenv/group_vars/cvmfsstratum1servers.yml R galaxyenv/group_vars/ec2hosts.yml R galaxyenv/group_vars/jenkinsservers.yml R galaxyenv/group_vars/jenkinsslaves.yml R galaxyenv/group_vars/listservers.yml R galaxyenv/group_vars/liteenv.yml R galaxyenv/group_vars/mailservers.yml R galaxyenv/group_vars/starforgebuilders.yml R galaxyenv/host_vars/athena.galaxyproject.org.yml R galaxyenv/host_vars/chouffe.galaxyproject.org.yml R galaxyenv/host_vars/cvmfs0-psu0.galaxyproject.org.yml R galaxyenv/host_vars/cvmfs0-tacc0.galaxyproject.org.yml R galaxyenv/host_vars/cvmfs1-iu0.galaxyproject.org.yml R galaxyenv/host_vars/cvmfs1-psu0.galaxyproject.org.yml R galaxyenv/host_vars/cvmfs1-tacc0.galaxyproject.org.yml R galaxyenv/host_vars/delirium.galaxyproject.org.yml R galaxyenv/host_vars/duvel.galaxyproject.org.yml R galaxyenv/host_vars/jetstream-iu0.galaxyproject.org.yml R galaxyenv/host_vars/jetstream-tacc0.galaxyproject.org.yml R galaxyenv/host_vars/leeroy.galaxyproject.org.yml R galaxyenv/host_vars/n4.galaxyproject.org.yml R galaxyenv/host_vars/n6.galaxyproject.org.yml R galaxyenv/host_vars/orval.galaxyproject.org.yml R galaxyenv/host_vars/westvleteren.galaxyproject.org.yml R galaxyenv/inventory R galaxyenv/library/README R galaxyenv/library/cron.py R galaxyenv/playbook.yml R galaxyenv/secret_group_vars/all.yml R galaxyenv/secret_group_vars/dockersslservers.yml R galaxyenv/secret_group_vars/dockerswarmmanagers.yml R galaxyenv/secret_group_vars/jenkinsslaves.yml R galaxyenv/secret_group_vars/sslwebservers.yml R galaxyenv/secret_host_vars/athena.galaxyproject.org.yml R galaxyenv/secret_host_vars/biostar.usegalaxy.org.yml R galaxyenv/secret_host_vars/chouffe.galaxyproject.org.yml R galaxyenv/secret_host_vars/cvmfs0-psu0.galaxyproject.org.yml R galaxyenv/secret_host_vars/cvmfs0-tacc0.galaxyproject.org.yml R galaxyenv/secret_host_vars/cvmfs1-iu0.galaxyproject.org.yml R galaxyenv/secret_host_vars/cvmfs1-psu0.galaxyproject.org.yml R galaxyenv/secret_host_vars/cvmfs1-tacc0.galaxyproject.org.yml R galaxyenv/secret_host_vars/default.yml R galaxyenv/secret_host_vars/delirium.galaxyproject.org.yml R galaxyenv/secret_host_vars/leeroy.galaxyproject.org.yml R galaxyenv/secret_host_vars/mjolnir0.galaxyproject.org.yml R galaxyenv/secret_host_vars/orval.galaxyproject.org.yml R galaxyenv/secret_host_vars/radegast.galaxyproject.org.yml R galaxyenv/secret_host_vars/westvleteren.galaxyproject.org.yml R galaxyenv/templates/nginx/bioarchive.j2 R galaxyenv/templates/nginx/cloudlaunch.j2 R galaxyenv/templates/nginx/depot.j2 R galaxyenv/templates/nginx/docs.j2 R galaxyenv/templates/nginx/duvel.j2 R galaxyenv/templates/nginx/eggs.j2 R galaxyenv/templates/nginx/galaxy.tools.j2 R galaxyenv/templates/nginx/galaxydomains.j2 R galaxyenv/templates/nginx/galaxyproject.j2 R galaxyenv/templates/nginx/images-proxy.j2 R galaxyenv/templates/nginx/images.j2 R galaxyenv/templates/nginx/intron.j2 R galaxyenv/templates/nginx/jenkins.j2 R galaxyenv/templates/nginx/lists.j2 R galaxyenv/templates/nginx/moin.j2 R galaxyenv/templates/nginx/new.j2 R galaxyenv/templates/nginx/orval.j2 R galaxyenv/templates/nginx/sample-data.j2 R galaxyenv/templates/nginx/screencast.j2 R galaxyenv/templates/nginx/snpeff-data.j2 R galaxyenv/templates/nginx/toolshed.tools.j2 R galaxyenv/templates/nginx/training.j2 R galaxyenv/templates/nginx/wheels.j2 R galaxyenv/templates/nginx/wiki.j2 R galaxyenv/templates/nginx/wiki_hub_rewrites.conf.j2 R galaxyenv/templates/supervisor/pypiserver.j2 Log Message: ----------- Relocate galaxyenv to env/galaxy Commit: a42ef24ee9383f66633bcdbe21af20fea637b873 https://github.com/galaxyproject/infrastructure-playbook/commit/a42ef24ee93… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-26 (Thu, 26 Oct 2017) Changed paths: A common_env R common_env/files/ssl/docker/ca-key.pem R common_env/files/ssl/docker/ca.pem R common_env/files/ssl/docker/ca.srl R common_env/files/ssl/docker/client.pem R common_env/files/ssl/docker/client_privatekey.yml R common_env/files/ssl/docker/cvmfs1-psu0.galaxyproject.org/server.pem R common_env/files/ssl/docker/cvmfs1-psu0.galaxyproject.org/server_privatekey… R common_env/files/ssl/docker/jetstream-iu0.galaxyproject.org/server.pem R common_env/files/ssl/docker/jetstream-iu0.galaxyproject.org/server_privatek… R common_env/files/ssl/docker/jetstream-tacc0.galaxyproject.org/server-cert.p… R common_env/files/ssl/docker/jetstream-tacc0.galaxyproject.org/server_privat… R common_env/files/ssl/docker_test/ca-key.pem R common_env/files/ssl/docker_test/ca.pem R common_env/files/ssl/docker_test/ca.srl R common_env/files/ssl/docker_test/client.pem R common_env/files/ssl/docker_test/client_privatekey.yml R common_env/files/ssl/docker_test/iu-gie-test/server.pem R common_env/files/ssl/docker_test/iu-gie-test/server_privatekey.yml R common_env/files/ssl/rabbitmq/ca-key.pem R common_env/files/ssl/rabbitmq/ca.pem R common_env/files/ssl/rabbitmq/ca.srl R common_env/files/ssl/rabbitmq/galaxy08.tacc.utexas.edu/server.pem R common_env/files/ssl/rabbitmq/galaxy08.tacc.utexas.edu/server_privatekey.yml R common_env/files/ssl/wildcard_cert.pem R common_env/group_vars/baseenv/vars.yml R common_env/group_vars/baseenv/vault.yml R common_env/group_vars/sslservers/vars.yml R common_env/group_vars/sslservers/vault.yml R common_env/secret_group_vars/sslwebservers.yml R env/common A env/common/files/ssl/docker/ca-key.pem A env/common/files/ssl/docker/ca.pem A env/common/files/ssl/docker/ca.srl A env/common/files/ssl/docker/client.pem A env/common/files/ssl/docker/client_privatekey.yml A env/common/files/ssl/docker/cvmfs1-psu0.galaxyproject.org/server.pem A env/common/files/ssl/docker/cvmfs1-psu0.galaxyproject.org/server_privatekey… A env/common/files/ssl/docker/jetstream-iu0.galaxyproject.org/server.pem A env/common/files/ssl/docker/jetstream-iu0.galaxyproject.org/server_privatek… A env/common/files/ssl/docker/jetstream-tacc0.galaxyproject.org/server-cert.p… A env/common/files/ssl/docker/jetstream-tacc0.galaxyproject.org/server_privat… A env/common/files/ssl/docker_test/ca-key.pem A env/common/files/ssl/docker_test/ca.pem A env/common/files/ssl/docker_test/ca.srl A env/common/files/ssl/docker_test/client.pem A env/common/files/ssl/docker_test/client_privatekey.yml A env/common/files/ssl/docker_test/iu-gie-test/server.pem A env/common/files/ssl/docker_test/iu-gie-test/server_privatekey.yml A env/common/files/ssl/rabbitmq/ca-key.pem A env/common/files/ssl/rabbitmq/ca.pem A env/common/files/ssl/rabbitmq/ca.srl A env/common/files/ssl/rabbitmq/galaxy08.tacc.utexas.edu/server.pem A env/common/files/ssl/rabbitmq/galaxy08.tacc.utexas.edu/server_privatekey.yml A env/common/files/ssl/wildcard_cert.pem A env/common/group_vars/sshservers/vars.yml A env/common/group_vars/sshservers/vault.yml A env/common/group_vars/sslservers/vars.yml A env/common/group_vars/sslservers/vault.yml A env/common/secret_group_vars/sslwebservers.yml Log Message: ----------- Reverse common_env <-> env/common symlink Commit: a0ba5b2bd9a792c608339b4323daedecf921c0e1 https://github.com/galaxyproject/infrastructure-playbook/commit/a0ba5b2bd9a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-26 (Thu, 26 Oct 2017) Changed paths: M env/common/group_vars/sshservers/vars.yml M env/common/group_vars/sshservers/vault.yml A env/galaxy/group_vars/sshclients/vars.yml A env/galaxy/group_vars/sshclients/vault.yml A env/galaxy/group_vars/sshservers/common_vars.yml A env/galaxy/group_vars/sshservers/common_vault.yml A env/galaxy/group_vars/sshservers/vars.yml A env/galaxy/group_vars/sshservers/vault.yml M env/galaxy/inventory R env/galaxy/secret_group_vars/all.yml R jetstreamiuenv/group_vars/baseenv A jetstreamiuenv/group_vars/sshservers/common_vars.yml A jetstreamiuenv/group_vars/sshservers/common_vault.yml A jetstreamiuenv/group_vars/sshservers/vars.yml M jetstreamiuenv/inventory R jetstreamtaccenv/group_vars/baseenv A jetstreamtaccenv/group_vars/sshservers/common_vars.yml A jetstreamtaccenv/group_vars/sshservers/common_vault.yml A jetstreamtaccenv/group_vars/sshservers/vars.yml M jetstreamtaccenv/inventory R taccenv/group_vars/baseenv A taccenv/group_vars/sshservers/common_vars.yml A taccenv/group_vars/sshservers/common_vault.yml A taccenv/group_vars/sshservers/vars.yml M taccenv/inventory Log Message: ----------- Convert ssh keys out of the baseenv group to a separate sshkeys group, allow hash merging by renaming to common_sshkeys Commit: 99fe08fd5b10ce15eed7d70cec11263b11cf6c06 https://github.com/galaxyproject/infrastructure-playbook/commit/99fe08fd5b1… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-26 (Thu, 26 Oct 2017) Changed