From 22489a721e9388b0f516f45c842129d6471b4cde Mon Sep 17 00:00:00 2001 From: Martin Cech Date: Wed, 24 Jan 2018 09:47:22 -0500 Subject: [PATCH] add generated sample --- config/galaxy.yml.sample | 29 ++++++++++++++++------------- 1 file changed, 16 insertions(+), 13 deletions(-) diff --git a/config/galaxy.yml.sample b/config/galaxy.yml.sample index 086b2f5667d..2fa325d812c 100644 --- a/config/galaxy.yml.sample +++ b/config/galaxy.yml.sample @@ -1511,11 +1511,14 @@ galaxy: # is 5MB, but as low as 1MB seems to be a reasonable size. #max_metadata_value_size: 5242880 - # If (for example) you run on a cluster and your datasets (by default, - # database/files/) are mounted read-only, this option will override - # tool output paths to write outputs to the working directory instead, - # and the job manager will move the outputs to their proper place in - # the dataset directory on the Galaxy server after the job completes. + # This option will override tool output paths to write outputs to the + # job working directory (instead of to the file_path) and the job + # manager will move the outputs to their proper place in the dataset + # directory on the Galaxy server after the job completes. This is + # necessary (for example) if jobs run on a cluster and datasets can + # not be created by the user running the jobs (e.g. if the filesystem + # is mounted read-only or the jobs are run by a different user than + # the galaxy user). #outputs_to_working_directory: false # If your network filesystem's caching prevents the Galaxy server from @@ -1547,27 +1550,27 @@ galaxy: #cleanup_job: always # When running DRMAA jobs as the Galaxy user - # (https://galaxyproject.org/admin/config/performance/cluster - # /#submitting-jobs-as-the-real-user) this script is used to run the + # (https://docs.galaxyproject.org/en/latest/admin/cluster.html + # #submitting-jobs-as-the-real-user) this script is used to run the # job script Galaxy generates for a tool execution. #drmaa_external_runjob_script: sudo -E scripts/drmaa_external_runner.py --assign_all_groups # When running DRMAA jobs as the Galaxy user - # (https://galaxyproject.org/admin/config/performance/cluster - # /#submitting-jobs-as-the-real-user) this script is used to kill such + # (https://docs.galaxyproject.org/en/latest/admin/cluster.html + # #submitting-jobs-as-the-real-user) this script is used to kill such # jobs by Galaxy (e.g. if the user cancels the job). #drmaa_external_killjob_script: sudo -E scripts/drmaa_external_killer.py # When running DRMAA jobs as the Galaxy user - # (https://galaxyproject.org/admin/config/performance/cluster - # /#submitting-jobs-as-the-real-user) this script is used transfer + # (https://docs.galaxyproject.org/en/latest/admin/cluster.html + # #submitting-jobs-as-the-real-user) this script is used transfer # permissions back and forth between the Galaxy user and the user that # is running the job. #external_chown_script: sudo -E scripts/external_chown_script.py # When running DRMAA jobs as the Galaxy user - # (https://galaxyproject.org/admin/config/performance/cluster - # /#submitting-jobs-as-the-real-user) Galaxy can extract the user name + # (https://docs.galaxyproject.org/en/latest/admin/cluster.html + # #submitting-jobs-as-the-real-user) Galaxy can extract the user name # from the email address (actually the local-part before the @) or the # username which are both stored in the Galaxy data base. The latter # option is particularly useful for installations that get the