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.