paths: M common_roles Log Message: ----------- Update common_roles for users role improvements Commit: 7dcb2ac12002fec9ea230fbec1c40b836e822e2a https://github.com/galaxyproject/infrastructure-playbook/commit/7dcb2ac1200… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-26 (Thu, 26 Oct 2017) Changed paths: A env/galaxy/group_vars/dockersslservers/vars.yml A env/galaxy/group_vars/dockersslservers/vault.yml A env/galaxy/group_vars/dockerswarmmanagers/vars.yml A env/galaxy/group_vars/dockerswarmmanagers/vault.yml R env/galaxy/group_vars/jenkinsslaves.yml A env/galaxy/group_vars/jenkinsslaves/vars.yml A env/galaxy/group_vars/jenkinsslaves/vault.yml R env/galaxy/secret_group_vars/dockersslservers.yml R env/galaxy/secret_group_vars/dockerswarmmanagers.yml R env/galaxy/secret_group_vars/jenkinsslaves.yml Log Message: ----------- Mostly convert the galaxy env to standard vars/vault group_vars Commit: 34342b8a13b1dc3ec2a5fe86023d492d85b78c9c https://github.com/galaxyproject/infrastructure-playbook/commit/34342b8a13b… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-27 (Fri, 27 Oct 2017) Changed paths: M ansible.cfg M common_roles M env/galaxy/secret_host_vars/mjolnir0.galaxyproject.org.yml Log Message: ----------- Merge branch 'master' into galaxyenv Commit: 0b47750f8f09715ddcaea949280c692d62506492 https://github.com/galaxyproject/infrastructure-playbook/commit/0b47750f8f0… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-27 (Fri, 27 Oct 2017) Changed paths: M env/galaxy/playbook.yml Log Message: ----------- Remove manual inclusion of secret variables in galaxy env playbook Commit: 1647adbf58e9494de222d1ae83e47138390dc09b https://github.com/galaxyproject/infrastructure-playbook/commit/1647adbf58e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-27 (Fri, 27 Oct 2017) Changed paths: M env/galaxy/group_vars/all.yml Log Message: ----------- Drop unncessary deploy_env Commit: 6c73e832fbe10ee23d770ca3fcacd7e04820dc5b https://github.com/galaxyproject/infrastructure-playbook/commit/6c73e832fbe… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-27 (Fri, 27 Oct 2017) Changed paths: M env/common/group_vars/sslservers/vars.yml M env/common/group_vars/sslservers/vault.yml R env/common/secret_group_vars/sslwebservers.yml M env/galaxy/inventory R env/galaxy/secret_group_vars/sslwebservers.yml M taccenv/inventory R taccenv/secret_group_vars/sslwebservers.yml Log Message: ----------- Convert sslkeys to automatic vault files Commit: 46d754c2b74c11c09d274bb3f09de07d668418bf https://github.com/galaxyproject/infrastructure-playbook/commit/46d754c2b74… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-27 (Fri, 27 Oct 2017) Changed paths: R env/galaxy/group_vars/baseenv.yml A env/galaxy/group_vars/baseenv/vars.yml A env/galaxy/group_vars/baseenv/vault.yml A env/galaxy/group_vars/cvmfsservers/vars.yml A env/galaxy/group_vars/cvmfsservers/vault.yml R env/galaxy/group_vars/jenkinsservers.yml A env/galaxy/group_vars/jenkinsservers/vars.yml A env/galaxy/group_vars/jenkinsservers/vault.yml A env/galaxy/group_vars/jetstreamhosts/vars.yml A env/galaxy/group_vars/jetstreamhosts/vault.yml R env/galaxy/host_vars/athena.galaxyproject.org.yml A env/galaxy/host_vars/athena.galaxyproject.org/vars.yml A env/galaxy/host_vars/athena.galaxyproject.org/vault.yml A env/galaxy/host_vars/biostar.usegalaxy.org/vars.yml A env/galaxy/host_vars/biostar.usegalaxy.org/vault.yml R env/galaxy/host_vars/chouffe.galaxyproject.org.yml A env/galaxy/host_vars/chouffe.galaxyproject.org/vars.yml A env/galaxy/host_vars/chouffe.galaxyproject.org/vault.yml R env/galaxy/host_vars/cvmfs0-psu0.galaxyproject.org.yml A env/galaxy/host_vars/cvmfs0-psu0.galaxyproject.org/vars.yml A env/galaxy/host_vars/cvmfs0-psu0.galaxyproject.org/vault.yml R env/galaxy/host_vars/cvmfs0-tacc0.galaxyproject.org.yml A env/galaxy/host_vars/cvmfs0-tacc0.galaxyproject.org/vars.yml A env/galaxy/host_vars/cvmfs0-tacc0.galaxyproject.org/vault.yml R env/galaxy/host_vars/cvmfs1-psu0.galaxyproject.org.yml A env/galaxy/host_vars/cvmfs1-psu0.galaxyproject.org/vars.yml A env/galaxy/host_vars/cvmfs1-psu0.galaxyproject.org/vault.yml R env/galaxy/host_vars/delirium.galaxyproject.org.yml A env/galaxy/host_vars/delirium.galaxyproject.org/vars.yml A env/galaxy/host_vars/delirium.galaxyproject.org/vault.yml M env/galaxy/host_vars/leeroy.galaxyproject.org.yml A env/galaxy/host_vars/mjolnir0.galaxyproject.org/vars.yml A env/galaxy/host_vars/mjolnir0.galaxyproject.org/vault.yml R env/galaxy/host_vars/orval.galaxyproject.org.yml A env/galaxy/host_vars/orval.galaxyproject.org/vars.yml A env/galaxy/host_vars/orval.galaxyproject.org/vault.yml A env/galaxy/host_vars/radegast.galaxyproject.org/vars.yml A env/galaxy/host_vars/radegast.galaxyproject.org/vault.yml R env/galaxy/host_vars/westvleteren.galaxyproject.org.yml A env/galaxy/host_vars/westvleteren.galaxyproject.org/vars.yml A env/galaxy/host_vars/westvleteren.galaxyproject.org/vault.yml M env/galaxy/playbook.yml R env/galaxy/secret_host_vars/athena.galaxyproject.org.yml R env/galaxy/secret_host_vars/biostar.usegalaxy.org.yml R env/galaxy/secret_host_vars/chouffe.galaxyproject.org.yml R env/galaxy/secret_host_vars/cvmfs0-psu0.galaxyproject.org.yml R env/galaxy/secret_host_vars/cvmfs0-tacc0.galaxyproject.org.yml R env/galaxy/secret_host_vars/cvmfs1-iu0.galaxyproject.org.yml R env/galaxy/secret_host_vars/cvmfs1-psu0.galaxyproject.org.yml R env/galaxy/secret_host_vars/cvmfs1-tacc0.galaxyproject.org.yml R env/galaxy/secret_host_vars/default.yml R env/galaxy/secret_host_vars/delirium.galaxyproject.org.yml R env/galaxy/secret_host_vars/leeroy.galaxyproject.org.yml R env/galaxy/secret_host_vars/mjolnir0.galaxyproject.org.yml R env/galaxy/secret_host_vars/orval.galaxyproject.org.yml R env/galaxy/secret_host_vars/radegast.galaxyproject.org.yml R env/galaxy/secret_host_vars/westvleteren.galaxyproject.org.yml Log Message: ----------- Remove secret_host_vars from galaxy env Commit: 629aee142143ce08dbd781688d22126a4351bfaf https://github.com/galaxyproject/infrastructure-playbook/commit/629aee14214… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-30 (Mon, 30 Oct 2017) Changed paths: M env/galaxy/inventory Log Message: ----------- nventory documentation improvements and fixes for authorized keys Commit: b5b266f439840b839f1394ee497f8864c9fc4960 https://github.com/galaxyproject/infrastructure-playbook/commit/b5b266f4398… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-30 (Mon, 30 Oct 2017) Changed paths: M env/galaxy/inventory M env/galaxy/playbook.yml Log Message: ----------- Add a "fullenv" group to the Galaxy env ("liteenv" + AFS) Commit: b6c8a7134dfd9cf3ebc57ca756ef3ef24d5bd85a https://github.com/galaxyproject/infrastructure-playbook/commit/b6c8a7134df… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-30 (Mon, 30 Oct 2017) Changed paths: M env/galaxy/inventory M env/galaxy/playbook.yml A roles/kerberos_kdc/defaults/main.yml A roles/kerberos_kdc/handlers/main.yml A roles/kerberos_kdc/meta/main.yml A roles/kerberos_kdc/tasks/debian.yml A roles/kerberos_kdc/tasks/heimdal.yml A roles/kerberos_kdc/tasks/main.yml A roles/kerberos_kdc/templates/kadmind.acl.j2 A roles/kerberos_kdc/templates/kdc.conf.j2 A roles/kerberos_kdc/vars/debian.yml A roles/kerberos_kdc/vars/heimdal.yml Log Message: ----------- Add the Kerberos KDC role from the pre-vault playbook and update it. Commit: 9d32f3fd87d9298bd32899ede324b1f5813cf9a7 https://github.com/galaxyproject/infrastructure-playbook/commit/9d32f3fd87d… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-11-01 (Wed, 01 Nov 2017) Changed paths: M ansible.cfg M common_roles Log Message: ----------- Include fixes for inheritance chain vars Commit: d371844a507ea06459c1f97061ccf358c206a758 https://github.com/galaxyproject/infrastructure-playbook/commit/d371844a507… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-11-02 (Thu, 02 Nov 2017) Changed paths: M common_roles Log Message: ----------- Update common_roles again Commit: ff0e0168086421bcc2c2e0bbc729bd2a41ab5686 https://github.com/galaxyproject/infrastructure-playbook/commit/ff0e0168086… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-11-02 (Thu, 02 Nov 2017) Changed paths: A env/galaxy/_inc_baseenv.yml M env/galaxy/playbook.yml Log Message: ----------- Start splitting galaxy env playbook into different purposes Commit: e2c5215c9ebe97f7e57dfd64bdf6834ebfcc87ec https://github.com/galaxyproject/infrastructure-playbook/commit/e2c5215c9eb… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-11-02 (Thu, 02 Nov 2017) Changed paths: A .pass M ansible.cfg Log Message: ----------- Automatically