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

[galaxyproject/galaxy] 3f172c: Fix job stopping from DRMAA jobs broken in
by GitHub 24 Oct '18

24 Oct '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: 3f172cc9880e58396e7f71b7480bea9e7163dda4 https://github.com/galaxyproject/galaxy/commit/3f172cc9880e58396e7f71b7480b… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-10-23 (Tue, 23 Oct 2018) Changed paths: M lib/galaxy/jobs/runners/drmaa.py Log Message: ----------- Fix job stopping from DRMAA jobs broken in a1c58a708829d79859426ecb7c39b5c5f69ad735 and improve logging around it. Commit: 36383785697bed5db7e99461c3483f19836a016b https://github.com/galaxyproject/galaxy/commit/36383785697bed5db7e99461c348… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-10-23 (Tue, 23 Oct 2018) Changed paths: M lib/galaxy/jobs/runners/drmaa.py Log Message: ----------- Merge pull request #6912 from natefoo/fix-drmaa-job-stop [18.09] Fix stopping DRMAA jobs Compare: https://github.com/galaxyproject/galaxy/compare/ecb56d80a103...36383785697b **NOTE:** This service has 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.

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[galaxyproject/usegalaxy-playbook] 29d04a: Updated all installed data managers.
by GitHub 24 Oct '18

24 Oct '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 29d04a9079607b385ecf1e4a275f7d9767386f3c https://github.com/galaxyproject/usegalaxy-playbook/commit/29d04a9079607b38… Author: Dave B <dave(a)bx.psu.edu> Date: 2018-10-23 (Tue, 23 Oct 2018) Changed paths: M env/test/files/galaxy/var/shed_tool_data_table_conf.xml Log Message: ----------- Updated all installed data managers. **NOTE:** This service has 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.

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[galaxyproject/usegalaxy-playbook] 8daa82: Fix DM destinations
by GitHub 23 Oct '18

23 Oct '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 8daa82a3c453d3840fb50f75dbcff84424377f46 https://github.com/galaxyproject/usegalaxy-playbook/commit/8daa82a3c453d384… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-10-23 (Tue, 23 Oct 2018) Changed paths: M env/test/templates/galaxy/config/job_conf.xml.j2 Log Message: ----------- Fix DM destinations **NOTE:** This service has 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.

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[galaxyproject/galaxy] 126ee5: Create composite file archives in new_file_path in...
by GitHub 23 Oct '18

