Hi David,
can you open an issue at
https://github.com/galaxyproject/docker-build ?


18.06.2015 21:55 David Trudgian ha scritto: 

> 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? 
> Cheers, 
> -- 
David Trudgian Ph.D. 
> Computational Scientist, BioHPC 
> UT
Southwestern Medical Center 
> Dallas, TX 75390-9039 
> Tel: (214)
> Please contact biohpc-help@utsouthwestern with general
BioHPC inquries. 
> -------------------------
> UT Southwestern 

> Medical Center 
> The future of medicine, today.

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