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

[galaxyproject/infrastructure-playbook] 9c0b13: Use consumable resources on Jetstream but make the...
by GitHub 15 Jun '18

15 Jun '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 9c0b13b5506d779fadd62856e372ad50ef57b5de https://github.com/galaxyproject/infrastructure-playbook/commit/9c0b13b5506… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-06-15 (Fri, 15 Jun 2018) Changed paths: M env/jsiu/templates/slurm/slurm.conf.j2 Log Message: ----------- Use consumable resources on Jetstream but make the small/multi partitions exclusive (only normal will use cons_res) **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

1 0

[galaxyproject/usegalaxy-playbook] d29c5f: Run fastx collapse on Jetstream @ IU
by GitHub 14 Jun '18

14 Jun '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: d29c5f207266d526a8d32890f77e95b503669791 https://github.com/galaxyproject/usegalaxy-playbook/commit/d29c5f207266d526… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-06-14 (Thu, 14 Jun 2018) Changed paths: M env/main/host_vars/jetstream-iu0.galaxyproject.org.yml M env/main/templates/galaxy/config/job_conf.xml.j2 Log Message: ----------- Run fastx collapse on Jetstream @ IU **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

1 0

[galaxyproject/infrastructure-playbook] 825a3d: Slurmscale: Attempt to handle failures on spawn
by GitHub 13 Jun '18

13 Jun '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 825a3df102e36032b2c655df47c6ffb1f3f89372 https://github.com/galaxyproject/infrastructure-playbook/commit/825a3df102e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-06-13 (Wed, 13 Jun 2018) Changed paths: M roles/slurmscale/files/roles/galaxynodeconfig/tasks/main.yml Log Message: ----------- Slurmscale: Attempt to handle failures on spawn Commit: aad3956aa9bfe48a66a7b4ccb4ce12cca857fb9c https://github.com/galaxyproject/infrastructure-playbook/commit/aad3956aa9b… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-06-13 (Wed, 13 Jun 2018) Changed paths: M roles/slurmscale/files/group_vars/all/cluster.yml M roles/slurmscale/templates/group_vars/all/cloud.yml.j2 Log Message: ----------- Slurm user fix Compare: https://github.com/galaxyproject/infrastructure-playbook/compare/c2b543d1a1… **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

1 0

[galaxyproject/usegalaxy-playbook] 76a0ed: Fixes for running Test jobs on new autoscaling Jet...
by GitHub 13 Jun '18

13 Jun '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 76a0edeb4c11d063e1678861d930b28a75621055 https://github.com/galaxyproject/usegalaxy-playbook/commit/76a0edeb4c11d063… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-06-13 (Wed, 13 Jun 2018) Changed paths: M env/common/templates/pulsar/config/jetstream_dependency_resolvers_conf.xml.j2 A env/test/files/galaxy/dynamic_rules/multi_dynamic_walltime.py R env/test/files/galaxy/dynamic_rules/multi_dynamic_walltime.py M env/test/host_vars/jetstream-iu0.galaxyproject.org.yml Log Message: ----------- Fixes for running Test jobs on new autoscaling Jetstream @ IU **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

1 0

[galaxyproject/infrastructure-playbook] c2b543: Pulsar fixes
by GitHub 13 Jun '18

13 Jun '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: c2b543d1a119b2dffe597b79408191119a378390 https://github.com/galaxyproject/infrastructure-playbook/commit/c2b543d1a11… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-06-13 (Wed, 13 Jun 2018) Changed paths: M env/jscommon/group_vars/controllers.yml M env/jscommon/templates/supervisor/pulsar.j2 Log Message: ----------- Pulsar fixes **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

1 0

[galaxyproject/infrastructure-playbook] 9f4837: Deduplicate
by GitHub 13 Jun '18

13 Jun '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 9f4837a12fdbcfe9303d9bd88afc67f475b688e3 https://github.com/galaxyproject/infrastructure-playbook/commit/9f4837a12fd… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-06-13 (Wed, 13 Jun 2018) Changed paths: A env/jscommon/group_vars/all/vars.yml A env/jscommon/group_vars/all/vault.yml M env/jscommon/group_vars/controllers.yml M env/jscommon/group_vars/slurmclients/vars.yml A env/jsiu/group_vars/all/common_vars.yml A env/jsiu/group_vars/all/common_vault.yml M env/jsiu/group_vars/all/vars.yml M env/jsiu/group_vars/all/vault.yml A env/jsiu/group_vars/controllers.yml R env/jsiu/group_vars/controllers.yml M roles/slurmscale/files/group_vars/all/cluster.yml M roles/slurmscale/templates/group_vars/all/cloud.yml.j2 Log Message: ----------- Deduplicate **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

1 0

[galaxyproject/galaxy] 43d23b: Stop listening to history changes after job submis...
by GitHub 13 Jun '18

