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:
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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