[Bioclusters] Bioinformactic Roll for NPACI Rock

mason j. katz mason.katz at gmail.com
Thu Jul 7 13:43:13 EDT 2005


There were some Roll API changes from Rocks 3.3.0 to Rocks 4.0.0 so I  
would expect it not to install.  The BioBrew developers need to spin  
a new version for Rocks 4.0.0.

The specifics are (this is for Glen):  The graph itself has changed  
so the entry point may need to be modified for the new graph  
structure.  Also both the nodes and graph xml files have a line at  
the top that says @GRAPH_DTD@ or @KICKSTART_DTD@ this entire line  
needs to be removed for the new XML parser to work.  We had these in  
as placeholders and never used them, unfortunately the new XML engine  
breaks with them.  Also Glen, we are thinking more about a bioroll  
for Rocks we should talk about the future of BioBrew, give me a call  
sometime.

     -mjk

On Jul 6, 2005, at 07:00 p, Alan Ng wrote:

> Has anyone tried inserting the Biobrew-3.3 roll on Rocks 4.0. Would  
> be a
> nice stop-gap measure for some bioinformatics clusters we're  
> running if
> it works
>
> "Leadership & Life-long Learning"
>
> Alan Ng
> Assistant Manager, Systems
> Linux Certified Professional
> Open Source Systems Sdn Bhd
> www.aldrix.net  Tel: 6 03-8656 0139   Fax: 6 03-8656 0132
>
> -------------------------------------------
>
> "Carpe Diem: Seize the Day!!"
>
>
>
> Glen Otero wrote:
>
>
>> BioBrew rolls for x86 and x86_64 are available for Rocks-3.3. Rolls
>> for Rocks-4.0 are not available yet. The rolls contains BLAST,
>> mpiBLAST, HMMER, EMBOSS, ClustalW, Gromacs, wise, and Phylip
>> applications, among others. The main website is biobrew.org.
>>
>> Glen
>>
>> On Jul 1, 2005, at 7:00 AM, Kurata Sung wrote:
>>
>>
>>> Hello
>>>
>>>      I study faculty of Computer Engineer at Kasetsart
>>> University,Bangkok Thailand.
>>>      I want information with bioinformatics roll on NPACI rock
>>> because my project do this.
>>>         - What have bioinformatics roll on NPACI rock ?(example :
>>> biobrew(This is only bioinformatics  roll on NPACI rock which I can
>>> find from Internet))
>>>
>>> Thank you very much
>>>
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>>> _______________________________________________
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>>>
>>
>> _______________________________________________
>> Bioclusters maillist  -  Bioclusters at bioinformatics.org
>> https://bioinformatics.org/mailman/listinfo/bioclusters
>>
>
>
> <alan.vcf>
> _______________________________________________
> Bioclusters maillist  -  Bioclusters at bioinformatics.org
> https://bioinformatics.org/mailman/listinfo/bioclusters
>



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