13 Jun '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 43d23b24d14b72bc59f98b4faa89a54dd1e58b25 https://github.com/galaxyproject/galaxy/commit/43d23b24d14b72bc59f98b4faa89… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-06-05 (Tue, 05 Jun 2018) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js Log Message: ----------- Stop listening to history changes after job submission Commit: b41af6abe9c144c76fbedff7d6a5e41d9a3d6071 https://github.com/galaxyproject/galaxy/commit/b41af6abe9c144c76fbedff7d6a5… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-06-13 (Wed, 13 Jun 2018) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js Log Message: ----------- Merge pull request #6303 from guerler/history_polling Stop listening to history changes after job submission Compare: https://github.com/galaxyproject/galaxy/compare/f8bc0656f9cf...b41af6abe9c1 **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

1 0

[galaxyproject/galaxy] 81864e: Update dependencies to versions with Python3 manyl...
by GitHub 13 Jun '18

13 Jun '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 81864e9713e63b3478a3e8ec8ed672516b2c6853 https://github.com/galaxyproject/galaxy/commit/81864e9713e63b3478a3e8ec8ed6… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-06-13 (Wed, 13 Jun 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt Log Message: ----------- Update dependencies to versions with Python3 manylinux wheels on PyPI Commit: d66a63012af8f538572458650d47801a5d2cd396 https://github.com/galaxyproject/galaxy/commit/d66a63012af8f538572458650d47… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-06-13 (Wed, 13 Jun 2018) Changed paths: M config/galaxy.yml.sample M config/tool_shed.yml.sample M doc/source/admin/galaxy_options.rst M lib/galaxy/datatypes/display_applications/util.py M lib/galaxy/dependencies/pipfiles/default/Pipfile M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/flake8/Pipfile.lock M lib/galaxy/web/security/__init__.py M lib/galaxy/webapps/galaxy/config_schema.yml M scripts/api/common.py M test/unit/test_security_helper.py M test/unit/unittest_utils/galaxy_mock.py Log Message: ----------- Replace unmaintained pycrypto dependency with pycryptodome Minimum secret key length for Blowfish was increased from 4 to 5 bytes. First argument to Blowfish.new() must be a bytestring, and the `mode` argument is no more optional. Remove unused `encode_id` function from `scripts/api/common.py` . Documentation updated, then rebuilt with `make config-rebuild` . Commit: 39b70d7193c223e4013391afcb90cc932f7ac650 https://github.com/galaxyproject/galaxy/commit/39b70d7193c223e4013391afcb90… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-06-13 (Wed, 13 Jun 2018) Changed paths: M lib/tool_shed/util/common_util.py M lib/tool_shed/util/encoding_util.py Log Message: ----------- Python3 Unicode/binary fixes Commit: cffeb6edc8b72534385d6aa5e978d25cb20b5479 https://github.com/galaxyproject/galaxy/commit/cffeb6edc8b72534385d6aa5e978… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-06-13 (Wed, 13 Jun 2018) Changed paths: M lib/tool_shed/util/hg_util.py Log Message: ----------- Move mercurial imports inside the functions that use them Because Galaxy under Python3 would fail otherwise. Commit: 6120183182bf643b6abb995283c7798da71f0211 https://github.com/galaxyproject/galaxy/commit/6120183182bf643b6abb995283c7… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-06-13 (Wed, 13 Jun 2018) Changed paths: M scripts/check_python.py Log Message: ----------- Allow Python 3 if in a virtualenv Commit: 594daa85bf5de0acfb0a76aeea8cb55d7aa4684a https://github.com/galaxyproject/galaxy/commit/594daa85bf5de0acfb0a76aeea8c… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-06-13 (Wed, 13 Jun 2018) Changed paths: M .travis.yml M tox.ini Log Message: ----------- Add py34-first_startup to Travis and default tox tests. Commit: f8bc0656f9cf5336cac667b1be46ad2bb5bfb7ff https://github.com/galaxyproject/galaxy/commit/f8bc0656f9cf5336cac667b1be46… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-06-13 (Wed, 13 Jun 2018) Changed paths: M .travis.yml M config/galaxy.yml.sample M config/tool_shed.yml.sample M doc/source/admin/galaxy_options.rst M lib/galaxy/datatypes/display_applications/util.py M lib/galaxy/dependencies/pipfiles/default/Pipfile M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/flake8/Pipfile.lock M lib/galaxy/web/security/__init__.py M lib/galaxy/webapps/galaxy/config_schema.yml M lib/tool_shed/util/common_util.py M lib/tool_shed/util/encoding_util.py M lib/tool_shed/util/hg_util.py M scripts/api/common.py M scripts/check_python.py M test/unit/test_security_helper.py M test/unit/unittest_utils/galaxy_mock.py M tox.ini Log Message: ----------- Merge pull request #6325 from mvdbeek/py3_fixes2 Add py34-first_startup to Travis and default tox tests Compare: https://github.com/galaxyproject/galaxy/compare/b5214867c9ff...f8bc0656f9cf **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

