[Biodevelopers] Is it source available for blastall

[Abhik Shah]

Looks like you already found your answer but for future reference, you can
download the source code for blast at
ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools/ncbi.tar.gz

It includes the NCBI Toolbox and tools (including Blast 2.0.x)..

As for .ncbirc, you put it in your home directory or the directory where
the blastall executable is located.  The file is described in the NCBI
Tools Readme file (ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools/README)..
search for the "CONFIGURATION OR SETTINGS FILES" section of the file..


abhik.

On Wed, 9 Oct 2002, Bala wrote:

> Hi Joe,
>        Thanks for the information,
> I found out the solution for that command
> line parameter problem, the command I am
> trying to run is
>
> #blastall -p blastp -d /usr/local/sge/db/pataa -i
> /usr/local/sge/QUERY -M /usr/local/sge/db/BLOSUM62
>
> the solotion is, instead of giving the matrix path
> in the command line, set the enviroinment variable
> "BLASTMAT".
>
>   I didn't find .ncbirc file in my stand allown blast
> download from NCBI site, can you give me some info
> regrading .ncbirc file content and where to
> put(location) of the file.
>
> Thanks,
> Bala.
>
>
>
>
>
> --- Joe Landman <landman at scalableinformatics.com>
> wrote:
> > Hi Bala:
> >
> >   Look on http://www.ncbi.nlm.nih.gov for the BLAST
> > (standalone) bit.
> >
> >   It looks to me like you may have some command line
> > parameter problems,
> > or problems with you .ncbirc file.  The data.tar.Z
> > file on the ftp site
> > contains the scoring matrices, and the tarball
> > contains the code.
> >
> >   What are you running, including the complete
> > command line?
> >
> > Joe
> >
> > On Wed, 2002-10-09 at 22:05, Bala wrote:
> > > Hi All,
> > >         I am new to this list,
> > > I wondering is it source available
> > > for blastall executable from NCBI site.
> > > I am getting some error with the one
> > > of the parameter(Matrix value) to
> > > blastall.
> > >
> > >    If that default file BLOSUM62 is
> > > available locally, then it is working,
> > > if I am running from some other location
> > > and specifing that file location, then it
> > > is giving error.
> > >
> > > [blastall] ERROR: gi|532319|pir|TVFV2E|TVFV2E:
> > > BlastKarlinBlkGappedCalc: test/BLOSUM62 is not a
> > > supported matrix
> > >
> > > any suggestion! help!
> > >
> > > -bala-
> > >
> > > __________________________________________________
> > > Do you Yahoo!?
> > > Faith Hill - Exclusive Performances, Videos & More
> > > http://faith.yahoo.com
> > > _______________________________________________
> > > Biodevelopers mailing list
> > > Biodevelopers at bioinformatics.org
> > >
> >
> https://bioinformatics.org/mailman/listinfo/biodevelopers
> > --
> > Joseph Landman, Ph.D
> > email: landman at scalableinformatics.com
> > web  : http://scalableinformatics.com
> > phone: +1 734 612 4615
> >
> > _______________________________________________
> > Biodevelopers mailing list
> > Biodevelopers at bioinformatics.org
> >
> https://bioinformatics.org/mailman/listinfo/biodevelopers
>
>
> __________________________________________________
> Do you Yahoo!?
> Faith Hill - Exclusive Performances, Videos & More
> http://faith.yahoo.com
> _______________________________________________
> Biodevelopers mailing list
> Biodevelopers at bioinformatics.org
> https://bioinformatics.org/mailman/listinfo/biodevelopers
>