read vault password from pass, or prompt if pass is not installed or doesn't work Commit: 307ccf6db7b987294ef0fd98796e035fd09658dd https://github.com/galaxyproject/infrastructure-playbook/commit/307ccf6db7b… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-11-02 (Thu, 02 Nov 2017) Changed paths: M common_roles M env/galaxy/playbook.yml A roles/kerberos_kdc/meta/required_vars.yml Log Message: ----------- Check kerberos_kdc required vars Commit: 74a26b2310b2ec823d9ff5a7a1e8791ed647007d https://github.com/galaxyproject/infrastructure-playbook/commit/74a26b2310b… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-11-02 (Thu, 02 Nov 2017) Changed paths: A env/galaxy/core.yml Log Message: ----------- Start a playbook for core infrastructure servers Commit: 24640abf6b83801fcd454701af832600caa4633b https://github.com/galaxyproject/infrastructure-playbook/commit/24640abf6b8… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-11-02 (Thu, 02 Nov 2017) Changed paths: M env/galaxy/inventory Log Message: ----------- Document the purpose of the virtual group and add duvel to it Commit: c8e17bbd96626c9fe80ebae6060ef4f3a331345c https://github.com/galaxyproject/infrastructure-playbook/commit/c8e17bbd966… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-11-02 (Thu, 02 Nov 2017) Changed paths: M roles/kerberos/defaults/main.yml A roles/kerberos/meta/required_vars.yml Log Message: ----------- Define required vars for kerberos role and set some defaults that can be easily set Commit: 8e0068ac5994f6c361a5bf8abdcf93d0ceea35c3 https://github.com/galaxyproject/infrastructure-playbook/commit/8e0068ac599… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-11-02 (Thu, 02 Nov 2017) Changed paths: A env/galaxy/group_vars/kerberosservers/vars.yml A env/galaxy/group_vars/kerberosservers/vault.yml M roles/kerberos_kdc/defaults/main.yml M roles/kerberos_kdc/meta/main.yml M roles/kerberos_kdc/tasks/heimdal.yml A roles/kerberos_kdc/tasks/heimdal_keytab.yml M roles/kerberos_kdc/tasks/main.yml M roles/kerberos_kdc/templates/kadmind.acl.j2 M roles/kerberos_kdc/templates/kdc.conf.j2 A roles/kerberos_kdc/templates/slaves.j2 M roles/kerberos_kdc/vars/debian.yml M roles/kerberos_kdc/vars/heimdal.yml Log Message: ----------- Allow Ansible to generate iprop principals/keytabs, and other kerberos_kdc role improvements. Commit: 11a090947ac0ba95dabd2e119d987e6456d1aa3a https://github.com/galaxyproject/infrastructure-playbook/commit/11a090947ac… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-11-02 (Thu, 02 Nov 2017) Changed paths: A roles/dns/defaults/main.yml A roles/dns/tasks/bind.yml A roles/dns/tasks/debian.yml A roles/dns/tasks/main.yml A roles/dns/templates/named_options.conf.j2 A roles/dns/templates/named_views.conf.j2 A roles/dns/vars/bind.yml A roles/dns/vars/debian.yml Log Message: ----------- WIP untested DNS role Commit: 1a8ffca684f616e0c76427c50e45bd6e56d2b7a7 https://github.com/galaxyproject/infrastructure-playbook/commit/1a8ffca684f… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-11-03 (Fri, 03 Nov 2017) Changed paths: M common_roles Log Message: ----------- Update common_roles for ordered filter Commit: 1520279873385c678558415bc330a2bb41bdb378 https://github.com/galaxyproject/infrastructure-playbook/commit/15202798733… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-11-03 (Fri, 03 Nov 2017) Changed paths: M env/galaxy/core.yml A env/galaxy/group_vars/dnsservers.yml M env/galaxy/inventory A roles/dns/handlers/main.yml M roles/dns/tasks/main.yml M roles/dns/templates/named_options.conf.j2 M roles/dns/templates/named_views.conf.j2 M roles/dns/vars/bind.yml M roles/dns/vars/debian.yml Log Message: ----------- dns role is working Commit: a5058f56e16ac985f2a643dec756e5b56d569feb https://github.com/galaxyproject/infrastructure-playbook/commit/a5058f56e16… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-11-03 (Fri, 03 Nov 2017) Changed paths: M env/galaxy/host_vars/athena.galaxyproject.org/vars.yml A env/galaxy/templates/nginx/gxy.io.j2 Log Message: ----------- Merge branch 'master' into galaxyenv Commit: c6fd1ff76b85ec0b92d192fb50314e7158ca076a https://github.com/galaxyproject/infrastructure-playbook/commit/c6fd1ff76b8… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-11-06 (Mon, 06 Nov 2017) Changed paths: M env/galaxy/core.yml A env/galaxy/group_vars/ldapservers/vars.yml A env/galaxy/group_vars/ldapservers/vault.yml M env/galaxy/inventory A roles/ldap_server/defaults/main.yml A roles/ldap_server/files/autofs.ldif A roles/ldap_server/files/dhcp.ldif A roles/ldap_server/files/galaxy.ldif A roles/ldap_server/files/postfix.ldif A roles/ldap_server/files/rfc2307bis.ldif A roles/ldap_server/files/sudo.ldif A roles/ldap_server/handlers/main.yml A roles/ldap_server/meta/required_vars.yml A roles/ldap_server/tasks/debian.yml A roles/ldap_server/tasks/main.yml A roles/ldap_server/tasks/openldap.yml A roles/ldap_server/vars/debian.yml A roles/ldap_server/vars/openldap.yml Log Message: ----------- LDAP server role is working. Skipped auditlog/ldap2pts stuff as I plan to have Ansible create LDAP/AFS users Commit: ffeeed5b2e00db66f8b84a9b6034fbd237870498 https://github.com/galaxyproject/infrastructure-playbook/commit/ffeeed5b2e0… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-11-09 (Thu, 09 Nov 2017) Changed paths: M env/common/group_vars/sshservers/vault.yml Log Message: ----------- Add missing people from common sshkeys Commit: 93480aed148c9dd839adeaaf7b7fd9c9d8aa820d https://github.com/galaxyproject/infrastructure-playbook/commit/93480aed148… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-11-09 (Thu, 09 Nov 2017) Changed paths: M env/galaxy/group_vars/starforgebuilders.yml Log Message: ----------- Stop using removed local_users syntax and note an annoyance with the new inheritance merging. Commit: afeab93d32e03c0a2198b2eb4cc082774c5fcc0c https://github.com/galaxyproject/infrastructure-playbook/commit/afeab93d32e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-11-28 (Tue, 28 Nov 2017) Changed paths: A env/common/files/ssl/incommon_chain.pem A env/galaxy/files/ssl/incommon_chain.pem M env/galaxy/host_vars/athena.galaxyproject.org/vars.yml M env/galaxy/host_vars/chouffe.galaxyproject.org/vars.yml M env/galaxy/host_vars/delirium.galaxyproject.org/vars.yml M env/galaxy/host_vars/duvel.galaxyproject.org.yml M env/galaxy/host_vars/orval.galaxyproject.org/vars.yml M env/galaxy/playbook.yml M env/galaxy/templates/nginx/training.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/ssl.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 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 M roles/stats/templates/galaxy_slurp.py.j2 M taccenv/group_vars/galaxyservers.yml M taccenv/host_vars/galaxy-db-02.tacc.utexas.edu/vars.yml M taccenv/host_vars/galaxy04.tacc.utexas.edu.yml M taccenv/host_vars/galaxy06.tacc.utexas.edu.yml M taccenv/playbook.yml Log Message: ----------- Merge remote-tracking branch 'origin/master' into galaxyenv Commit: 297484ca90d5540a9871729320571f443c011a45 https://github.com/galaxyproject/infrastructure-playbook/commit/297484ca90d… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-01-16 (Tue, 16 Jan 2018) Changed paths: M env/galaxy/inventory M roles/nfs/tasks/main.yml Log Message: ----------- Set up nn14 as a liteenv host Commit: dbabd0075f3a25a94bb930e805e55531fe96c5bf https://github.com/galaxyproject/infrastructure-playbook/commit/dbabd0075f3… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: M common_roles M env/galaxy/group_vars/sshservers/vault.yml M env/galaxy/host_vars/westvleteren.galaxyproject.org/vars.yml M env/galaxy/host_vars/westvleteren.galaxyproject.org/vault.yml M env/galaxy/inventory A taccenv/group_vars/sshclients/vars.yml A taccenv/group_vars/sshclients/vault.yml A taccenv/host_vars/galaxy-web-05.tacc.utexas.edu/vars.yml A taccenv/host_vars/galaxy-web-05.tacc.utexas.edu/vault.yml M taccenv/inventory A taccenv/zfsdump-gxmain.yml Log Message: ----------- Backup Main public libraries Commit: e2992640880d0df95df4256a16219e4059bbb90a https://github.com/galaxyproject/infrastructure-playbook/commit/e2992640880… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: M common_roles M env/galaxy/host_vars/orval.galaxyproject.org/vars.yml M env/galaxy/host_vars/westvleteren.galaxyproject.org/vars.yml Log Message: ----------- Updates for the zfs admin module Commit: 1cfe001988c2692eed4cbfa04eaf5acfbf194e06 https://github.com/galaxyproject/infrastructure-playbook/commit/1cfe001988c… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-02-15 (Thu, 15 Feb 2018) Changed paths: M