Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: 02410b270d025e5fb8cb4e2036fb627051c7850a https://github.com/galaxyproject/galaxy/commit/02410b270d025e5fb8cb4e2036fb6... Author: mvdbeek <m.vandenbeek@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: 5844bdc7aa0a90d992c3b36e041abb8d103e3b95 https://github.com/galaxyproject/galaxy/commit/5844bdc7aa0a90d992c3b36e041ab... Author: mvdbeek <m.vandenbeek@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/57a1f19b069597bde97852b3e0d0a... Author: mvdbeek <m.vandenbeek@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/fc28e0bd83a2df59f11b80f0119e6... Author: mvdbeek <m.vandenbeek@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/5e12e509bf20d7e4f4464a60f04c7... Author: mvdbeek <m.vandenbeek@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/b08c6219c3fe771e00d0b6d8b9adb... Author: mvdbeek <m.vandenbeek@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/ac3e1ca1d0d7bb85cc00e2e113f70... Author: Nicola Soranzo <nicola.soranzo@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: a1f7634fd7dca45902a2d3f67d2279db3aa2270d https://github.com/galaxyproject/galaxy/commit/a1f7634fd7dca45902a2d3f67d227... Author: thobalose <lose.thoba@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/fe6c1738c0ea3ee35fa34fec8a2c2... Author: Dannon <dannon.baker@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 Commit: fd0b24ecd2bff2f8baa636304e45eb2dbdcaf3a9 https://github.com/galaxyproject/galaxy/commit/fd0b24ecd2bff2f8baa636304e45e... Author: Dannon <dannon.baker@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 Commit: baa992d217032b809d321cb800cd2f41af401c63 https://github.com/galaxyproject/galaxy/commit/baa992d217032b809d321cb800cd2... Author: Nate Coraor <nate@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 Commit: a8fa5a1d4a6c801fc230c037129671978955916c https://github.com/galaxyproject/galaxy/commit/a8fa5a1d4a6c801fc230c03712967... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2018-10-12 (Fri, 12 Oct 2018) Changed paths: M lib/galaxy/util/monitors.py Log Message: ----------- Merge branch 'release_18.01' into release_18.05 Commit: d22f652f918f7a49d80ede8652d335d41c478546 https://github.com/galaxyproject/galaxy/commit/d22f652f918f7a49d80ede8652d33... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2018-10-12 (Fri, 12 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 M lib/galaxy/jobs/runners/util/cli/shell/local.py M lib/galaxy/jobs/runners/util/cli/shell/rsh.py M lib/galaxy/util/monitors.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 branch 'release_18.05' into release_18.09 Compare: https://github.com/galaxyproject/galaxy/compare/2c14c2afc4d3...d22f652f918f **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.