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

[galaxyproject/galaxy] 02410b: Register job monitor as postfork function
by GitHub 11 Oct '18

11 Oct '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: 02410b270d025e5fb8cb4e2036fb627051c7850a https://github.com/galaxyproject/galaxy/commit/02410b270d025e5fb8cb4e2036fb… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-10-08 (Mon, 08 Oct 2018) Changed paths: M lib/galaxy/util/monitors.py Log Message: ----------- Register job monitor as postfork function This should fix https://github.com/galaxyproject/galaxy/issues/6831, and might fix https://github.com/galaxyproject/galaxy/issues/6261. Commit: baa992d217032b809d321cb800cd2f41af401c63 https://github.com/galaxyproject/galaxy/commit/baa992d217032b809d321cb800cd… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-10-11 (Thu, 11 Oct 2018) Changed paths: M lib/galaxy/util/monitors.py Log Message: ----------- Merge pull request #6836 from mvdbeek/fix_job_monitor_thread [18.01] Register job monitor thread as postfork function Compare: https://github.com/galaxyproject/galaxy/compare/ac46d21ece75...baa992d21703 **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] c6193c: Update DEVTEAM, rebuild, include a few new PRs.
by GitHub 11 Oct '18

11 Oct '18

Branch: refs/heads/18.09_release_notes Home: https://github.com/galaxyproject/galaxy Commit: c6193ca4406450cdaa01b9c27bcfb871c916544c https://github.com/galaxyproject/galaxy/commit/c6193ca4406450cdaa01b9c27bcf… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-11 (Thu, 11 Oct 2018) Changed paths: M doc/source/releases/18.09.rst M scripts/bootstrap_history.py Log Message: ----------- Update DEVTEAM, rebuild, include a few new PRs. Commit: 7cb2eb57aca559c86b3d938912d8f7bde5da9f74 https://github.com/galaxyproject/galaxy/commit/7cb2eb57aca559c86b3d938912d8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-11 (Thu, 11 Oct 2018) Changed paths: M doc/source/releases/18.09_announce.rst Log Message: ----------- Merge branch '18.09_release_notes' of github.com:galaxyproject/galaxy into 18.09_release_notes Compare: https://github.com/galaxyproject/galaxy/compare/c1383bc2d55c...7cb2eb57aca5 **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] c1383b: Small fixes
by GitHub 11 Oct '18

11 Oct '18

Branch: refs/heads/18.09_release_notes Home: https://github.com/galaxyproject/galaxy Commit: c1383bc2d55cb6565fbd63eb4088c734a805700e https://github.com/galaxyproject/galaxy/commit/c1383bc2d55cb6565fbd63eb4088… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2018-10-11 (Thu, 11 Oct 2018) Changed paths: M doc/source/releases/18.09_announce.rst Log Message: ----------- Small fixes **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] 5844bd: Add integration test for remote shell CLI runners
by GitHub 11 Oct '18

