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

[galaxyproject/galaxy] b463be: Add nodeenv to dev requirements
by GitHub 08 Feb '18

08 Feb '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: b463be78a5066c7e6c389c43af2bd863f05e4a80 https://github.com/galaxyproject/galaxy/commit/b463be78a5066c7e6c389c43af2b… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-02-08 (Thu, 08 Feb 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/develop/Pipfile M lib/galaxy/dependencies/pipfiles/develop/Pipfile.lock M lib/galaxy/dependencies/pipfiles/develop/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pipfiles/develop/pinned-requirements.txt Log Message: ----------- Add nodeenv to dev requirements Commit: 977bbf1481b2fd36512f869c01f0af6ba4099a92 https://github.com/galaxyproject/galaxy/commit/977bbf1481b2fd36512f869c01f0… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-02-08 (Thu, 08 Feb 2018) Changed paths: M scripts/common_startup.sh Log Message: ----------- Install node and yarn in common_startup.sh using nodeenv and the venv's npm. Commit: eba3fb4b35570fc704dbb9a70c733293a2ee4514 https://github.com/galaxyproject/galaxy/commit/eba3fb4b35570fc704dbb9a70c73… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-02-08 (Thu, 08 Feb 2018) Changed paths: M client/package.json M scripts/common_startup.sh Log Message: ----------- Fix common_startup.sh for galaxy tarballs Do not assume git is installed and the `.git` directory is present. Fix https://github.com/galaxyproject/galaxy/issues/5466 Commit: d91078024bf3e9404aaca1c8655a5bc2b451ebc8 https://github.com/galaxyproject/galaxy/commit/d91078024bf3e9404aaca1c8655a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-02-08 (Thu, 08 Feb 2018) Changed paths: M client/package.json M lib/galaxy/dependencies/pipfiles/develop/Pipfile M lib/galaxy/dependencies/pipfiles/develop/Pipfile.lock M lib/galaxy/dependencies/pipfiles/develop/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pipfiles/develop/pinned-requirements.txt M scripts/common_startup.sh Log Message: ----------- Merge pull request #5491 from nsoranzo/release_18.01_fix_common_startup_for_bare_clone [18.01] Fix common_startup.sh for galaxy tarballs Compare: https://github.com/galaxyproject/galaxy/compare/3f50b45a4e30...d91078024bf3

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[galaxyproject/galaxy] b5945a: Add IdeasPre datatype subclassed from Rgenetics
by GitHub 08 Feb '18

08 Feb '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: b5945ad3e3a972acb41c87c2ddeeff222779020c https://github.com/galaxyproject/galaxy/commit/b5945ad3e3a972acb41c87c2ddee… Author: greg <ghv2(a)psu.edu> Date: 2018-02-02 (Fri, 02 Feb 2018) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/genetics.py Log Message: ----------- Add IdeasPre datatype subclassed from Rgenetics Commit: 3fdd4edc5c1954dc750dfeff03cb3205ee1b6042 https://github.com/galaxyproject/galaxy/commit/3fdd4edc5c1954dc750dfeff03cb… Author: greg <ghv2(a)psu.edu> Date: 2018-02-02 (Fri, 02 Feb 2018) Changed paths: M lib/galaxy/datatypes/genetics.py Log Message: ----------- Subclass IdeasPre from Html Commit: 3f50b45a4e3016a211dcbd0876bb95acb29cf900 https://github.com/galaxyproject/galaxy/commit/3f50b45a4e3016a211dcbd0876bb… Author: Dave B <dave(a)bx.psu.edu> Date: 2018-02-08 (Thu, 08 Feb 2018) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/genetics.py Log Message: ----------- Merge pull request #5445 from gregvonkuster/add-ideaspre [18.01] Add support for the ideaspre datatype Compare: https://github.com/galaxyproject/galaxy/compare/64e4e8b572b8...3f50b45a4e30

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[galaxyproject/infrastructure-playbook] 84730b: Update postgresql_objects role
by GitHub 08 Feb '18

08 Feb '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook 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 Compare: https://github.com/galaxyproject/infrastructure-playbook/compare/b27e8c6159…

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[galaxyproject/galaxy] bb9d10: Initial work towards slow request logging into sen...
by GitHub 08 Feb '18

08 Feb '18

Branch: refs/heads/usegalaxy Home: https://github.com/galaxyproject/galaxy Commit: bb9d10790b2948250c7fd3c945d8190dfa8c7f3c https://github.com/galaxyproject/galaxy/commit/bb9d10790b2948250c7fd3c945d8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-02-08 (Thu, 08 Feb 2018) Changed paths: M lib/galaxy/web/framework/middleware/sentry.py Log Message: ----------- Initial work towards slow request logging into sentry Commit: 2b3a2833acf871d5c6520ea489d1c287f0b41d76 https://github.com/galaxyproject/galaxy/commit/2b3a2833acf871d5c6520ea489d1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-02-08 (Thu, 08 Feb 2018) Changed paths: M config/galaxy.yml.sample M lib/galaxy/web/framework/middleware/sentry.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Make sloreq_threshold configurable Compare: https://github.com/galaxyproject/galaxy/compare/64e4e8b572b8...2b3a2833acf8

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[galaxyproject/galaxy]
by GitHub 08 Feb '18

08 Feb '18

Branch: refs/heads/usegalaxy Home: https://github.com/galaxyproject/galaxy

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[galaxyproject/galaxy] 3f80a4: Add configuration for slow request timing to schem...
by GitHub 08 Feb '18