env/galaxy/inventory M roles/cvmfs/tasks/stratum1.yml Log Message: ----------- Use `cvmfs_server snapshot -a` instead of snapshotting each repo individually Commit: 8f224099bde598ead8fd29402b25ed3ec7089f11 https://github.com/galaxyproject/infrastructure-playbook/commit/8f224099bde… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-03-16 (Fri, 16 Mar 2018) Changed paths: A env/galaxy/group_vars/sslservers M env/galaxy/templates/nginx/galaxyproject.j2 Log Message: ----------- Enable GCC2019 redirect on Hub Commit: b763fb25cfc72d65ff9207293e03410dec3642eb https://github.com/galaxyproject/infrastructure-playbook/commit/b763fb25cfc… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-03-21 (Wed, 21 Mar 2018) Changed paths: M env/galaxy/group_vars/cvmfsstratum0servers.yml M env/galaxy/host_vars/cvmfs0-tacc0.galaxyproject.org/vars.yml M roles/cvmfs/tasks/stratum0.yml Log Message: ----------- Stratum 0 upgrades I forgot to commit Commit: bc9ad65d929be306b8429e15fba596073bce3610 https://github.com/galaxyproject/infrastructure-playbook/commit/bc9ad65d929… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-03-21 (Wed, 21 Mar 2018) Changed paths: A env/common/files/ssl/athena.galaxyproject.org_cert.pem M env/common/files/ssl/docker/ca-key.pem M env/common/files/ssl/docker/ca.pem M env/common/files/ssl/docker/ca.srl R env/common/files/ssl/docker/client.pem R env/common/files/ssl/docker/client_privatekey.yml M env/common/files/ssl/docker/cvmfs1-psu0.galaxyproject.org/server.pem M env/common/files/ssl/docker/cvmfs1-psu0.galaxyproject.org/server_privatekey… M env/common/files/ssl/docker/jetstream-iu0.galaxyproject.org/server.pem M env/common/files/ssl/docker/jetstream-iu0.galaxyproject.org/server_privatek… R env/common/files/ssl/docker/jetstream-tacc0.galaxyproject.org/server-cert.p… A env/common/files/ssl/docker/jetstream-tacc0.galaxyproject.org/server.pem M env/common/files/ssl/docker/jetstream-tacc0.galaxyproject.org/server_privat… A env/galaxy/files/ssl R env/galaxy/files/ssl/athena.galaxyproject.org_cert.pem R env/galaxy/files/ssl/wildcard_cert.pem M env/galaxy/group_vars/dockersslservers/vars.yml M env/galaxy/inventory Log Message: ----------- New Docker CA and server certs Commit: 6a60eaaf69dbeb7cac1c09802990bac1e9bd9474 https://github.com/galaxyproject/infrastructure-playbook/commit/6a60eaaf69d… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-11 (Wed, 11 Apr 2018) Changed paths: M common_roles A env/galaxy/files/sites/datacache/index.html M env/galaxy/group_vars/jenkinsslaves/vars.yml M env/galaxy/host_vars/athena.galaxyproject.org/vars.yml M env/galaxy/host_vars/chouffe.galaxyproject.org/vars.yml M env/galaxy/host_vars/cvmfs1-psu0.galaxyproject.org/vars.yml M env/galaxy/host_vars/westvleteren.galaxyproject.org/vars.yml M env/galaxy/inventory A env/galaxy/templates/nginx/datacache.j2 A env/galaxy/templates/squid/cvmfs1-psu0_squid.conf.j2 M roles/cvmfs/tasks/stratum1.yml Log Message: ----------- - Serve datacache via HTTP as well as rsync - Switch to inheritance chain for directories and files common role tasks Commit: 346402da28015558326dbb1f8c3ec1ca678538b1 https://github.com/galaxyproject/infrastructure-playbook/commit/346402da280… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-12 (Thu, 12 Apr 2018) Changed paths: M env/galaxy/templates/squid/cvmfs1-psu0_squid.conf.j2 Log Message: ----------- Fix squid conf for cvmfs1-psu0 localhost (cvmfs_server) access Commit: 8108c8f4cef4ee4aeb876303c0e19e3f08cc055c https://github.com/galaxyproject/infrastructure-playbook/commit/8108c8f4cef… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-13 (Fri, 13 Apr 2018) Changed paths: M common_roles Log Message: ----------- Update common roles Commit: 6874c540a2b24559c0b2640d647d9d4b4484a8fe https://github.com/galaxyproject/infrastructure-playbook/commit/6874c540a2b… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-13 (Fri, 13 Apr 2018) Changed paths: M common_roles A env/common/files/ssl/athena.galaxyproject.org_cert.pem M env/common/files/ssl/docker/ca-key.pem M env/common/files/ssl/docker/ca.pem M env/common/files/ssl/docker/ca.srl R env/common/files/ssl/docker/client.pem R env/common/files/ssl/docker/client_privatekey.yml M env/common/files/ssl/docker/cvmfs1-psu0.galaxyproject.org/server.pem M env/common/files/ssl/docker/cvmfs1-psu0.galaxyproject.org/server_privatekey… M env/common/files/ssl/docker/jetstream-iu0.galaxyproject.org/server.pem M env/common/files/ssl/docker/jetstream-iu0.galaxyproject.org/server_privatek… R env/common/files/ssl/docker/jetstream-tacc0.galaxyproject.org/server-cert.p… A env/common/files/ssl/docker/jetstream-tacc0.galaxyproject.org/server.pem M env/common/files/ssl/docker/jetstream-tacc0.galaxyproject.org/server_privat… A env/galaxy/files/sites/datacache/index.html A env/galaxy/files/ssl R env/galaxy/files/ssl/athena.galaxyproject.org_cert.pem R env/galaxy/files/ssl/incommon_chain.pem R env/galaxy/files/ssl/wildcard_cert.pem M env/galaxy/group_vars/cvmfsstratum0servers.yml M env/galaxy/group_vars/dockersslservers/vars.yml M env/galaxy/group_vars/jenkinsslaves/vars.yml M env/galaxy/group_vars/sshservers/vault.yml A env/galaxy/group_vars/sslservers M env/galaxy/host_vars/athena.galaxyproject.org/vars.yml M env/galaxy/host_vars/chouffe.galaxyproject.org/vars.yml M env/galaxy/host_vars/cvmfs0-tacc0.galaxyproject.org/vars.yml M env/galaxy/host_vars/cvmfs1-psu0.galaxyproject.org/vars.yml M env/galaxy/host_vars/orval.galaxyproject.org/vars.yml M env/galaxy/host_vars/westvleteren.galaxyproject.org/vars.yml M env/galaxy/host_vars/westvleteren.galaxyproject.org/vault.yml M env/galaxy/inventory A env/galaxy/templates/nginx/datacache.j2 M env/galaxy/templates/nginx/galaxyproject.j2 A env/galaxy/templates/squid/cvmfs1-psu0_squid.conf.j2 M roles/cvmfs/tasks/stratum0.yml M roles/cvmfs/tasks/stratum1.yml M roles/nfs/tasks/main.yml A taccenv/group_vars/sshclients/vars.yml A taccenv/group_vars/sshclients/vault.yml A taccenv/host_vars/galaxy-web-05.tacc.utexas.edu/vars.yml A taccenv/host_vars/galaxy-web-05.tacc.utexas.edu/vault.yml M taccenv/inventory A taccenv/zfsdump-gxmain.yml Log Message: ----------- Merge branch 'galaxyenv' of github.com:galaxyproject/infrastructure-playbook into galaxyenv Commit: a76b216a470f83a57c24b1e894226602b8ecef98 https://github.com/galaxyproject/infrastructure-playbook/commit/a76b216a470… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-13 (Fri, 13 Apr 2018) Changed paths: M env/common/files/ssl/docker/ca.srl A env/common/files/ssl/status.galaxyproject.org_cert.pem M env/common/group_vars/sshservers/vars.yml M env/common/group_vars/sshservers/vault.yml M env/common/group_vars/sslservers/vault.yml A env/galaxy/host_vars/status.galaxyproject.org.yml M env/galaxy/inventory M env/galaxy/templates/nginx/gxy.io.j2 A env/galaxy/templates/nginx/status.j2 A env/jsdocker/.snapshot_base.yml.swp M env/jsdocker/group_vars/all/vars.yml M env/jsdocker/group_vars/baseinstances.yml M env/jsdocker/group_vars/imageinstances.yml A env/tacc/files/galaxy/cancelled.sh A env/tacc/files/monitoring/mailoom.py A env/tacc/files/slurm/spartbalance A env/tacc/files/ssl A env/tacc/group_vars/all.yml A env/tacc/group_vars/dockerclients.yml A env/tacc/group_vars/galaxynodes.yml A env/tacc/group_vars/galaxyservers.yml A env/tacc/group_vars/maingalaxyservers.yml A env/tacc/group_vars/rabbitmqservers/vars.yml A env/tacc/group_vars/rabbitmqservers/vault.yml A env/tacc/group_vars/slurmclients/vars.yml A env/tacc/group_vars/slurmclients/vault.yml A env/tacc/group_vars/slurmdbdservers/vars.yml A env/tacc/group_vars/slurmdbdservers/vault.yml A env/tacc/group_vars/slurmservers.yml A env/tacc/group_vars/sshclients/vars.yml A env/tacc/group_vars/sshclients/vault.yml A env/tacc/group_vars/sshservers/common_vars.yml A env/tacc/group_vars/sshservers/common_vault.yml A env/tacc/group_vars/sshservers/vars.yml A env/tacc/group_vars/sslservers A env/tacc/group_vars/stats/vars.yml A env/tacc/group_vars/stats/vault.yml A env/tacc/group_vars/statsservers.yml A env/tacc/group_vars/testgalaxyservers.yml A env/tacc/host_vars/galaxy-db-02.tacc.utexas.edu/vars.yml A env/tacc/host_vars/galaxy-db-02.tacc.utexas.edu/vault.yml A env/tacc/host_vars/galaxy-web-05.tacc.utexas.edu/vars.yml A env/tacc/host_vars/galaxy-web-05.tacc.utexas.edu/vault.yml A env/tacc/host_vars/galaxy04.tacc.utexas.edu/vars.yml A env/tacc/host_vars/galaxy04.tacc.utexas.edu/vault.yml A env/tacc/host_vars/galaxy06.tacc.utexas.edu.yml A env/tacc/host_vars/galaxy07.tacc.utexas.edu.yml A env/tacc/inventory A env/tacc/playbook.yml A env/tacc/templates/nginx/galaxy-installers.j2 A