1 0

[galaxyproject/galaxy] 847d0e: Fix target update for rule collection builder afte...
by GitHub 13 Jun '18

13 Jun '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 847d0e987e21056948a2859d91b39c3b7d41ab69 https://github.com/galaxyproject/galaxy/commit/847d0e987e21056948a2859d91b3… Author: Sebastian Kapust <sebastian(a)kapust.org> Date: 2018-06-13 (Wed, 13 Jun 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-rules-edit.js Log Message: ----------- Fix target update for rule collection builder after input selection Commit: b5214867c9ffea3cb9008acc3efa9928781ff513 https://github.com/galaxyproject/galaxy/commit/b5214867c9ffea3cb9008acc3efa… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-06-13 (Wed, 13 Jun 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-rules-edit.js Log Message: ----------- Merge pull request #6326 from scrathat/rule.builder.selection.update Fix target update for rule collection builder after input selection Compare: https://github.com/galaxyproject/galaxy/compare/5a27b0cf4d41...b5214867c9ff **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

1 0

[galaxyproject/infrastructure-playbook] 14f78d: Relaunch JS@IU, now with more elastic
by GitHub 12 Jun '18

12 Jun '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 14f78d9d7e140b7028c11df75cb7a03869247685 https://github.com/galaxyproject/infrastructure-playbook/commit/14f78d9d7e1… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-06-11 (Mon, 11 Jun 2018) Changed paths: M env/galaxy/group_vars/cvmfsservers/vars.yml M env/galaxy/group_vars/cvmfsstratum1servers/vars.yml M env/galaxy/group_vars/dockerswarmmanagers/vars.yml M env/galaxy/group_vars/dockerswarmmanagers/vault.yml M env/galaxy/group_vars/jetstreamhosts/vault.yml M env/galaxy/inventory M env/galaxy/playbook.yml R env/jsiu/group_vars/all.yml A env/jsiu/group_vars/all/vars.yml A env/jsiu/group_vars/all/vault.yml A env/jsiu/group_vars/controllers.yml R env/jsiu/group_vars/controllers/vars.yml R env/jsiu/group_vars/controllers/vault.yml M env/jsiu/group_vars/cvmfsclients.yml A env/jsiu/group_vars/cvmfsservers.yml M env/jsiu/inventory M env/jsiu/playbook.yml M env/jsiu/templates/slurm/slurm.conf.j2 M roles/docker_swarm/tasks/main.yml M roles/jetstream_nfs/tasks/server.yml M roles/openstack/tasks/spawn.yml M roles/slurmscale/files/ansible.cfg M roles/slurmscale/files/config.yml M roles/slurmscale/files/group_vars/all/cluster.yml M roles/slurmscale/files/spawn.yml M roles/slurmscale/files/start.yml R roles/slurmscale/files/templates/slurm/slurm.conf.j2 M roles/slurmscale/tasks/main.yml M roles/slurmscale/templates/group_vars/all/cloud.yml.j2 M roles/slurmscale/templates/slurm_resume.sh.j2 M roles/slurmscale/templates/slurm_suspend.sh.j2 Log Message: ----------- Relaunch JS@IU, now with more elastic Commit: bbd846f535c968b540c51263e2a7e2df7e5f855e https://github.com/galaxyproject/infrastructure-playbook/commit/bbd846f535c… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-06-12 (Tue, 12 Jun 2018) Changed paths: M env/jsiu/templates/slurm/slurm.conf.j2 M roles/slurmscale/files/ansible.cfg R roles/slurmscale/files/config.yml M roles/slurmscale/files/group_vars/all/cluster.yml M roles/slurmscale/files/group_vars/all/spawn.yml R roles/slurmscale/files/group_vars/jetstream-large.yml R roles/slurmscale/files/group_vars/jetstream-medium.yml R roles/slurmscale/files/group_vars/jetstream-small.yml R roles/slurmscale/files/inventory/flavors A roles/slurmscale/files/inventory/openstack.yml R roles/slurmscale/files/inventory/openstack_inventory.py A roles/slurmscale/files/resume.yml A roles/slurmscale/files/roles/galaxynodeconfig/tasks/main.yml R roles/slurmscale/files/spawn.yml R roles/slurmscale/files/start.yml R roles/slurmscale/files/stop.yml A roles/slurmscale/files/suspend.yml M roles/slurmscale/tasks/main.yml R roles/slurmscale/templates/slurm_resume.sh.j2 R roles/slurmscale/templates/slurm_suspend.sh.j2 A roles/slurmscale/templates/suspend_resume.sh.j2 Log Message: ----------- Simplify slurm suspend/resume process and reduce some duplication. Compare: https://github.com/galaxyproject/infrastructure-playbook/compare/f495dd5166… **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

1 0