From 3fa5d9e1423746c05305922d7f7142c1a4174b79 Mon Sep 17 00:00:00 2001 From: M Bernt Date: Mon, 9 Sep 2019 13:58:17 +0200 Subject: [PATCH] Apply suggestions from code review Co-Authored-By: Nicola Soranzo --- doc/source/admin/cluster.md | 2 +- lib/galaxy/config/sample/galaxy.yml.sample | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/doc/source/admin/cluster.md b/doc/source/admin/cluster.md index 2ba43a21a14..e61bf49e451 100644 --- a/doc/source/admin/cluster.md +++ b/doc/source/admin/cluster.md @@ -330,7 +330,7 @@ Since this is a complex problem, the current solution does have some caveats: ### Configuration -You'll need to ensure that all datasets are stored on the filesystem such that they are readable by all users that will use Galaxy: either made readable by a group, or world-readable. If using a group, set your `umask(1)` to `027` or for world-readable, use `022` Setting the umask assumes your underlying filesystem uses POSIX permissions, so if this is not the case, your environment changes may be different. For uWSGI setups (which are the default since release 19.01) the default umask is set in galaxy.yml (with a default of `027`). +You'll need to ensure that all datasets are stored on the filesystem such that they are readable by all users that will use Galaxy: either made readable by a group, or world-readable. If using a group, set your `umask(1)` to `027` or for world-readable, use `022` Setting the umask assumes your underlying filesystem uses POSIX permissions, so if this is not the case, your environment changes may be different. For uWSGI setups (which are the default since release 19.01) the default umask is set in the `uwsgi:` section of `galaxy.yml` . The directory specified in `new_file_path` in the Galaxy config should be world-writable, cluster-accessible (via the same absolute path) and have its sticky bit (+t) set. This directory should also be cleaned regularly using a script or program as is appropriate for your site, since temporary files created here may not always be cleaned up under certain conditions. diff --git a/lib/galaxy/config/sample/galaxy.yml.sample b/lib/galaxy/config/sample/galaxy.yml.sample index 872eb530635..5193c9ca073 100644 --- a/lib/galaxy/config/sample/galaxy.yml.sample +++ b/lib/galaxy/config/sample/galaxy.yml.sample @@ -99,9 +99,9 @@ uwsgi: # On some systems uWSGI has a default umask of 000, for Galaxy a # somewhat safer default is chosen. If Galaxy submits jobs as real # user then all users needs to be able to read the files, i.e. - # the the umask needs to be 0o022 or the Galaxy users need to be in the + # the the umask needs to be '022' or the Galaxy users need to be in the # same group as the Galaxy system user - umask: 027 + umask: '027' galaxy: # The directory that will be prepended to relative paths in options