[ensembl-dev] Newbie: Possible to use Condor instead of LSF with Blast?

[William Spooner]

Hi Bob,

Any reason why you want to submit blasts to a cluster rather than run in-line? The latter works well for Ensembl sites with a reasonable load, and is easy to configure in the DEFAULTS.ini file using the following;

[ENSEMBL_BLAST_METHODS]
; Registers BlastView methods. Key values are the
; Bio::Tools::Run::Search classes used to run the search
BLASTN  = wublastn
BLASTX  = wublastx
BLASTP  = wublastp
TBLASTN = wutblastn
TBLASTX = wutblastx 

If you want to use condor, then the public-plugins/sge_blast plugin might work with a few tweaks, although it's not been touched since I wrote it in 2005.

Will

On 7 Feb 2012, at 16:33, Giulietta wrote:

> Hello,
> 
> Apologies for the delay.
> Thanks for your message. We don't have experience with with systems other than LSF. I did talk with some of the developers on the project and they suggest that Lava might be sufficient, but as this hasn't been tested, we are unsure.
> 
> I hope this helps and best of luck with your project.
> 
> Regards,
> Giulietta
> 
> On 13/01/2012 10:23, Martin Steele wrote:
>> Hi All,
>> 
>> I notice from the file ${ENSEMBL_ROOT}/ctrl_scripts/start_server that an LSF installation is expected, i.e.:
>> 
>> # LOAD LSF ENVIRONMENT - REQUIRED FOR BLAST
>> my $cmd = ". /usr/local/lsf/conf/profile.lsf;" if -e '/usr/local/lsf/conf/profile.lsf';
>> 
>> I would like to use a different batch system if possible, namely Condor, and I notice that there's a company that offers such a service commercially, so it should be possible. However, I can't find any online resource describing how to perform the switch. Does anyone on this list know how to, and would they care to share the information?
>> 
>> Failing that, is Platform Lava (LSF's watered-down free version) a suitable alternative?
>> 
>> TIA,
>> Bob
>> 
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--
William Spooner
william.spooner at eaglegenomics.com
http://www.eaglegenomics.com