23 Oct '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 126ee5fe2bb6d8c1c2874545cd5a583389d45bca https://github.com/galaxyproject/galaxy/commit/126ee5fe2bb6d8c1c2874545cd5a… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-10-17 (Wed, 17 Oct 2018) Changed paths: M lib/galaxy/datatypes/data.py Log Message: ----------- Create composite file archives in new_file_path instead of TMP Commit: d19effdf3c042538ffa0ba1351a2f3433ad19fd1 https://github.com/galaxyproject/galaxy/commit/d19effdf3c042538ffa0ba1351a2… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-17 (Wed, 17 Oct 2018) Changed paths: M doc/source/releases/18.09.rst Log Message: ----------- One last batch of PRs. Commit: 89fbe9c9344d1e8ad88fe88a0685cf85aa1edcb3 https://github.com/galaxyproject/galaxy/commit/89fbe9c9344d1e8ad88fe88a0685… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2018-10-17 (Wed, 17 Oct 2018) Changed paths: M doc/source/releases/18.09.rst Log Message: ----------- Merge pull request #6890 from dannon/18.09_release_notes_updates [18.09] One last batch of PRs added to RN Commit: 9735146f2848beca367ac84c066d10a4b5008a25 https://github.com/galaxyproject/galaxy/commit/9735146f2848beca367ac84c066d… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-10-17 (Wed, 17 Oct 2018) Changed paths: M doc/source/releases/18.09_announce.rst Log Message: ----------- add discovered tool vulnerabilities to RN Commit: fa212c3c31b78f885b7aff2681430bc9e54fec89 https://github.com/galaxyproject/galaxy/commit/fa212c3c31b78f885b7aff268143… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-10-17 (Wed, 17 Oct 2018) Changed paths: M doc/source/releases/18.09_announce.rst Log Message: ----------- specify which gemini tools were fixed Commit: 0aca12ce96f0c2a860453a15022bbd5e693493ed https://github.com/galaxyproject/galaxy/commit/0aca12ce96f0c2a860453a15022b… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-10-17 (Wed, 17 Oct 2018) Changed paths: M doc/source/releases/18.09_announce.rst Log Message: ----------- Merge pull request #6892 from martenson/security-notes [18.09] add discovered tool vulnerabilities to RN Commit: 46e56417dddfa88c9b093c612eb006c9f471579d https://github.com/galaxyproject/galaxy/commit/46e56417dddfa88c9b093c612eb0… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-10-17 (Wed, 17 Oct 2018) Changed paths: M lib/galaxy/web/base/controller.py Log Message: ----------- Use hasattr instead of relying on value Commit: 3411852fedf31c93ec506aa4f8f8a922d4b57ad7 https://github.com/galaxyproject/galaxy/commit/3411852fedf31c93ec506aa4f8f8… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-10-21 (Sun, 21 Oct 2018) Changed paths: M lib/galaxy/datatypes/data.py Log Message: ----------- Merge pull request #6885 from mvdbeek/create_in_new_file_path [18.05] Create composite file archives in new_file_path instead of TMP Commit: 88b840d2c6cc18184c71772d96301a9f9a71cbdc https://github.com/galaxyproject/galaxy/commit/88b840d2c6cc18184c71772d9630… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-10-22 (Mon, 22 Oct 2018) Changed paths: M lib/galaxy/web/base/controller.py Log Message: ----------- Merge pull request #6893 from martenson/backport-6884 [18.09] check presence of attribute in addition to value Commit: 4dd2ecb13f1cac23730debd107dd150e46c47568 https://github.com/galaxyproject/galaxy/commit/4dd2ecb13f1cac23730debd107dd… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-10-23 (Tue, 23 Oct 2018) Changed paths: M config/galaxy.yml.sample M doc/source/admin/galaxy_options.rst M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- Fix ``make config-validate`` Commit: 194358703450ff8fef553d92531fc6e6a0938612 https://github.com/galaxyproject/galaxy/commit/194358703450ff8fef553d92531f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-10-23 (Tue, 23 Oct 2018) Changed paths: M config/galaxy.yml.sample M doc/source/admin/galaxy_options.rst M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- Merge pull request #6908 from nsoranzo/release_18.09_config_validate [18.09] Fix ``make config-validate`` Commit: ecb56d80a103dc3b11091beb3de06a086ed48953 https://github.com/galaxyproject/galaxy/commit/ecb56d80a103dc3b11091beb3de0… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-10-23 (Tue, 23 Oct 2018) Changed paths: M lib/galaxy/datatypes/data.py Log Message: ----------- Merge branch 'release_18.05' into release_18.09 Commit: 02c71e2429bad6caf07ce9a66e788d26af8b21b3 https://github.com/galaxyproject/galaxy/commit/02c71e2429bad6caf07ce9a66e78… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-10-23 (Tue, 23 Oct 2018) Changed paths: M config/galaxy.yml.sample M doc/source/admin/galaxy_options.rst M doc/source/releases/18.09.rst M doc/source/releases/18.09_announce.rst M lib/galaxy/datatypes/data.py M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- Merge branch 'release_18.09' into dev Compare: https://github.com/galaxyproject/galaxy/compare/3759db3297b2...02c71e2429ba **NOTE:** This service has 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.

