Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 9c81089ed1c9d5c434ecb991be8fd542bbe3c75e https://github.com/galaxyproject/galaxy/commit/9c81089ed1c9d5c434ecb991be8fd... Author: Luca Pireddu <pireddu@crs4.it> Date: 2018-10-17 (Wed, 17 Oct 2018) Changed paths: M lib/galaxy/jobs/runners/kubernetes.py Log Message: ----------- Catch IOErrors when the k8s runner tries to collect job logs This commit should fix cases where successful job can't be marked as done by Galaxy because the logs have gone missing. Commit: ac7c2d0473d09e8a3b4b39734527a383835478ab https://github.com/galaxyproject/galaxy/commit/ac7c2d0473d09e8a3b4b39734527a... Author: Luca Pireddu <pireddu@crs4.it> Date: 2018-10-17 (Wed, 17 Oct 2018) Changed paths: M lib/galaxy/jobs/runners/kubernetes.py Log Message: ----------- Print full job object to the DEBUG log if k8s runner finds it in an unrecognized state Commit: cd6c4d4db8bcb72ae931797c216b9829313850cf https://github.com/galaxyproject/galaxy/commit/cd6c4d4db8bcb72ae931797c216b9... Author: Luca Pireddu <pireddu@crs4.it> Date: 2018-10-22 (Mon, 22 Oct 2018) Changed paths: M lib/galaxy/jobs/runners/kubernetes.py Log Message: ----------- Add job id to missing k8s log text Commit: c434c271598d95130439ac86c8b9060f42455e9a https://github.com/galaxyproject/galaxy/commit/c434c271598d95130439ac86c8b90... Author: Luca Pireddu <pireddu@gmail.com> Date: 2018-10-26 (Fri, 26 Oct 2018) Changed paths: M lib/galaxy/jobs/runners/kubernetes.py Log Message: ----------- Improve k8s runner debug log message Commit: e235343f7674a5b74a707a693e94b80633d1ca2b https://github.com/galaxyproject/galaxy/commit/e235343f7674a5b74a707a693e94b... Author: Luca Pireddu <pireddu@crs4.it> Date: 2018-10-26 (Fri, 26 Oct 2018) Changed paths: M lib/galaxy/jobs/runners/kubernetes.py Log Message: ----------- Push k8s log IOError handling into `__produce_log_file` Handling the IOError within the function should result in other call sites within the kubernets.py module properly setting the job state even if the job directory has been removed. Commit: cf02c9812759505d61f284d6d33ee9ce2dc994e8 https://github.com/galaxyproject/galaxy/commit/cf02c9812759505d61f284d6d33ee... Author: Luca Pireddu <pireddu@crs4.it> Date: 2018-10-26 (Fri, 26 Oct 2018) Changed paths: M lib/galaxy/jobs/runners/kubernetes.py Log Message: ----------- Prefer `with open` syntax within kubernetes.py Commit: c13da94fd75d4b0010e4e3284649366c213a205d https://github.com/galaxyproject/galaxy/commit/c13da94fd75d4b0010e4e32846493... Author: Luca Pireddu <pireddu@crs4.it> Date: 2018-10-26 (Fri, 26 Oct 2018) Changed paths: M lib/galaxy/jobs/runners/kubernetes.py Log Message: ----------- Fix inverted log message arguments Thanks @pcm32! Commit: 4dce069209c4da228629e7dddfbeda836098aedc https://github.com/galaxyproject/galaxy/commit/4dce069209c4da228629e7dddfbed... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-10-29 (Mon, 29 Oct 2018) Changed paths: M doc/source/releases/18.09_announce.rst Log Message: ----------- Adjust code block to try to fix release doc formatting -- I hate RST Commit: cea9521b1a0194c93c5e2bf7b7f02fa88bd2c0b9 https://github.com/galaxyproject/galaxy/commit/cea9521b1a0194c93c5e2bf7b7f02... Author: Nate Coraor <nate@bx.psu.edu> Date: 2018-10-29 (Mon, 29 Oct 2018) Changed paths: M doc/source/releases/18.09_announce.rst Log Message: ----------- Merge pull request #6938 from dannon/codeblock_formatting [18.09] Release announce codeblock formatting fix Commit: 1482cacee51a9fd91f65d54704c7bc36120f3a34 https://github.com/galaxyproject/galaxy/commit/1482cacee51a9fd91f65d54704c7b... Author: Marius van den Beek <m.vandenbeek@gmail.com> Date: 2018-10-30 (Tue, 30 Oct 2018) Changed paths: M lib/galaxy/jobs/runners/kubernetes.py Log Message: ----------- Merge pull request #6886 from ilveroluca/fix/k8s_error_handling Improve k8s job error handling Commit: 49d9409f007dfe6288de4d6a2c0e15a4b45af022 https://github.com/galaxyproject/galaxy/commit/49d9409f007dfe6288de4d6a2c0e1... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-10-30 (Tue, 30 Oct 2018) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Bam index is only available for coordinate sorted bam files Commit: 4c7ba6f0fe4a99c1324f70785d27b655ac8b5538 https://github.com/galaxyproject/galaxy/commit/4c7ba6f0fe4a99c1324f70785d27b... Author: John Chilton <jmchilton@gmail.com> Date: 2018-10-30 (Tue, 30 Oct 2018) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Merge pull request #6946 from mvdbeek/bam_index_for_coordinate_sorted_only [18.09] Make Bam index only available for coordinate sorted bam files Commit: b47efd4adedb781056423bda4112a5b46a72489b https://github.com/galaxyproject/galaxy/commit/b47efd4adedb781056423bda4112a... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2018-10-31 (Wed, 31 Oct 2018) Changed paths: M doc/source/releases/18.09_announce.rst M lib/galaxy/datatypes/binary.py M lib/galaxy/jobs/runners/kubernetes.py Log Message: ----------- Merge branch 'release_18.09' into dev Compare: https://github.com/galaxyproject/galaxy/compare/17efac853ad1...b47efd4adedb **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.