08 Feb '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 3f80a43bda5e7d32cf9f1317666e5fa618f38bd6 https://github.com/galaxyproject/galaxy/commit/3f80a43bda5e7d32cf9f1317666e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-02-08 (Thu, 08 Feb 2018) Changed paths: M config/galaxy.yml.sample M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- Add configuration for slow request timing to schema, regenerate Commit: 8ce7f96353f3d31e6b41bd19c611c33a57411cb6 https://github.com/galaxyproject/galaxy/commit/8ce7f96353f3d31e6b41bd19c611… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-02-08 (Thu, 08 Feb 2018) Changed paths: M doc/source/admin/galaxy_options.rst Log Message: ----------- Rebuild rst for new configuration options Commit: 0ca7afb343d865a7d1bd4cc6b5170f9bf03a0cf3 https://github.com/galaxyproject/galaxy/commit/0ca7afb343d865a7d1bd4cc6b517… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2018-02-08 (Thu, 08 Feb 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 #5487 from dannon/slow_request_timing_sentry Add configuration for slow request timing to schema, regenerate Compare: https://github.com/galaxyproject/galaxy/compare/55ca8132a38c...0ca7afb343d8

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[galaxyproject/usegalaxy-playbook] 182fa5: Reenable sentry on Main
by GitHub 08 Feb '18

08 Feb '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 182fa5c142032153df350d7eeb11d12d29157c15 https://github.com/galaxyproject/usegalaxy-playbook/commit/182fa5c142032153… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-02-08 (Thu, 08 Feb 2018) Changed paths: M env/main/group_vars/galaxyservers/vars.yml Log Message: ----------- Reenable sentry on Main

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[galaxyproject/usegalaxy-playbook] 02da13: Update Test and Main
by GitHub 08 Feb '18

08 Feb '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 02da1321b7b7de422833f96137d8213998fd7e1f https://github.com/galaxyproject/usegalaxy-playbook/commit/02da1321b7b7de42… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-02-08 (Thu, 08 Feb 2018) Changed paths: M env/main/files/galaxy/galaxy_version.yml M env/test/files/galaxy/galaxy_version.yml Log Message: ----------- Update Test and Main

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[galaxyproject/galaxy] 8b0e3b: Fix recursion bug in BamNative datatype
by GitHub 08 Feb '18

08 Feb '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 8b0e3bd28f551864b5c989d756a69ad87115af10 https://github.com/galaxyproject/galaxy/commit/8b0e3bd28f551864b5c989d756a6… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-02-07 (Wed, 07 Feb 2018) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Fix recursion bug in BamNative datatype We introduced this in https://github.com/galaxyproject/galaxy/pull/5180/ where we moved a lot of code form the Bam class into the BamNative class. Reported by @natefoo Commit: db069198af913238515faf6077521a2a2754631f https://github.com/galaxyproject/galaxy/commit/db069198af913238515faf607752… Author: Jelle Scholtalbers <j.scholtalbers(a)gmail.com> Date: 2018-02-08 (Thu, 08 Feb 2018) Changed paths: M lib/galaxy/jobs/actions/post.py Log Message: ----------- fix #5484 Commit: e9ed97f533c00a66db4f6aee81429f61e74835cb https://github.com/galaxyproject/galaxy/commit/e9ed97f533c00a66db4f6aee8142… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-02-08 (Thu, 08 Feb 2018) Changed paths: M lib/galaxy/jobs/actions/post.py Log Message: ----------- Merge pull request #5485 from scholtalbers/fix/#5484_rename_post_actions [18.01] Fix #5484 Commit: 64e4e8b572b85d09da53af95332c37b4dc8ecff0 https://github.com/galaxyproject/galaxy/commit/64e4e8b572b85d09da53af95332c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-02-08 (Thu, 08 Feb 2018) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Merge pull request #5482 from mvdbeek/bam_recursion_bug [18.01] Fix recursion bug in BamNative datatype Commit: 55ca8132a38c67d7e30e6ee59f1497d58f6158df https://github.com/galaxyproject/galaxy/commit/55ca8132a38c67d7e30e6ee59f14… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-02-08 (Thu, 08 Feb 2018) Changed paths: M lib/galaxy/datatypes/binary.py M lib/galaxy/jobs/actions/post.py Log Message: ----------- Merge remote-tracking branch 'origin/release_18.01' into dev Compare: https://github.com/galaxyproject/galaxy/compare/d1f120108735...55ca8132a38c

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[galaxyproject/galaxy] 8b0e3b: Fix recursion bug in BamNative datatype
by GitHub 08 Feb '18

08 Feb '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: 8b0e3bd28f551864b5c989d756a69ad87115af10 https://github.com/galaxyproject/galaxy/commit/8b0e3bd28f551864b5c989d756a6… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-02-07 (Wed, 07 Feb 2018) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Fix recursion bug in BamNative datatype We introduced this in https://github.com/galaxyproject/galaxy/pull/5180/ where we moved a lot of code form the Bam class into the BamNative class. Reported by @natefoo Commit: 64e4e8b572b85d09da53af95332c37b4dc8ecff0 https://github.com/galaxyproject/galaxy/commit/64e4e8b572b85d09da53af95332c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-02-08 (Thu, 08 Feb 2018) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Merge pull request #5482 from mvdbeek/bam_recursion_bug [18.01] Fix recursion bug in BamNative datatype Compare: https://github.com/galaxyproject/galaxy/compare/e9ed97f533c0...64e4e8b572b8

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