[BioBrew Users] Re: BioBrew-Users digest, Vol 1 #55 - 2 msgs
Glen Otero
gotero at linuxprophet.com
Wed Sep 8 13:28:06 EDT 2004
Gareth-
Is the Fasta rpm in the repository? Can you find it under
/home/install/rocks-dist/enterprise/3/en/os/i386/RedHat/RPMS? If not,
then the rpm didn't make it into the build for some reason, which is
puzzling...If that is the case, then:
1) remove the line containing the Fasta tag in the biobrew.xml file
2) cd to /home/install
3) rm -f rocks-dist
4) rocks-dist dist
5) reinstall compute nodes
This should take care of the installation problem, but the Fasta
package won't be installed. If you would like to install the Fasta
package, then:
1) do not remove the line containing the Fasta tag in the biobrew.xml
file
2) download the Fasta-3.4-1.cld.i386.rpm from
http://ftp.bioinformatics.org/pub/biobrew/rpms/ and place it in
/home/install/rocks-dist/enterprise/3/en/os/i386/RedHat/RPMS
3) install the Fasta package on the head node:
rpm -ivh
/home/install/rocks-dist/enterprise/3/en/os/i386/RedHat/RPMS/Fasta-3.4
-1.cld.i386.rpm
4) cd to /home/install
5) rm -f rocks-dist
6) rocks-dist dist
7) reinstall compute nodes
Glen
On Sep 8, 2004, at 9:46 AM, Palidwor, Gareth wrote:
> Glen:
>
> Requested file appended below. I've mailed this directly to you to as
> requested.
>
> Mine looks pretty much identical to yours...
>
> gp
>
>
> [root at frontend-0 /]# cat /home/install/profiles/3.1.0/nodes/biobrew.xml
> <?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>
>
>
> Message: 2
> From: Glen Otero <gotero at linuxprophet.com>
> Subject: Re: [BioBrew Users] Biobrew roll
> Date: Tue, 7 Sep 2004 17:06:33 -0700
> To: BioBrew-Users at bioinformatics.org
> Reply-To: BioBrew-Users at bioinformatics.org
>
> 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
>
>
>
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> BioBrew-Users at bioinformatics.org
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>
>
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>
>
>
Glen Otero, Ph.D.
Linux Prophet
619.917.1772
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