In this case the code change is straightforward and doesn't require any
change to Bio::Tools::Run::RemoteBlast. The constructor can take a
URL_BASE argument, so just pass in the new URL (http://blast.ncbi.nlm.nih.gov/Blast.cgi).
This will overwrite the old URL (http://www.ncbi.nlm.nih.gov/blast/Blast.cgi)
hard-coded in Bio::Tools::Run::RemoteBlast. We made this change to the
remote BLAST components in the Pipeline Pilot Sequence Analysis collection
and things have been fine.
my @parameters = ("-prog" => $program,
"-data" => $database,
"-readmethod" => 'xml',
"-URL_BASE" => $url);
my $blastFactory = Bio::Tools::Run::RemoteBlast->new(@parameters);
Hope this helps.
Scott Markel, Ph.D.
Principal Bioinformatics Architect email: [email protected]
Accelrys (Pipeline Pilot R&D) mobile: +1 858 205 3653
5005 Wateridge Vista Drive voice: +1 858 799 5603
San Diego, CA 92121 fax: +1 858 799
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From: [email protected]
[mailto:[email protected]] On Behalf Of Jason Stajich
Sent: Wednesday, 14 May 14 2014 7:49 AM
To: Jolyon Holdstock
Cc: [email protected]
Subject: Re: [Bioperl-l] remoteblast
So the BLAST services changed - not sure if we will still even support perl
based - it will require a developer tracking and testing to the new NCBI
resources since the have discontinued the older submission CGI resource.
You can run remote blast with commandline tool from NCBI as an alternative.
I think we will need to have a developer volunteer who wants to keep
working on tracking the webservices for NCBI to keep this module working.
On Thu, May 8, 2014 at 8:34 AM, Jolyon Holdstock
> I have a script that runs blast jobs against the databases at the NCBI.
> I use the Bio::Tools::Run::RemoteBlast module for the blasting.
> It was working but is not now.
> The following is an example of the response I now get:
> --------------------- WARNING ---------------------
> MSG: req was POST http://www.ncbi.nlm.nih.gov/blast/Blast.cgi
> User-Agent: bioperl-Bio_Tools_Run_RemoteBlast/1.006901
> Content-Length: 788
> Content-Type: application/x-www-form-urlencoded
> An Error Occurred
An Error Occurred
301 Moved Permanently
> Can anyone suggest a fix?
> Dr. Jolyon Holdstock,
> Oxford Gene Technology
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