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.


________________________________

UT Southwestern


Medical Center



The future of medicine, today.

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