Installed bowtie2 from the toolshed, which brings in package_bowtie_2_2_4,
which downloads bowtie binaries from depot.galaxyproject.org
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.
The future of medicine, today.
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