we are running our own local galaxy service in a multi-user environment at version 21.09 currently.
We want to use the following setup to allow user import of data:
a mounted network drive at:
our galaxy is installed at
/.../galaxy/ and config/galaxy.yml has set:
/.../galaxy/database/files/ we created a symlink to the mounted network share:
firstname.lastname@example.org -> /galaxy-clients/user1
now if we try to upload data to a data library from user directory for user1 we receive the error:
The specified directory does not exist [/.../email@example.com.].
The mounted drive is accessible by the user thats running the galaxy process, following the symlink to the mount is working fine.
The exact same setup with only change of a symlink email-address pointing to a directory simply on the machine instead of a mounted share is working fine.
The same setup using an older galaxy instance of version 19.01 is working fine.
We are quite at a loss why its not working, maybe someone of you has encountered a similar problem?
I’ve asked our administrative group for help at their chat. They may reply here or there, and feel free to join the chat in either of these:
You might have seen these resources already, but for reference:
Let’s start there
I’ve recreated pretty much your exact setup locally and I’m unable to reproduce the error. Is
/.../ just a collapsing of a real path? If so, can you verify that there are no typos in there? If not, I actually tested with that as a path and could not reproduce the issue:
$ tree /...
└── firstname.lastname@example.org -> /galaxy-clients/nate-test
4 directories, 0 files
$ tree /galaxy-clients
1 directory, 1 file
Importing as my
email@example.com user works in this scenario using the latest 21.09 (
Unrelated to the problem, but if
/.../galaxy/database/files is really the
database/files directory in your Galaxy server clone, this is not a good path to use for this purpose. Although newer Galaxy servers store datasets in
files dir is the default for older installations. The
user_library_import_dir can be anywhere (especially since you’re just symlinking from it), preferably outside the Galaxy clone entirely.
Hi, thank you for looking into it!
Yes the /…/ is just a collapsed normal path.
I have moved the user import dir to just
/data/galaxy_upload and the galaxy installation at
/srv/galaxy and unfortunately also with a symlink in
/firstname.lastname@example.org -> /galaxy-clients/user1 i get the same error.
I tried mounting something else to make sure its not just this one specific mount and if I point the symlink to
/mnt/home/tux without having it in the allow_list i get the apropriate error
directory (/email@example.com/.) is a symlink to a location not on the allowlist
After adding it to the allow_list i no longer receive an error and can import data from the symlink-ed mountpoint.
So in conclusion I think it must have something to do with how the mountpoint at /galaxy-clients is set up on our system, if other mountpoints work just fine.