Installed bowtie2 from the toolshed, which brings in package_bowtie_2_2_4, 
which downloads bowtie binaries from

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?


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.


UT Southwestern

Medical Center

The future of medicine, today.

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