env/tacc/templates/nginx/sentry.j2 A env/tacc/templates/nginx/stats.j2 A env/tacc/templates/slurm/slurm.conf.j2 A env/tacc/templates/supervisor/sentry.j2 A env/tacc/templates/supervisor/stats.j2 A env/tacc/zfsdump-gxmain.yml M jetstreamiuenv/group_vars/controllers.yml M jetstreamiuenv/group_vars/galaxynodes.yml M jetstreamtaccenv/group_vars/controllers.yml M jetstreamtaccenv/group_vars/galaxynodes.yml M roles/cvmfs/defaults/main.yml A roles/cvmfs/files/cvmfs_remount_sync.c A roles/cvmfs/files/cvmfs_remount_sync.centos_6 A roles/cvmfs/files/cvmfs_remount_sync.centos_7 M roles/cvmfs/tasks/client.yml M roles/cvmfs/tasks/stratum0.yml M roles/cvmfs/tasks/stratum1.yml M roles/docker/defaults/main.yml M roles/docker/tasks/install_debian.yml M roles/docker/tasks/install_redhat.yml M roles/galaxyproject.nginx/defaults/main.yml M roles/galaxyproject.nginx/meta/.galaxy_install_info M roles/galaxyproject.nginx/tasks/pkgin.yml M roles/galaxyproject.nginx/tasks/ssl.yml M roles/galaxyproject.nginx/vars/pkgin.yml M roles/natefoo.postgresql_objects/README.md M roles/natefoo.postgresql_objects/meta/.galaxy_install_info M roles/natefoo.postgresql_objects/tasks/main.yml M roles/sentry/tasks/main.yml M roles/sentry/templates/sentry.conf.py.j2 M roles/stats/tasks/main.yml M roles/stats/templates/grafana.conf.j2 M roles/stats/templates/influxdb.conf.j2 R taccenv/files/galaxy/cancelled.sh R taccenv/files/monitoring/mailoom.py R taccenv/files/ssl R taccenv/group_vars/all.yml R taccenv/group_vars/dockerclients.yml R taccenv/group_vars/galaxynodes.yml R taccenv/group_vars/galaxyservers.yml R taccenv/group_vars/maingalaxyservers/vars.yml R taccenv/group_vars/maingalaxyservers/vault.yml R taccenv/group_vars/rabbitmqservers/vars.yml R taccenv/group_vars/rabbitmqservers/vault.yml R taccenv/group_vars/slurmclients.yml R taccenv/group_vars/slurmdbdservers/vars.yml R taccenv/group_vars/slurmdbdservers/vault.yml R taccenv/group_vars/sshclients/vars.yml R taccenv/group_vars/sshclients/vault.yml R taccenv/group_vars/sshservers/common_vars.yml R taccenv/group_vars/sshservers/common_vault.yml R taccenv/group_vars/sshservers/vars.yml R taccenv/group_vars/sslservers R taccenv/group_vars/statsservers.yml R taccenv/group_vars/testgalaxyservers/vars.yml R taccenv/group_vars/testgalaxyservers/vault.yml R taccenv/host_vars/galaxy-db-02.tacc.utexas.edu/vars.yml R taccenv/host_vars/galaxy-db-02.tacc.utexas.edu/vault.yml R taccenv/host_vars/galaxy-web-05.tacc.utexas.edu/vars.yml R taccenv/host_vars/galaxy-web-05.tacc.utexas.edu/vault.yml R taccenv/host_vars/galaxy04.tacc.utexas.edu.yml R taccenv/host_vars/galaxy06.tacc.utexas.edu.yml R taccenv/host_vars/galaxy07.tacc.utexas.edu.yml R taccenv/inventory R taccenv/playbook.yml R taccenv/secret_group_vars/dockersslclients.yml R taccenv/secret_group_vars/slurmclients.yml R taccenv/secret_group_vars/stats.yml R taccenv/secret_host_vars/default.yml R taccenv/secret_host_vars/galaxy04.tacc.utexas.edu.yml R taccenv/templates/nginx/galaxy-installers.j2 R taccenv/templates/nginx/sentry.j2 R taccenv/templates/nginx/stats.j2 R taccenv/templates/slurm/slurm.conf.j2 R taccenv/templates/supervisor/sentry.j2 R taccenv/templates/supervisor/stats.j2 R taccenv/zfsdump-gxmain.yml Log Message: ----------- Merge remote-tracking branch 'origin/master' into galaxyenv Compare: https://github.com/galaxyproject/infrastructure-playbook/compare/de352bfcd4…

1 0

[galaxyproject/infrastructure-playbook] 4a07bb: Update nginx role for SmartOS fixes
by GitHub 13 Apr '18

13 Apr '18

Branch: refs/heads/galaxyenv Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 4a07bbd01fbac0e0ea18a02c02749a352b8c8cd5 https://github.com/galaxyproject/infrastructure-playbook/commit/4a07bbd01fb… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-11-28 (Tue, 28 Nov 2017) Changed paths: M roles/galaxyproject.nginx/defaults/main.yml M roles/galaxyproject.nginx/meta/.galaxy_install_info M roles/galaxyproject.nginx/tasks/pkgin.yml M roles/galaxyproject.nginx/tasks/ssl.yml M roles/galaxyproject.nginx/vars/pkgin.yml Log Message: ----------- Update nginx role for SmartOS fixes Commit: 84239ffd6793dda8b8ab46bf18a1e0908a637d11 https://github.com/galaxyproject/infrastructure-playbook/commit/84239ffd679… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-11-28 (Tue, 28 Nov 2017) Changed paths: M common_env/secret_group_vars/sslwebservers.yml A galaxyenv/files/ssl/status.galaxyproject.org_cert.pem A galaxyenv/host_vars/status.galaxyproject.org.yml M galaxyenv/inventory A galaxyenv/templates/nginx/status.j2 Log Message: ----------- Add status.galaxyproject.org to the inventory Commit: e3cb79ce021454db04c554f00373ff883d87fcd0 https://github.com/galaxyproject/infrastructure-playbook/commit/e3cb79ce021… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: M galaxyenv/templates/nginx/gxy.io.j2 Log Message: ----------- Add toolshed redirect to gxy.io Commit: 8b1d7203ee90d92a15d8f6b6fba2e26f6b8a546e https://github.com/galaxyproject/infrastructure-playbook/commit/8b1d7203ee9… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: A taccenv/files/slurm/spartbalance A taccenv/group_vars/slurmservers.yml Log Message: ----------- Automatically balance normal/multi partitions on roundup to try to avoid waiting normal jobs. Commit: cbf3e016a8ccf8d9f90b0f157ff517c105cf5d72 https://github.com/galaxyproject/infrastructure-playbook/commit/cbf3e016a8c… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-02-03 (Sat, 03 Feb 2018) Changed paths: M taccenv/files/slurm/spartbalance Log Message: ----------- Bug fixes for slurm partition balancing Commit: b27e8c6159fe40c52870b5eeba8c463256e8de45 https://github.com/galaxyproject/infrastructure-playbook/commit/b27e8c6159f… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-02-05 (Mon, 05 Feb 2018) Changed paths: M taccenv/files/slurm/spartbalance Log Message: ----------- More stdout/stderr handling for spartbalance Commit: 84730b8a7f17d3d60dab304ffa7c2e23b4eed8a0 https://github.com/galaxyproject/infrastructure-playbook/commit/84730b8a7f1… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-02-08 (Thu, 08 Feb 2018) Changed paths: 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 postgresql_objects role Commit: 7c023ee85662f5165e71a7eea8b7cd101c3ba3ea https://github.com/galaxyproject/infrastructure-playbook/commit/7c023ee8566… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-02-08 (Thu, 08 Feb 2018) Changed paths: M roles/sentry/tasks/main.yml M roles/sentry/templates/sentry.conf.py.j2 M roles/stats/tasks/main.yml M roles/stats/templates/grafana.conf.j2 M taccenv/group_vars/statsservers.yml Log Message: ----------- Email and other fixes for stats/sentry Commit: db9646bca42d6a61e3de2d89fe8d1dfdcea84014 https://github.com/galaxyproject/infrastructure-playbook/commit/db9646bca42… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-02-08 (Thu, 08 Feb 2018) Changed paths: M roles/stats/templates/influxdb.conf.j2 Log Message: ----------- Enable the monitor for influxdb Commit: ff188630f138398352f9a94c4cac19dd67fc553f https://github.com/galaxyproject/infrastructure-playbook/commit/ff188630f13… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-02-15 (Thu, 15 Feb 2018) Changed paths: M common_env/group_vars/baseenv/vault.yml Log Message: ----------- Commit missing key change Commit: 550f81cbfb0745eeebfdeeb4342b09f9c34c54ed https://github.com/galaxyproject/infrastructure-playbook/commit/550f81cbfb0… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-02-15 (Thu, 15 Feb 2018) Changed paths: M roles/cvmfs/defaults/main.yml A roles/cvmfs/files/cvmfs_remount_sync.c A roles/cvmfs/files/cvmfs_remount_sync.centos_6 A roles/cvmfs/files/cvmfs_remount_sync.centos_7 M roles/cvmfs/tasks/client.yml M roles/cvmfs/tasks/stratum0.yml M roles/cvmfs/tasks/stratum1.yml M taccenv/group_vars/galaxyservers.yml Log Message: ----------- Use new and improved cvmfs_talk remount sync functionality over cvmfs_config wipecache. Include a setuid binary for unprivileged users to call remount. Commit: 669ca93ed1e988e9159633abf51306b06617aecf https://github.com/galaxyproject/infrastructure-playbook/commit/669ca93ed1e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-02-16 (Fri, 16 Feb 2018) Changed paths: M roles/cvmfs/tasks/client.yml M taccenv/group_vars/galaxyservers.yml Log Message: ----------- Remove cvmfs_wipecache setuid binary Commit: 6ae3b1a0c18f6ad7b428c5041b65b2b977d6a037 https://github.com/galaxyproject/infrastructure-playbook/commit/6ae3b1a0c18… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-02-19 (Mon, 19 Feb 2018) Changed paths: M roles/stats/tasks/main.yml Log