Installed bowtie2 from the toolshed, which brings in package_bowtie_2_2_4, which downloads bowtie binaries from depot.galaxyproject.org

 

http://depot.galaxyproject.org/package/linux/x86_64/bowtie2/bowtie2-2.2.4-linux-x86_64.tgz

 

Jobs submitted on our setup, running as a ‘real user’ (not galaxy user) via pulsar + SLURM fail with a permissions error. This is due to the permissions on some of the bowtie executables in the .tar.gz from depot being owner/group executable only. Other users cannot run bowtie2:

 

-rwxrwx---. 1 galaxy galaxy  18K Oct 22  2014 bowtie2

 

If I download the tar.gz from depot manually and extract then I get:

 

-rwxrwx--- 1 dtrudgian biohpc_admin  18K Oct 22  2014 bowtie2

 

Could the .tar.gz be fixed, so that the executables will work in a run as real user configuration? Is there any sensible way Galaxy could enforce permissions to guard against this issue?

 

Cheers,

 

--

David Trudgian Ph.D.

Computational Scientist, BioHPC

UT Southwestern Medical Center

Dallas, TX 75390-9039

Tel: (214) 648-4833

 

Please contact biohpc-help@utsouthwestern with general BioHPC inquries.