[BioBrew Users] Biobrew roll

[Palidwor, Gareth]

I'm experiencing this problem with installing the biobrew roll
as well with rocks 3.1 as well. 
Glen Otero mentioned  that this is likely due to a bug in the
biobrew.xml 
file.  
Is there a fix available for this yet?
Can anyone tell me what is *not* being installed when this error
shows up?

Thanks 

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