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[galaxyproject/galaxy] 126ee5: Create composite file archives in new_file_path in...
by GitHub 23 Oct '18

23 Oct '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: 126ee5fe2bb6d8c1c2874545cd5a583389d45bca https://github.com/galaxyproject/galaxy/commit/126ee5fe2bb6d8c1c2874545cd5a… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-10-17 (Wed, 17 Oct 2018) Changed paths: M lib/galaxy/datatypes/data.py Log Message: ----------- Create composite file archives in new_file_path instead of TMP Commit: 3411852fedf31c93ec506aa4f8f8a922d4b57ad7 https://github.com/galaxyproject/galaxy/commit/3411852fedf31c93ec506aa4f8f8… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-10-21 (Sun, 21 Oct 2018) Changed paths: M lib/galaxy/datatypes/data.py Log Message: ----------- Merge pull request #6885 from mvdbeek/create_in_new_file_path [18.05] Create composite file archives in new_file_path instead of TMP Commit: ecb56d80a103dc3b11091beb3de06a086ed48953 https://github.com/galaxyproject/galaxy/commit/ecb56d80a103dc3b11091beb3de0… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-10-23 (Tue, 23 Oct 2018) Changed paths: M lib/galaxy/datatypes/data.py Log Message: ----------- Merge branch 'release_18.05' into release_18.09 Compare: https://github.com/galaxyproject/galaxy/compare/194358703450...ecb56d80a103 **NOTE:** This service has 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.

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[galaxyproject/galaxy] 429ef9: WIP pgcleanup improvements
by GitHub 23 Oct '18

23 Oct '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 429ef96a106d0bf094145a7fd8a65143b113e6e5 https://github.com/galaxyproject/galaxy/commit/429ef96a106d0bf094145a7fd8a6… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-10-15 (Mon, 15 Oct 2018) Changed paths: M scripts/cleanup_datasets/pgcleanup.py Log Message: ----------- WIP pgcleanup improvements Commit: 941d68ad358155f6577fb89f1778625b805035fe https://github.com/galaxyproject/galaxy/commit/941d68ad358155f6577fb89f1778… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-10-15 (Mon, 15 Oct 2018) Changed paths: M scripts/cleanup_datasets/pgcleanup.py Log Message: ----------- WIP pgcleanup improvements Commit: ba83310d53488ccc62dd52907746a3ca63baaf28 https://github.com/galaxyproject/galaxy/commit/ba83310d53488ccc62dd52907746… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-10-15 (Mon, 15 Oct 2018) Changed paths: M scripts/cleanup_datasets/pgcleanup.py Log Message: ----------- Mostly refactored pgcleanup.py Commit: e1a197676ec3f6f35dafaa6cb58d60c7d9d44fb2 https://github.com/galaxyproject/galaxy/commit/e1a197676ec3f6f35dafaa6cb58d… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-10-15 (Mon, 15 Oct 2018) Changed paths: M scripts/cleanup_datasets/pgcleanup.py Log Message: ----------- Refactor repetitive HDA purging stuff and add a function to purge HDAs with null history_ids Commit: 4d0538cc4f74c183495c9df33c1055a9441766d8 https://github.com/galaxyproject/galaxy/commit/4d0538cc4f74c183495c9df33c10… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-10-15 (Mon, 15 Oct 2018) Changed paths: A lib/galaxy/model/migrate/versions/0144_add_cleanup_event_user_table.py Log Message: ----------- Add a table for logging user cleanup events Commit: e72d52c6dfe9332c5cd1c3f42d4e0276e9a75008 https://github.com/galaxyproject/galaxy/commit/e72d52c6dfe9332c5cd1c3f42d4e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-10-15 (Mon, 15 Oct 2018) Changed paths: M lib/galaxy/model/migrate/versions/0144_add_cleanup_event_user_table.py M scripts/cleanup_datasets/pgcleanup.py Log Message: ----------- Lint Commit: 3759db3297b2d277ae3039f54e203dc7493cb3dc https://github.com/galaxyproject/galaxy/commit/3759db3297b2d277ae3039f54e20… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-10-23 (Tue, 23 Oct 2018) Changed paths: A lib/galaxy/model/migrate/versions/0144_add_cleanup_event_user_table.py M scripts/cleanup_datasets/pgcleanup.py Log Message: ----------- Merge pull request #6877 from natefoo/pgcleanup-inactive-users Refactor pgcleanup.py and add new routines Compare: https://github.com/galaxyproject/galaxy/compare/99bc4b33d2fa...3759db3297b2 **NOTE:** This service has 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.

