[BioBrew Users] Biobrew roll

[Humberto Ortiz Zuazaga]

I'm testing the biobrew roll with rocks 3.1

http://ftp.bioinformatics.org/pub/biobrew/BioBrew-v3.0/roll-biobrew-3.1.0-0.i38
6.iso

I installed Rocks 3.1 base and the biobrew, hpc, sge, java rolls.

When installing, each compute node complains that the Fasta package is 
selected for installation but not available, and I select continue.

After installation, sge jobs don't run, I get the following error in the 
standard error stream of each job:

Bad : modifier in $ (/).

Following some recommendations on the rocks mailing list archives, I think I 
found the problem:

/etc/profile.d/z-biomodules.csh has a line that reads:

setenv MODULEPATH $MODULEPATH:/opt/BioBrew/modulefiles

this line causes the error.

I think this file should read:

--
# Additional modules for biobrew
#

if ( ${?MODULEPATH} ) then
    setenv MODULEPATH "${MODULEPATH}:/opt/BioBrew/modulefiles"
else
    setenv MODULEPATH "/opt/BioBrew/modulefiles"
endif
--

See for example the rocks-pythonpath.csh script.


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