11 Oct '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: 5844bdc7aa0a90d992c3b36e041abb8d103e3b95 https://github.com/galaxyproject/galaxy/commit/5844bdc7aa0a90d992c3b36e041a… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-10-10 (Wed, 10 Oct 2018) Changed paths: M test/functional/tools/job_environment_default.xml M test/functional/tools/job_environment_default_legacy.xml M test/functional/tools/job_environment_explicit_shared_home.xml A test/integration/test_cli_runners.py M test/integration/test_job_environments.py Log Message: ----------- Add integration test for remote shell CLI runners This tests both the SecureShell and Paramiko shell plugins and the Slurm and Torque CLI runner. Commit: 57a1f19b069597bde97852b3e0d0a3e1c0068bc4 https://github.com/galaxyproject/galaxy/commit/57a1f19b069597bde97852b3e0d0… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-10-10 (Wed, 10 Oct 2018) Changed paths: M lib/galaxy/jobs/runners/util/cli/shell/local.py M lib/galaxy/jobs/runners/util/cli/shell/rsh.py Log Message: ----------- Fix slurm cli plugin by avoiding `shell=True` in subprocess Fixes the remaining issue in https://github.com/galaxyproject/galaxy/issues/6831#issuecomment-428097520 Commit: fc28e0bd83a2df59f11b80f0119e67da1326887f https://github.com/galaxyproject/galaxy/commit/fc28e0bd83a2df59f11b80f0119e… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-10-10 (Wed, 10 Oct 2018) Changed paths: M lib/galaxy/jobs/runners/util/cli/shell/rsh.py Log Message: ----------- Use long-form options Commit: 5e12e509bf20d7e4f4464a60f04c7479cb4e232d https://github.com/galaxyproject/galaxy/commit/5e12e509bf20d7e4f4464a60f04c… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-10-10 (Wed, 10 Oct 2018) Changed paths: M test/integration/test_cli_runners.py Log Message: ----------- Fix selection of job plugin and image Thanks @nsoranzo. Commit: b08c6219c3fe771e00d0b6d8b9adb1c97e38e9a6 https://github.com/galaxyproject/galaxy/commit/b08c6219c3fe771e00d0b6d8b9ad… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-10-10 (Wed, 10 Oct 2018) Changed paths: M test/integration/test_cli_runners.py Log Message: ----------- Simplify ssh key handling in integration test Commit: ac3e1ca1d0d7bb85cc00e2e113f70e3576f0b048 https://github.com/galaxyproject/galaxy/commit/ac3e1ca1d0d7bb85cc00e2e113f7… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-10-10 (Wed, 10 Oct 2018) Changed paths: M test/integration/test_cli_runners.py Log Message: ----------- Use Crypto to generate SSH keys Also remove key files in `stop_ssh_docker()`. Commit: fd0b24ecd2bff2f8baa636304e45eb2dbdcaf3a9 https://github.com/galaxyproject/galaxy/commit/fd0b24ecd2bff2f8baa636304e45… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-10-11 (Thu, 11 Oct 2018) Changed paths: M lib/galaxy/jobs/runners/util/cli/shell/local.py M lib/galaxy/jobs/runners/util/cli/shell/rsh.py M test/functional/tools/job_environment_default.xml M test/functional/tools/job_environment_default_legacy.xml M test/functional/tools/job_environment_explicit_shared_home.xml A test/integration/test_cli_runners.py M test/integration/test_job_environments.py Log Message: ----------- Merge pull request #6845 from mvdbeek/fix_slurm_cli_on_secure_shell [18.05] Fix slurm cli on secure shell Compare: https://github.com/galaxyproject/galaxy/compare/fe6c1738c0ea...fd0b24ecd2bf **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] a1f763: Updated volume kwds.
by GitHub 11 Oct '18

11 Oct '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: a1f7634fd7dca45902a2d3f67d2279db3aa2270d https://github.com/galaxyproject/galaxy/commit/a1f7634fd7dca45902a2d3f67d22… Author: thobalose <lose.thoba(a)gmail.com> Date: 2018-10-10 (Wed, 10 Oct 2018) Changed paths: M config/plugins/interactive_environments/bam_iobio/templates/bam_iobio.mako M config/plugins/interactive_environments/hicbrowser/templates/hicbrowser.mako M config/plugins/interactive_environments/neo/templates/neo.mako Log Message: ----------- Updated volume kwds. Commit: fe6c1738c0ea3ee35fa34fec8a2c2e8eb97ec044 https://github.com/galaxyproject/galaxy/commit/fe6c1738c0ea3ee35fa34fec8a2c… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-10-11 (Thu, 11 Oct 2018) Changed paths: M config/plugins/interactive_environments/bam_iobio/templates/bam_iobio.mako M config/plugins/interactive_environments/hicbrowser/templates/hicbrowser.mako M config/plugins/interactive_environments/neo/templates/neo.mako Log Message: ----------- Merge pull request #6851 from martenson/backport-gie-kwds [18.05] Updated volume kwds for GIEs Compare: https://github.com/galaxyproject/galaxy/compare/4a345b99c3cc...fe6c1738c0ea **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] d60699: Don't create jobs for inactive users
by GitHub 11 Oct '18

