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-li...
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.
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