Message: ----------- update grafana Commit: f9205a79e9cf8791c9ab1b5d929e9bfaba208ebc https://github.com/galaxyproject/infrastructure-playbook/commit/f9205a79e9c… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-02-19 (Mon, 19 Feb 2018) Changed paths: M roles/stats/tasks/main.yml Log Message: ----------- Merge pull request #20 from galaxyproject/grafana-update update grafana Commit: 9146d1938f4bfa8b4d894295f3a68e7f709792de https://github.com/galaxyproject/infrastructure-playbook/commit/9146d1938f4… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-03-14 (Wed, 14 Mar 2018) Changed paths: A env/jsdocker/.snapshot_base.yml.swp M env/jsdocker/group_vars/all/vars.yml M env/jsdocker/group_vars/baseinstances.yml M env/jsdocker/group_vars/imageinstances.yml Log Message: ----------- New Jetstream docker image Commit: 50e71d72720c8a657ad8111200bbe8613d1e1852 https://github.com/galaxyproject/infrastructure-playbook/commit/50e71d72720… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-03-21 (Wed, 21 Mar 2018) Changed paths: M common_env/files/ssl/docker/ca-key.pem M common_env/files/ssl/docker/ca.pem M common_env/files/ssl/docker/ca.srl M common_env/files/ssl/docker/client.pem M common_env/files/ssl/docker/client_privatekey.yml R common_env/files/ssl/docker/cvmfs1-psu0.galaxyproject.org/server.pem R common_env/files/ssl/docker/cvmfs1-psu0.galaxyproject.org/server_privatekey… R common_env/files/ssl/docker/jetstream-iu0.galaxyproject.org/server.pem R common_env/files/ssl/docker/jetstream-iu0.galaxyproject.org/server_privatek… R common_env/files/ssl/docker/jetstream-tacc0.galaxyproject.org/server-cert.p… R common_env/files/ssl/docker/jetstream-tacc0.galaxyproject.org/server_privat… M roles/docker/defaults/main.yml M roles/docker/tasks/install_debian.yml M roles/docker/tasks/install_redhat.yml M taccenv/group_vars/dockerclients.yml M taccenv/inventory Log Message: ----------- Client side changes for new Docker SSL certs Commit: fa3ed84610566507ec0b632dfb3a64c991d01bb3 https://github.com/galaxyproject/infrastructure-playbook/commit/fa3ed846105… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-11 (Wed, 11 Apr 2018) Changed paths: M common_roles M jetstreamiuenv/group_vars/controllers.yml M jetstreamiuenv/group_vars/galaxynodes.yml M jetstreamtaccenv/group_vars/controllers.yml M jetstreamtaccenv/group_vars/galaxynodes.yml M taccenv/group_vars/all.yml M taccenv/group_vars/galaxyservers.yml M taccenv/host_vars/galaxy-db-02.tacc.utexas.edu/vars.yml Log Message: ----------- Use inheritance vars for directories and links. Commit: cce10053db47c04f4a88118332ece417f246a39e https://github.com/galaxyproject/infrastructure-playbook/commit/cce10053db4… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-13 (Fri, 13 Apr 2018) Changed paths: A env/tacc/files/galaxy/cancelled.sh A env/tacc/files/monitoring/mailoom.py A env/tacc/files/slurm/spartbalance A env/tacc/files/ssl A env/tacc/group_vars/all.yml A env/tacc/group_vars/baseenv A env/tacc/group_vars/dockerclients.yml A env/tacc/group_vars/galaxynodes.yml A env/tacc/group_vars/galaxyservers.yml A env/tacc/group_vars/maingalaxyservers/vars.yml A env/tacc/group_vars/maingalaxyservers/vault.yml A env/tacc/group_vars/rabbitmqservers/vars.yml A env/tacc/group_vars/rabbitmqservers/vault.yml A env/tacc/group_vars/slurmclients.yml A env/tacc/group_vars/slurmdbdservers/vars.yml A env/tacc/group_vars/slurmdbdservers/vault.yml A env/tacc/group_vars/slurmservers.yml A env/tacc/group_vars/sslservers A env/tacc/group_vars/statsservers.yml A env/tacc/group_vars/testgalaxyservers/vars.yml A env/tacc/group_vars/testgalaxyservers/vault.yml A env/tacc/host_vars/galaxy-db-02.tacc.utexas.edu/vars.yml A env/tacc/host_vars/galaxy-db-02.tacc.utexas.edu/vault.yml A env/tacc/host_vars/galaxy04.tacc.utexas.edu.yml A env/tacc/host_vars/galaxy06.tacc.utexas.edu.yml A env/tacc/host_vars/galaxy07.tacc.utexas.edu.yml A env/tacc/inventory A env/tacc/playbook.yml A env/tacc/secret_group_vars/dockersslclients.yml A env/tacc/secret_group_vars/slurmclients.yml A env/tacc/secret_group_vars/sslwebservers.yml A env/tacc/secret_group_vars/stats.yml A env/tacc/secret_host_vars/default.yml A env/tacc/secret_host_vars/galaxy04.tacc.utexas.edu.yml A env/tacc/templates/nginx/galaxy-installers.j2 A env/tacc/templates/nginx/sentry.j2 A env/tacc/templates/nginx/stats.j2 A env/tacc/templates/slurm/slurm.conf.j2 A env/tacc/templates/supervisor/sentry.j2 A env/tacc/templates/supervisor/stats.j2 R taccenv/files/galaxy/cancelled.sh R taccenv/files/monitoring/mailoom.py R taccenv/files/slurm/spartbalance R taccenv/files/ssl R taccenv/group_vars/all.yml R taccenv/group_vars/baseenv R taccenv/group_vars/dockerclients.yml R taccenv/group_vars/galaxynodes.yml R taccenv/group_vars/galaxyservers.yml R taccenv/group_vars/maingalaxyservers/vars.yml R taccenv/group_vars/maingalaxyservers/vault.yml R taccenv/group_vars/rabbitmqservers/vars.yml R taccenv/group_vars/rabbitmqservers/vault.yml R taccenv/group_vars/slurmclients.yml R taccenv/group_vars/slurmdbdservers/vars.yml R taccenv/group_vars/slurmdbdservers/vault.yml R taccenv/group_vars/slurmservers.yml R taccenv/group_vars/sslservers R taccenv/group_vars/statsservers.yml R taccenv/group_vars/testgalaxyservers/vars.yml R taccenv/group_vars/testgalaxyservers/vault.yml R taccenv/host_vars/galaxy-db-02.tacc.utexas.edu/vars.yml R taccenv/host_vars/galaxy-db-02.tacc.utexas.edu/vault.yml R taccenv/host_vars/galaxy04.tacc.utexas.edu.yml R taccenv/host_vars/galaxy06.tacc.utexas.edu.yml R taccenv/host_vars/galaxy07.tacc.utexas.edu.yml R taccenv/inventory R taccenv/playbook.yml R taccenv/secret_group_vars/dockersslclients.yml R taccenv/secret_group_vars/slurmclients.yml R taccenv/secret_group_vars/sslwebservers.yml R taccenv/secret_group_vars/stats.yml R taccenv/secret_host_vars/default.yml R taccenv/secret_host_vars/galaxy04.tacc.utexas.edu.yml R taccenv/templates/nginx/galaxy-installers.j2 R taccenv/templates/nginx/sentry.j2 R taccenv/templates/nginx/stats.j2 R taccenv/templates/slurm/slurm.conf.j2 R taccenv/templates/supervisor/sentry.j2 R taccenv/templates/supervisor/stats.j2 Log Message: ----------- Move taccenv to env/tacc Commit: 264d07af3d765dcd6c97f27fc20c91700fc81b1c https://github.com/galaxyproject/infrastructure-playbook/commit/264d07af3d7… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-13 (Fri, 13 Apr 2018) Changed paths: M env/tacc/files/ssl M env/tacc/group_vars/baseenv M env/tacc/group_vars/sslservers Log Message: ----------- Fix symlinks broken by move Commit: dde2217e106444fc771370458a6f87d5fe8e5d70 https://github.com/galaxyproject/infrastructure-playbook/commit/dde2217e106… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-13 (Fri, 13 Apr 2018) Changed paths: R env/tacc/group_vars/slurmclients.yml A env/tacc/group_vars/slurmclients/vars.yml A env/tacc/group_vars/slurmclients/vault.yml A env/tacc/group_vars/stats/vars.yml A env/tacc/group_vars/stats/vault.yml R env/tacc/host_vars/galaxy04.tacc.utexas.edu.yml A env/tacc/host_vars/galaxy04.tacc.utexas.edu/vars.yml A env/tacc/host_vars/galaxy04.tacc.utexas.edu/vault.yml M env/tacc/playbook.yml R env/tacc/secret_group_vars/dockersslclients.yml R env/tacc/secret_group_vars/slurmclients.yml R env/tacc/secret_group_vars/sslwebservers.yml R env/tacc/secret_group_vars/stats.yml R env/tacc/secret_host_vars/default.yml R env/tacc/secret_host_vars/galaxy04.tacc.utexas.edu.yml Log Message: ----------- Remove secret_*_vars from tacc env Commit: 72a2bc06d5468fa94e1b59b260ce257e596ac1d4 https://github.com/galaxyproject/infrastructure-playbook/commit/72a2bc06d54… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-13 (Fri, 13 Apr 2018) Changed paths: M ansible.cfg Log Message: ----------- Include lookup plugins from common_roles Commit: e64e61d701d3261a84730992bd0e6f689778befd https://github.com/galaxyproject/infrastructure-playbook/commit/e64e61d701d… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-13 (Fri, 13 Apr 2018) Changed paths: M common_env/group_vars/baseenv/vars.yml M common_env/group_vars/baseenv/vault.yml M env/tacc/group_vars/galaxynodes.yml A env/tacc/group_vars/maingalaxyservers.yml R env/tacc/group_vars/maingalaxyservers/vars.yml R env/tacc/group_vars/maingalaxyservers/vault.yml A env/tacc/group_vars/testgalaxyservers.yml R env/tacc/group_vars/testgalaxyservers/vars.yml R env/tacc/group_vars/testgalaxyservers/vault.yml Log Message: ----------- Keep the list of team users in one place instead of 50 Commit: de352bfcd479460ba59a60758b0ac751abffd721 https://github.com/galaxyproject/infrastructure-playbook/commit/de352bfcd47… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-13 (Fri, 13 Apr 2018) Changed paths: M common_roles Log Message: ----------- Update common roles Commit: a76b216a470f83a57c24b1e894226602b8ecef98 https://github.com/galaxyproject/infrastructure-playbook/commit/a76b216a470… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-13 (Fri, 13 Apr 2018) Changed paths: M env/common/files/ssl/docker/ca.srl A env/common/files/ssl/status.galaxyproject.org_cert.pem M env/common/group_vars/sshservers/vars.yml M env/common/group_vars/sshservers/vault.yml M env/common/group_vars/sslservers/vault.yml A env/galaxy/host_vars/status.galaxyproject.org.yml M env/galaxy/inventory M env/galaxy/templates/nginx/gxy.io.j2 A env/galaxy/templates/nginx/status.j2 A env/jsdocker/.snapshot_base.yml.swp M env/jsdocker/group_vars/all/vars.yml M env/jsdocker/group_vars/baseinstances.yml M env/jsdocker/group_vars/imageinstances.yml A env/tacc/files/galaxy/cancelled.sh A env/tacc/files/monitoring/mailoom.py A env/tacc/files/slurm/spartbalance A env/tacc/files/ssl A env/tacc/group_vars/all.yml A env/tacc/group_vars/dockerclients.yml A env/tacc/group_vars/galaxynodes.yml A env/tacc/group_vars/galaxyservers.yml A env/tacc/group_vars/maingalaxyservers.yml A env/tacc/group_vars/rabbitmqservers/vars.yml A env/tacc/group_vars/rabbitmqservers/vault.yml A env/tacc/group_vars/slurmclients/vars.yml A env/tacc/group_vars/slurmclients/vault.yml A env/tacc/group_vars/slurmdbdservers/vars.yml A env/tacc/group_vars/slurmdbdservers/vault.yml A env/tacc/group_vars/slurmservers.yml A env/tacc/group_vars/sshclients/vars.yml A env/tacc/group_vars/sshclients/vault.yml A env/tacc/group_vars/sshservers/common_vars.yml A env/tacc/group_vars/sshservers/common_vault.yml A env/tacc/group_vars/sshservers/vars.yml A env/tacc/group_vars/sslservers A env/tacc/group_vars/stats/vars.yml A env/tacc/group_vars/stats/vault.yml A env/tacc/group_vars/statsservers.yml A env/tacc/group_vars/testgalaxyservers.yml A env/tacc/host_vars/galaxy-db-02.tacc.utexas.edu/vars.yml A env/tacc/host_vars/galaxy-db-02.tacc.utexas.edu/vault.yml A env/tacc/host_vars/galaxy-web-05.tacc.utexas.edu/vars.yml A env/tacc/host_vars/galaxy-web-05.tacc.utexas.edu/vault.yml A env/tacc/host_vars/galaxy04.tacc.utexas.edu/vars.yml A env/tacc/host_vars/galaxy04.tacc.utexas.edu/vault.yml A env/tacc/host_vars/galaxy06.tacc.utexas.edu.yml A env/tacc/host_vars/galaxy07.tacc.utexas.edu.yml A env/tacc/inventory A env/tacc/playbook.yml A env/tacc/templates/nginx/galaxy-installers.j2 A env/tacc/templates/nginx/sentry.j2 A env/tacc/templates/nginx/stats.j2 A env/tacc/templates/slurm/slurm.conf.j2 A env/tacc/templates/supervisor/sentry.j2 A env/tacc/templates/supervisor/stats.j2 A env/tacc/zfsdump-gxmain.yml M jetstreamiuenv/group_vars/controllers.yml M jetstreamiuenv/group_vars/galaxynodes.yml M jetstreamtaccenv/group_vars/controllers.yml M jetstreamtaccenv/group_vars/galaxynodes.yml M roles/cvmfs/defaults/main.yml A roles/cvmfs/files/cvmfs_remount_sync.c A roles/cvmfs/files/cvmfs_remount_sync.centos_6 A roles/cvmfs/files/cvmfs_remount_sync.centos_7 M roles/cvmfs/tasks/client.yml M roles/cvmfs/tasks/stratum0.yml M roles/cvmfs/tasks/stratum1.yml M roles/docker/defaults/main.yml M roles/docker/tasks/install_debian.yml M roles/docker/tasks/install_redhat.yml M roles/galaxyproject.nginx/defaults/main.yml M roles/galaxyproject.nginx/meta/.galaxy_install_info M roles/galaxyproject.nginx/tasks/pkgin.yml M roles/galaxyproject.nginx/tasks/ssl.yml M roles/galaxyproject.nginx/vars/pkgin.yml M roles/natefoo.postgresql_objects/README.md M roles/natefoo.postgresql_objects/meta/.galaxy_install_info M roles/natefoo.postgresql_objects/tasks/main.yml M roles/sentry/tasks/main.yml M roles/sentry/templates/sentry.conf.py.j2 M roles/stats/tasks/main.yml M roles/stats/templates/grafana.conf.j2 M roles/stats/templates/influxdb.conf.j2 R taccenv/files/galaxy/cancelled.sh R taccenv/files/monitoring/mailoom.py R taccenv/files/ssl R taccenv/group_vars/all.yml R taccenv/group_vars/dockerclients.yml R taccenv/group_vars/galaxynodes.yml R taccenv/group_vars/galaxyservers.yml R taccenv/group_vars/maingalaxyservers/vars.yml R taccenv/group_vars/maingalaxyservers/vault.yml R taccenv/group_vars/rabbitmqservers/vars.yml R taccenv/group_vars/rabbitmqservers/vault.yml R taccenv/group_vars/slurmclients.yml R taccenv/group_vars/slurmdbdservers/vars.yml R taccenv/group_vars/slurmdbdservers/vault.yml R taccenv/group_vars/sshclients/vars.yml R taccenv/group_vars/sshclients/vault.yml R taccenv/group_vars/sshservers/common_vars.yml R taccenv/group_vars/sshservers/common_vault.yml R taccenv/group_vars/sshservers/vars.yml R taccenv/group_vars/sslservers R taccenv/group_vars/statsservers.yml R taccenv/group_vars/testgalaxyservers/vars.yml R taccenv/group_vars/testgalaxyservers/vault.yml R taccenv/host_vars/galaxy-db-02.tacc.utexas.edu/vars.yml R taccenv/host_vars/galaxy-db-02.tacc.utexas.edu/vault.yml R taccenv/host_vars/galaxy-web-05.tacc.utexas.edu/vars.yml R taccenv/host_vars/galaxy-web-05.tacc.utexas.edu/vault.yml R taccenv/host_vars/galaxy04.tacc.utexas.edu.yml R taccenv/host_vars/galaxy06.tacc.utexas.edu.yml R taccenv/host_vars/galaxy07.tacc.utexas.edu.yml R taccenv/inventory R taccenv/playbook.yml R taccenv/secret_group_vars/dockersslclients.yml R taccenv/secret_group_vars/slurmclients.yml R taccenv/secret_group_vars/stats.yml R taccenv/secret_host_vars/default.yml R taccenv/secret_host_vars/galaxy04.tacc.utexas.edu.yml R taccenv/templates/nginx/galaxy-installers.j2 R taccenv/templates/nginx/sentry.j2 R taccenv/templates/nginx/stats.j2 R taccenv/templates/slurm/slurm.conf.j2 R taccenv/templates/supervisor/sentry.j2 R taccenv/templates/supervisor/stats.j2 R taccenv/zfsdump-gxmain.yml Log Message: ----------- Merge remote-tracking branch 'origin/master' into galaxyenv Compare: https://github.com/galaxyproject/infrastructure-playbook/compare/6874c540a2…

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[galaxyproject/infrastructure-playbook] 43cdd8: Move Main reports to galaxy-system mailing list
by GitHub 13 Apr '18

13 Apr '18

Branch: refs/heads/galaxyenv Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 43cdd844a66081d84781dff54382d4b525a55e92 https://github.com/galaxyproject/infrastructure-playbook/commit/43cdd844a66… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-11-06 (Mon, 06 Nov 2017) Changed paths: M taccenv/group_vars/galaxyservers.yml M taccenv/host_vars/galaxy-db-02.tacc.utexas.edu/vars.yml Log Message: ----------- Move Main reports to galaxy-system mailing list Commit: 372d7f4a229681558656375313160a52eddb31b5 https://github.com/galaxyproject/infrastructure-playbook/commit/372d7f4a229… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-11-06 (Mon, 06 Nov 2017) Changed paths: M taccenv/host_vars/galaxy-db-02.tacc.utexas.edu/vars.yml Log Message: ----------- Don't send memory reports on saturdays Commit: f54bfe05fd383af1439e84f31c4afcc27752b231 https://github.com/galaxyproject/infrastructure-playbook/commit/f54bfe05fd3… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-11-14 (Tue, 14 Nov 2017) Changed paths: M galaxyenv/templates/nginx/training.j2 Log Message: ----------- Redirect training.galaxyproject.org -> galaxyproject.github.io/training-material with the $request_uri appended (previously all pages redirected to the training root). Commit: 1892596434860fba38194bf5974640e6bb8164c5 https://github.com/galaxyproject/infrastructure-playbook/commit/18925964348… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-11-16 (Thu, 16 Nov 2017) Changed paths: M roles/stats/templates/galaxy_slurp.py.j2 Log Message: ----------- Fix grafana slurp database target for Main move Commit: c15b07641f91039d0acd69b379fff5cb9a0e1ac3 https://github.com/galaxyproject/infrastructure-playbook/commit/c15b07641f9… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-11-16 (Thu, 16 Nov 2017) Changed paths: M taccenv/playbook.yml Log Message: ----------- Set up additional mail forwards at TACC Commit: 3f7ee441636f9277fa56381f9d146df438f0728f https://github.com/galaxyproject/infrastructure-playbook/commit/3f7ee441636… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-11-28 (Tue, 28 Nov 2017) Changed paths: M galaxyenv/playbook.yml 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/ssl.