[BioBrew Users] Fixed modulefiles RPM or source?

Glen Otero glen at callident.com
Fri Oct 15 05:06:34 EDT 2004

On Oct 14, 2004, at 7:06 PM, Humberto Ortiz Zuazaga wrote:

> Glen Otero <gotero at linuxprophet.com> wrote:
>> I've attached the new modulefiles rpm. It includes the changes you
>> suggested. Let me know how it works for you. I'll build a new BioBrew
>> roll after I hear how it works.
>> Sorry again about the delay.
> No problem, we were testing on a fixed number of nodes, but just moved
> to a production system, which we're bringing online in parts. I keep
> forgetting to fix the z-biomodules.csh file and end up chasing strange
> bugs.
> There are a couple of problems with the new RPM.
> You need to increment the version or build number, it won't install the
> new one if it has the same version as the old one.
> You should also fix the z-biomodules.sh

Hmmm... The current one looks OK to me.
> # Additional modules for biobrew
> #
> export MODULEPATH=${MODULEPATH:+$MODULEPATH:}/opt/BioBrew/modulefiles

This syntax looks a little weird to me. Shouldn't this read:

> export MODULEPATH=${MODULEPATH:+$MODULEPATH}:/opt/BioBrew/modulefiles
(with the colon outside the braces)?

In any case, I put the above line in the file and commented out the 
original. I've attached the rpm and the SRPM in case you need to make 
further changes. Just look under modulefiles/profile.d/ in the source 
> The module files aren't actually being used, are they? I have none of
> the bioinformatics tools in my path, and can't run EMBOSS programs
> (library problems, ACD problems), because the environment isn't set up
> for EMBOSS.

ACD problems?

Modules doesn't put the apps in your execution path automatically. They 
are be used to switch between multiple versions of an application. 
That's why they're not much use right now, because there is only on 
version of BLAST, etc. in BioBrew (ClustalW may have a few versions). 
But in the future, when new versions are added or built with different 
compilers or mpi layers, then modulefiles will be very helpful. The 
modulefiles are there, but it's up to the user to actually use them. 
I'll forward you some references on modules once I dig them up.
> The modulefiles rpm has no documentation, so I can't figure out if I
> broke something. How do the modulefiles work? I'm willing to write up
> some of them if you'll tell me how (EMBOSS has no modulefile).

I'll dig out my modulefile notes and put a few examples together next 
chance I get.


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> -- 
> Humberto Ortiz Zuazaga
> Programmer-Archaeologist
> High Performance Computing facility
> University of Puerto Rico
> http://www.hpcf.upr.edu/~humberto/
Glen Otero, Ph.D.
Linux Prophet

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