Question: OMA Standalone 2.4.2: cannot write to .oma directory
1
gravatar for ed.eyles
12 days ago by
ed.eyles10
ed.eyles10 wrote:

I am a Linux system administrator supporting a scientist who is having problems with OMA. Our setup is an HPC cluster using the Slurm scheduler, with most application deployments being done via EasyBuild. The scientist got the following error when she tried to submit an OMA 2.1.1 job:

Darwin cannot open file /home/usern/easybuild/.oma//\ GOdata.drw-20210113 to write to: Permission denied

Here, /home/usern/easybuild is the home directory of the easybuild user. That user is the owner of all the executables installed via EasyBuild - including the oma executable. The scientist's user has no permissions to access the easybuild home directory.

She did find that a very similar issue was referred to in OMA error - download from gene ontology not working 404. That thread suggests that OMA had a problem that caused this, which was fixed in version 2.3.1. I therefore upgraded our OMA to the latest version, 2.4.2 - I deployed it using EasyBuild.

The scientist continued to get the same error, however. It was phrased very slightly differently:

Could not download Gene Ontology definitions: Darwin cannot open file /home/usern/easybuild/.oma/GOdata.drw-20210114 to write to: Permission denied

As a workaround, I have added the scientist's user to the group that owns the ~easybuild/.oma directory. OMA now seems to run for her. But this cannot be a permanent solution.

I am wondering whether the bug that was fixed in OMA 2.3.1 was regressed to in version 2.4.2? Failing that, is there any way to configure the download destination of the gene ontology definitions?

easybuild oma orthologs • 74 views
ADD COMMENTlink written 12 days ago by ed.eyles10

Hi ed,

thanks for pointing that out. It is unfortunately not the same problem than the one mentioned before. While installing, a path where to store some data files (like the GeneOntology hierachy) is set. However, this seems not to work in a multi-user setup, if the data is only loaded lazily by the user afterwards.

I'm checking the possible options. Would you mind getting in touch with me directly do maybe see what works best from a sys-admin point of view?

Best wishes Adrian

ADD REPLYlink written 6 days ago by adrian.altenhoff770

Thanks Adrian! I've sent you a direct e-mail about this.

Regards Ed

ADD REPLYlink written 5 days ago by ed.eyles10
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