[Bioclusters] Bioinformactic Roll for NPACI Rock

[mason j. katz]

The guide is correct with the exception of the inclusion of the line:

<!DOCTYPE kickstart SYSTEM "@KICKSTART_DTD@">

in the node files, and a similar line in the graph files.  We still  
need to update this part of the documentation.  This is in section  
2.1.3.1.

     -mjk


On Jul 7, 2005, at 02:55 p, Glen Otero wrote:

> Folks-
>
> I'll start working on a new BioBrew roll for Rocks-4.0 when I get  
> back from vacation in two weeks. Hopefully, I'll have a new roll by  
> mid August.
>
> Mason--At what point in the steps detailed in the Roll developer's  
> guide will I need to apply the changes you mentioned to the graph  
> and nodes xml files?
>
> Glen
>
> On Jul 7, 2005, at 10:43 AM, mason j. katz wrote:
>
>
>> 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
>>>>>
>>>>> _________________________________________________________________
>>>>> Express yourself instantly with MSN Messenger! Download today it's
>>>>> FREE! http://messenger.msn.click-url.com/go/onm00200471ave/ 
>>>>> direct/01/
>>>>>
>>>>> _______________________________________________
>>>>> Bioclusters maillist  -  Bioclusters at bioinformatics.org
>>>>> https://bioinformatics.org/mailman/listinfo/bioclusters
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>
>>>> _______________________________________________
>>>> 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
>>>
>>>
>>>
>>
>> _______________________________________________
>> Bioclusters maillist  -  Bioclusters at bioinformatics.org
>> https://bioinformatics.org/mailman/listinfo/bioclusters
>>
>>
>>
>
> _______________________________________________
> Bioclusters maillist  -  Bioclusters at bioinformatics.org
> https://bioinformatics.org/mailman/listinfo/bioclusters
>