Installed bowtie2 from

Hi David, can you open an issue at https://github.com/galaxyproject/docker-build ? Thanks, Nicola Il 18.06.2015 21:55 David Trudgian ha scritto: 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.

-------------------------

UT Southwestern

Medical Center

The future of medicine, today.

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