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 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 M taccenv/playbook.yml Log Message: ----------- Upgrade nginx role Commit: 651d0ef79fd9f784d86c3cea7e8293a558824d91 https://github.com/galaxyproject/infrastructure-playbook/commit/651d0ef79fd… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-11-28 (Tue, 28 Nov 2017) Changed paths: A common_env/files/ssl/incommon_chain.pem A galaxyenv/files/ssl/incommon_chain.pem M galaxyenv/host_vars/athena.galaxyproject.org.yml M galaxyenv/host_vars/chouffe.galaxyproject.org.yml M galaxyenv/host_vars/delirium.galaxyproject.org.yml M galaxyenv/host_vars/duvel.galaxyproject.org.yml M galaxyenv/host_vars/orval.galaxyproject.org.yml Log Message: ----------- Update galaxy env for updated nginx role Commit: 9b3e42b3400bddf1521d9f824b52fe25a099604f https://github.com/galaxyproject/infrastructure-playbook/commit/9b3e42b3400… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-11-28 (Tue, 28 Nov 2017) Changed paths: M taccenv/host_vars/galaxy04.tacc.utexas.edu.yml M taccenv/host_vars/galaxy06.tacc.utexas.edu.yml Log Message: ----------- Update tacc env for nginx role update Commit: afeab93d32e03c0a2198b2eb4cc082774c5fcc0c https://github.com/galaxyproject/infrastructure-playbook/commit/afeab93d32e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-11-28 (Tue, 28 Nov 2017) Changed paths: A env/common/files/ssl/incommon_chain.pem A env/galaxy/files/ssl/incommon_chain.pem M env/galaxy/host_vars/athena.galaxyproject.org/vars.yml M env/galaxy/host_vars/chouffe.galaxyproject.org/vars.yml M env/galaxy/host_vars/delirium.galaxyproject.org/vars.yml M env/galaxy/host_vars/duvel.galaxyproject.org.yml M env/galaxy/host_vars/orval.galaxyproject.org/vars.yml M env/galaxy/playbook.yml M env/galaxy/templates/nginx/training.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/ssl.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 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 M roles/stats/templates/galaxy_slurp.py.j2 M taccenv/group_vars/galaxyservers.yml M taccenv/host_vars/galaxy-db-02.tacc.utexas.edu/vars.yml M taccenv/host_vars/galaxy04.tacc.utexas.edu.yml M taccenv/host_vars/galaxy06.tacc.utexas.edu.yml M taccenv/playbook.yml Log Message: ----------- Merge remote-tracking branch 'origin/master' into galaxyenv Commit: 6874c540a2b24559c0b2640d647d9d4b4484a8fe https://github.com/galaxyproject/infrastructure-playbook/commit/6874c540a2b… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-13 (Fri, 13 Apr 2018) Changed paths: M common_roles A env/common/files/ssl/athena.galaxyproject.org_cert.pem M env/common/files/ssl/docker/ca-key.pem M env/common/files/ssl/docker/ca.pem M env/common/files/ssl/docker/ca.srl R env/common/files/ssl/docker/client.pem R env/common/files/ssl/docker/client_privatekey.yml M env/common/files/ssl/docker/cvmfs1-psu0.galaxyproject.org/server.pem M env/common/files/ssl/docker/cvmfs1-psu0.galaxyproject.org/server_privatekey… M env/common/files/ssl/docker/jetstream-iu0.galaxyproject.org/server.pem M env/common/files/ssl/docker/jetstream-iu0.galaxyproject.org/server_privatek… R env/common/files/ssl/docker/jetstream-tacc0.galaxyproject.org/server-cert.p… A env/common/files/ssl/docker/jetstream-tacc0.galaxyproject.org/server.pem M env/common/files/ssl/docker/jetstream-tacc0.galaxyproject.org/server_privat… A env/galaxy/files/sites/datacache/index.html A env/galaxy/files/ssl R env/galaxy/files/ssl/athena.galaxyproject.org_cert.pem R env/galaxy/files/ssl/incommon_chain.pem R env/galaxy/files/ssl/wildcard_cert.pem M env/galaxy/group_vars/cvmfsstratum0servers.yml M env/galaxy/group_vars/dockersslservers/vars.yml M env/galaxy/group_vars/jenkinsslaves/vars.yml M env/galaxy/group_vars/sshservers/vault.yml A env/galaxy/group_vars/sslservers M env/galaxy/host_vars/athena.galaxyproject.org/vars.yml M env/galaxy/host_vars/chouffe.galaxyproject.org/vars.yml M env/galaxy/host_vars/cvmfs0-tacc0.galaxyproject.org/vars.yml M env/galaxy/host_vars/cvmfs1-psu0.galaxyproject.org/vars.yml M env/galaxy/host_vars/orval.galaxyproject.org/vars.yml M env/galaxy/host_vars/westvleteren.galaxyproject.org/vars.yml M env/galaxy/host_vars/westvleteren.galaxyproject.org/vault.yml M env/galaxy/inventory A env/galaxy/templates/nginx/datacache.j2 M env/galaxy/templates/nginx/galaxyproject.j2 A env/galaxy/templates/squid/cvmfs1-psu0_squid.conf.j2 M roles/cvmfs/tasks/stratum0.yml M roles/cvmfs/tasks/stratum1.yml M roles/nfs/tasks/main.yml A taccenv/group_vars/sshclients/vars.yml A taccenv/group_vars/sshclients/vault.yml A taccenv/host_vars/galaxy-web-05.tacc.utexas.edu/vars.yml A taccenv/host_vars/galaxy-web-05.tacc.utexas.edu/vault.yml M taccenv/inventory A taccenv/zfsdump-gxmain.yml Log Message: ----------- Merge branch 'galaxyenv' of github.com:galaxyproject/infrastructure-playbook into galaxyenv Compare: https://github.com/galaxyproject/infrastructure-playbook/compare/8108c8f4ce…

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[galaxyproject/galaxy] ea1bfb: Framework for constrained memory, I/O sniffing.
by GitHub 13 Apr '18

13 Apr '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ea1bfb0056edbb69ab149d8664098127494e7b60 https://github.com/galaxyproject/galaxy/commit/ea1bfb0056edbb69ab149d866409… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M lib/galaxy/datatypes/annotation.py M lib/galaxy/datatypes/assembly.py M lib/galaxy/datatypes/blast.py M lib/galaxy/datatypes/constructive_solid_geometry.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/genetics.py M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/molecules.py M lib/galaxy/datatypes/mothur.py M lib/galaxy/datatypes/msa.py M lib/galaxy/datatypes/phylip.py M lib/galaxy/datatypes/plant_tribes.py M lib/galaxy/datatypes/proteomics.py M lib/galaxy/datatypes/qualityscore.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/tabular.py A lib/galaxy/datatypes/test/1.afg A lib/galaxy/datatypes/test/1.arff A lib/galaxy/datatypes/test/1.hdt A lib/galaxy/datatypes/test/1.obo A lib/galaxy/datatypes/test/1.owl A lib/galaxy/datatypes/test/1.phyloxml A lib/galaxy/datatypes/test/1.stockholm A lib/galaxy/datatypes/test/1.ttl A lib/galaxy/datatypes/test/1.xmfa A lib/galaxy/datatypes/test/2.tabular A lib/galaxy/datatypes/test/2.txt A lib/galaxy/datatypes/test/3.txt A lib/galaxy/datatypes/test/Acanium.hmm M lib/galaxy/datatypes/text.py M lib/galaxy/datatypes/triples.py M lib/galaxy/datatypes/xml.py M lib/galaxy/util/compression_utils.py Log Message: ----------- Framework for constrained memory, I/O sniffing. - Every unbound readline is a huge potential memory problem, this shrinks the number of such readlines down quite a bit. - There should be no reason to re-read the same file as much as we do, this keeps a fixed amount of the beginning of the file in memory and tries to use it as much as possible. - Lazy loads the size of the file and reuses that to reduce disc contention in that way also. With new sniffing tests for various types. Many datatypes will not just inspect the first GALAXY_SNIFF_PREFIX_BYTES of the file. This value defaults to 1 Mb but can be increased to increase the amount of memory and time used by the sniffers (getting more correctness also). Commit: 30e3658b8b0e2f6b975dc6ccccb0cc8cc040247c https://github.com/galaxyproject/galaxy/commit/30e3658b8b0e2f6b975dc6ccccb0… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-04-13 (Fri, 13 Apr 2018) Changed paths: M lib/galaxy/datatypes/annotation.py M lib/galaxy/datatypes/assembly.py M lib/galaxy/datatypes/blast.py M lib/galaxy/datatypes/constructive_solid_geometry.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/genetics.py M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/molecules.py M lib/galaxy/datatypes/mothur.py M lib/galaxy/datatypes/msa.py M lib/galaxy/datatypes/phylip.py M lib/galaxy/datatypes/plant_tribes.py M lib/galaxy/datatypes/proteomics.py M lib/galaxy/datatypes/qualityscore.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/tabular.py A lib/galaxy/datatypes/test/1.afg A lib/galaxy/datatypes/test/1.arff A lib/galaxy/datatypes/test/1.hdt A lib/galaxy/datatypes/test/1.obo A lib/galaxy/datatypes/test/1.owl A lib/galaxy/datatypes/test/1.phyloxml A lib/galaxy/datatypes/test/1.stockholm A lib/galaxy/datatypes/test/1.ttl A lib/galaxy/datatypes/test/1.xmfa A lib/galaxy/datatypes/test/2.tabular A lib/galaxy/datatypes/test/2.txt A lib/galaxy/datatypes/test/3.txt A lib/galaxy/datatypes/test/Acanium.hmm M lib/galaxy/datatypes/text.py M lib/galaxy/datatypes/triples.py M lib/galaxy/datatypes/xml.py M lib/galaxy/util/compression_utils.py Log Message: ----------- Merge pull request #5793 from jmchilton/bounded_memory_datatypes Sniffing framework with constrained memory and I/O. Compare: https://github.com/galaxyproject/galaxy/compare/225f6af3c07b...30e3658b8b0e

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