11 Oct '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d60699624139e09c1dd7d979eaaeecfeb77856ad https://github.com/galaxyproject/galaxy/commit/d60699624139e09c1dd7d979eaae… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-10-08 (Mon, 08 Oct 2018) Changed paths: M lib/galaxy/exceptions/__init__.py M lib/galaxy/exceptions/error_codes.json M lib/galaxy/managers/context.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/actions/history_imp_exp.py M lib/galaxy/tools/actions/metadata.py M lib/galaxy/tools/actions/upload.py Log Message: ----------- Don't create jobs for inactive users Commit: c4374f9a811762db7cc5dd999418ebe922d17a02 https://github.com/galaxyproject/galaxy/commit/c4374f9a811762db7cc5dd999418… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-10-08 (Mon, 08 Oct 2018) Changed paths: M lib/galaxy/tools/actions/upload.py Log Message: ----------- Fix tabs, wow Commit: c5700431c48cd0b2a2ebc2484a9e07d860c3aa9a https://github.com/galaxyproject/galaxy/commit/c5700431c48cd0b2a2ebc2484a9e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-10-09 (Tue, 09 Oct 2018) Changed paths: M lib/galaxy/managers/context.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/actions/history_imp_exp.py M lib/galaxy/tools/actions/metadata.py M lib/galaxy/tools/actions/model_operations.py M lib/galaxy/tools/actions/upload.py Log Message: ----------- check user activation with less duplication/imports Commit: 2bbabdae02bb08371429ddbda6737faea7ebc6b5 https://github.com/galaxyproject/galaxy/commit/2bbabdae02bb08371429ddbda673… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-10-09 (Tue, 09 Oct 2018) Changed paths: M test/unit/tools/test_actions.py Log Message: ----------- Fix unit tests for new job_is_active trans property and add a test for the feature. Commit: 8edeca024961a7f1856fc5586843137901fb6ff1 https://github.com/galaxyproject/galaxy/commit/8edeca024961a7f1856fc5586843… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-10-09 (Tue, 09 Oct 2018) Changed paths: M lib/galaxy/managers/context.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/actions/history_imp_exp.py M lib/galaxy/tools/actions/metadata.py M lib/galaxy/tools/actions/model_operations.py M lib/galaxy/tools/actions/upload.py Log Message: ----------- Merge pull request #9 from jmchilton/inactive-user-jobs check user activation with less duplication/imports Commit: 15944ce6e9d4bdf5818f3125efd63fc85c3161fe https://github.com/galaxyproject/galaxy/commit/15944ce6e9d4bdf5818f3125efd6… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-10-10 (Wed, 10 Oct 2018) Changed paths: M test/unit/tools/test_actions.py Log Message: ----------- Fix unit tests broken by the addition of trans.check_user_activation() Commit: 483a23a5a4bdfe2e74190cb7182fafd05d992461 https://github.com/galaxyproject/galaxy/commit/483a23a5a4bdfe2e74190cb7182f… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2018-10-11 (Thu, 11 Oct 2018) Changed paths: M lib/galaxy/exceptions/error_codes.json Log Message: ----------- Fix sorting of error codes Commit: 85d4706662969e953dd04a5266dddb7b73d16920 https://github.com/galaxyproject/galaxy/commit/85d4706662969e953dd04a5266dd… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-10-11 (Thu, 11 Oct 2018) Changed paths: M lib/galaxy/exceptions/__init__.py M lib/galaxy/exceptions/error_codes.json M lib/galaxy/managers/context.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/actions/history_imp_exp.py M lib/galaxy/tools/actions/metadata.py M lib/galaxy/tools/actions/model_operations.py M lib/galaxy/tools/actions/upload.py M test/unit/tools/test_actions.py Log Message: ----------- Merge pull request #6837 from natefoo/inactive-user-jobs Don't create jobs for inactive users Compare: https://github.com/galaxyproject/galaxy/compare/12929f9acb0b...85d470666296 **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] a46984: Clarify code used in output <filter> tags
by GitHub 10 Oct '18

