[BioBrew Users] Biobrew roll

[Glen Otero]

Humberto-

Thanks for testing the biobrew roll! I thought we took care of the  
FASTA installation problem, but I guess we'll have to look into it.  
It's likely an error in the biobrew.xml file.

When you make the changes to setting the MODULEPATH that you mention,  
can you then launch jobs with SGE?

Thanks!

Glen

On Aug 30, 2004, at 10:37 AM, Humberto Ortiz Zuazaga wrote:

> 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.
>
>
>
Glen Otero, Ph.D.
Linux Prophet
619.917.1772