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[galaxyproject/galaxy] 4dd2ec: Fix ``make config-validate``
by GitHub 23 Oct '18

23 Oct '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: 4dd2ecb13f1cac23730debd107dd150e46c47568 https://github.com/galaxyproject/galaxy/commit/4dd2ecb13f1cac23730debd107dd… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-10-23 (Tue, 23 Oct 2018) Changed paths: M config/galaxy.yml.sample M doc/source/admin/galaxy_options.rst M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- Fix ``make config-validate`` Commit: 194358703450ff8fef553d92531fc6e6a0938612 https://github.com/galaxyproject/galaxy/commit/194358703450ff8fef553d92531f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-10-23 (Tue, 23 Oct 2018) Changed paths: M config/galaxy.yml.sample M doc/source/admin/galaxy_options.rst M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- Merge pull request #6908 from nsoranzo/release_18.09_config_validate [18.09] Fix ``make config-validate`` Compare: https://github.com/galaxyproject/galaxy/compare/88b840d2c6cc...194358703450 **NOTE:** This service has 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.

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[galaxyproject/infrastructure-playbook] c6a4fe: Collect Galaxy handler process stats
by GitHub 23 Oct '18

23 Oct '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: c6a4fe030044926479872c4a60f95216887b893b https://github.com/galaxyproject/infrastructure-playbook/commit/c6a4fe03004… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-10-22 (Mon, 22 Oct 2018) Changed paths: M env/tacc/group_vars/galaxyservers.yml Log Message: ----------- Collect Galaxy handler process stats **NOTE:** This service has 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.

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[galaxyproject/usegalaxy-playbook] aa23d8: Configure workflow schedulers on Main
by GitHub 23 Oct '18

23 Oct '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: aa23d8cf0d1d857421b02c98bf278ea0d9923ba7 https://github.com/galaxyproject/usegalaxy-playbook/commit/aa23d8cf0d1d8574… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-10-22 (Mon, 22 Oct 2018) Changed paths: R env/common/templates/galaxy/config/workflow_schedulers_conf.xml.j2 A env/main/files/galaxy/config/workflow_schedulers_conf.xml M env/main/group_vars/galaxyjobservers.yml M env/main/group_vars/galaxyservers/vars.yml A env/test/files/galaxy/config/workflow_schedulers_conf.xml M env/test/group_vars/galaxyservers/vars.yml R env/test/templates/galaxy/config/workflow_schedulers_conf.xml.j2 Log Message: ----------- Configure workflow schedulers on Main **NOTE:** This service has 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.

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[galaxyproject/usegalaxy-playbook] 796070: Rename uWSGI logs from uwsgi_zerg*.log to zerg*.lo...
by GitHub 23 Oct '18

23 Oct '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 796070ba4ffacae52de4a889b89f271866a5bec3 https://github.com/galaxyproject/usegalaxy-playbook/commit/796070ba4ffacae5… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-10-22 (Mon, 22 Oct 2018) Changed paths: M env/common/templates/supervisor/galaxy.j2 M roles/usegalaxy_privileged/templates/archive_logs.sh.j2 Log Message: ----------- Rename uWSGI logs from uwsgi_zerg*.log to zerg*.log Commit: ecce49a63dc603bb6b0f2f4e2c08312179b7e634 https://github.com/galaxyproject/usegalaxy-playbook/commit/ecce49a63dc603bb… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-10-22 (Mon, 22 Oct 2018) Changed paths: A env/common/templates/galaxy/config/workflow_schedulers_conf.xml.j2 M env/common/templates/supervisor/galaxy_group.j2 A env/common/templates/supervisor/galaxy_workflow_scheduler.j2 M env/test/group_vars/galaxyservers/vars.yml A env/test/templates/galaxy/config/workflow_schedulers_conf.xml.j2 Log Message: ----------- Configure a workflow scheduler on Test Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/1634bc2fc07f...… **NOTE:** This service has 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.

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