Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 22a565d1a25a5eda466d49b69df3c3ab436e8b82 https://github.com/galaxyproject/galaxy/commit/22a565d1a25a5eda466d49b69df3c... Author: John Chilton <jmchilton@gmail.com> Date: 2015-10-07 (Wed, 07 Oct 2015) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh Log Message: ----------- Try harder to verify script integrity before running job scripts. These "Text file busy" errors are occasionally encountered in the wild in production settings and more commonly when running Galaxy in Docker containers. Simply sycning the file system has proven insufficient to prevent the problem and I do not want to add an arbitrary sleep. So this new strategy is used. - Inject special functionality into each job script that when executed with a certain environment variable set causes the script to exit with a specific return code. - Have Galaxy rerun this script in that configuration until it can succeed in executing the script. - In between each iteration sleep for a small amount of time and try to cause a file system sync. This entire is ... insane ... so I have added a configuration option to disable it entirely check_job_script_integrity=False. Commit: c53aeaef7737ff897dd2a754b16a9e077273e776 https://github.com/galaxyproject/galaxy/commit/c53aeaef7737ff897dd2a754b16a9... Author: John Chilton <jmchilton@gmail.com> Date: 2015-10-07 (Wed, 07 Oct 2015) Changed paths: M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh Log Message: ----------- Simplify shell expression thanks to suggestion by @nsoranzo. Commit: a5e75e8bbe6e465327c7ef783e7236ea2e467b53 https://github.com/galaxyproject/galaxy/commit/a5e75e8bbe6e465327c7ef783e723... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2015-10-07 (Wed, 07 Oct 2015) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh Log Message: ----------- Merge pull request #865 from jmchilton/script_integrity Try harder to verify script integrity before running job scripts. Compare: https://github.com/galaxyproject/galaxy/compare/495e3db97fdc...a5e75e8bbe6e