[ensembl-dev] [Hinxton #262456] How to make blast results be parsed?

[Anne Parker]

Hi Wally

I'm afraid we can't offer support on running BLAST with a queueing system at the moment. We are in the process of rewriting our BLAST application to make it much more modular, and hope to release something later this year, but at the moment the code is too closely tied to the setup we have at Sanger.

Sorry not to be of more help.

Cheers

Anne

On 23 Apr 2012, at 04:28, 邱艦瑩 via RT wrote:

> Hi Anne,
> 
> I got it, but I found "ncbiblast" is run locally. How can I do If I want to
> make it run on queuing system e.g. LSF?
> 
> 
> Sincerely,
> Wally
> 
> On Thu, Apr 19, 2012 at 9:15 PM, Anne Parker via RT <
> ensembl-webteam at sanger.ac.uk> wrote:
> 
>> On Thu Apr 19 09:10:56 2012, godinn66 at gmail.com wrote:
>>> Hello Mr. / Miss,
>>> 
>>> I have setup a local Ensembl server and I want to enable blast search.
>>> I tried to configure blast following the instructions in:
>>> http://www.ensembl.org/info/docs/webcode/install/blast.html
>>> 
>>> I found that I can get final results if I use "ncbiblastn" as blast
>> method.
>>> However, the status is always "parsing" and can't get the blast results
>>> display page when I used "ensembl_wublastn"as blast method. (I can
>>> get the blast raw results). I tried to trace the code
>>> in Bio::Tools::Run::Search
>>> , but I can't fine anywhere about doing the parsing. Could you help me
>>> to make the results be parsed? BTW, which method do you use in your
>>> blast?
>> 
>> Hi Wally
>> 
>> I'm afraid that wublast is no longer available as a downloadable binary,
>> so we
>> cannot support it for external installations. I recommend that you stick
>> with
>> ncbiblast, although it will of course return slightly different results.
>> 
>> Regards
>> 
>> Anne
>> 
>> --
>> 
>> 
>> Anne Parker
>> Ensembl Web Production Manager
>> 
>> --
>> Ticket Details <URL:
>> https://rt.sanger.ac.uk/SelfService/Display.html?id=262456 >
>> 
>> 
>> --
>> The Wellcome Trust Sanger Institute is operated by Genome Research
>> Limited, a charity registered in England with number 1021457 and a
>> company registered in England with number 2742969, whose registered
>> office is 215 Euston Road, London, NW1 2BE.
>> 
> 
> -- 
> Ticket Details <URL: https://rt.sanger.ac.uk/SelfService/Display.html?id=262456 >

Anne Parker
Ensembl Web Production Manager
http://www.ensembl.org