[BioBrew Users] Biobrew roll

[Glen Otero]

Can you send me the contents of the 
/home/install/profiles/3.1.0/nodes/biobrew.xml file? The contents of 
this file ( ) should look something like this:

<?xml version="1.0" standalone="no"?>
<!DOCTYPE kickstart SYSTEM "@KICKSTART_DTD@">

<kickstart>


         <description>
         Callident BioBrew
         </description>

         <copyright>

         </copyright>

         <changelog>
         </changelog>

<!-- There may be as many packages as needed here. -->
         <package roll="biobrew">clustalw-1.8.1</package>
         <package roll="biobrew">clustalw-1.8.2</package>
         <package roll="biobrew">clustalw-1.8.3</package>
         <package roll="biobrew">EMBOSS</package>
         <package roll="biobrew">Fasta</package>
         <package roll="biobrew">hmmer</package>
         <package roll="biobrew">ncbitools</package>
         <package roll="biobrew">wise</package>

         <package roll="biobrew">fftw</package>
         <package roll="biobrew">gromacs</package>
         <package roll="biobrew">lam</package>

         <package roll="biobrew">wwwblast</package>
         <package roll="biobrew">sgeblast</package>

         <package roll="biobrew">farmtools</package>
         <package roll="biobrew">modulefiles</package>

</kickstart>

There's probably a syntax error around the Fasta tag, or it's missing 
all together.

Glen

On Sep 7, 2004, at 11:02 AM, Palidwor, Gareth wrote:

>
> 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
>
> _______________________________________________
> BioBrew-Users mailing list
> BioBrew-Users at bioinformatics.org
> https://bioinformatics.org/mailman/listinfo/BioBrew-Users
>
>
>
Glen Otero, Ph.D.
Linux Prophet
619.917.1772