10 Oct '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a46984991ee976b80b06983e0548ec05724dce36 https://github.com/galaxyproject/galaxy/commit/a46984991ee976b80b06983e0548… Author: pvanheus <pvh(a)sanbi.ac.za> Date: 2018-10-07 (Sun, 07 Oct 2018) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Clarify code used in output <filter> tags Add extra detail to the explanation of how the Python code to ``<filter>`` tags works in outputs. Commit: 3b4ffc2565d8cb776d96b6540afe9aeaeb5b6792 https://github.com/galaxyproject/galaxy/commit/3b4ffc2565d8cb776d96b6540afe… Author: pvanheus <pvh(a)sanbi.ac.za> Date: 2018-10-07 (Sun, 07 Oct 2018) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Fix missing ] Commit: 12929f9acb0bed7373f1e600b90f4d3b917612f0 https://github.com/galaxyproject/galaxy/commit/12929f9acb0bed7373f1e600b90f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-10-10 (Wed, 10 Oct 2018) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Merge pull request #6827 from pvanheus/patch-9 Clarify code used in output <filter> tags Compare: https://github.com/galaxyproject/galaxy/compare/f41128a946d1...12929f9acb0b **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] e22def: add new welcome page using BS4 cards
by GitHub 10 Oct '18

10 Oct '18

Branch: refs/heads/new-welcome Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: e22defcd57210d9035b1388a7ab5c0afeced60de https://github.com/galaxyproject/usegalaxy-playbook/commit/e22defcd57210d90… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-10-10 (Wed, 10 Oct 2018) Changed paths: M env/common/templates/galaxy/static/welcome.html.j2 Log Message: ----------- add new welcome page using BS4 cards **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] 6b62a5: Should fix bug Jen saw with history panel being ma...
by GitHub 10 Oct '18

10 Oct '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: 6b62a57047f8877ba36e0767aaee04879bbc20c0 https://github.com/galaxyproject/galaxy/commit/6b62a57047f8877ba36e0767aaee… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-08 (Mon, 08 Oct 2018) Changed paths: M client/galaxy/style/scss/base.scss M static/style/blue/base.css Log Message: ----------- Should fix bug Jen saw with history panel being masked at bottom Commit: cd62461e8486bd4e44aee51907f7d515718ef3d8 https://github.com/galaxyproject/galaxy/commit/cd62461e8486bd4e44aee51907f7… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-10-10 (Wed, 10 Oct 2018) Changed paths: M client/galaxy/style/scss/base.scss M static/style/blue/base.css Log Message: ----------- Merge pull request #6839 from dannon/unified-panel-style-tweaks [18.09] Unified panel style bottom padding fix Compare: https://github.com/galaxyproject/galaxy/compare/a43a60656a49...cd62461e8486 **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] 6c580b: Updated volume kwds.
by GitHub 10 Oct '18

10 Oct '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 6c580b8c9d3b8ea509873683dba2a5d347017f03 https://github.com/galaxyproject/galaxy/commit/6c580b8c9d3b8ea509873683dba2… Author: thobalose <lose.thoba(a)gmail.com> Date: 2018-10-09 (Tue, 09 Oct 2018) Changed paths: M config/plugins/interactive_environments/bam_iobio/templates/bam_iobio.mako M config/plugins/interactive_environments/hicbrowser/templates/hicbrowser.mako M config/plugins/interactive_environments/neo/templates/neo.mako Log Message: ----------- Updated volume kwds. Commit: f41128a946d14cc7e45fc7f97c7368652bbfd49c https://github.com/galaxyproject/galaxy/commit/f41128a946d14cc7e45fc7f97c73… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-10-10 (Wed, 10 Oct 2018) Changed paths: M config/plugins/interactive_environments/bam_iobio/templates/bam_iobio.mako M config/plugins/interactive_environments/hicbrowser/templates/hicbrowser.mako M config/plugins/interactive_environments/neo/templates/neo.mako Log Message: ----------- Merge pull request #6840 from thobalose/volume Updated volume kwds. Compare: https://github.com/galaxyproject/galaxy/compare/c9b037923095...f41128a946d1 **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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