[Bioclusters] NCBI rpm?

Joe Landman bioclusters@bioinformatics.org
Wed, 18 Feb 2004 16:44:42 -0500

On Wed, 2004-02-18 at 14:38, Dan Bolser wrote:
> Hello, 
> I want to quickly find a sequence for a list of sequence id's, so I
> thought I would use formatdb to index the fasta format database and then
> use the sequence retreival tool to query this index.
> Is formatdb included in the NCBI rpm available from 
> http://downloads.scalableinformatics.com/downloads/ncbi/

Yes.  The binary RPMs contain compiled executables which install into
/usr/local/bin.  To run formatdb you would run


> When I try to install this rpm (src), it doesn't show up when I search rpm
> -q -a output.
> I am just doing  
> rpm -i NCBI-2.2.7-6.src.rpm (returns no error messages)
> Is this correct?

Only if you intend to rebuild from source :).  If you have a look in the
/usr/src/redhat/SOURCES directory, you will see ncbi.tar.gz (the NCBI
tools tarball of source).  In /usr/src/redhat/SPECS you will see
ncbi-toolkit.spec which will happily turn this tarball into a binary
RPM, after a long compilation process.

It might be simpler to grab
http://downloads.scalableinformatics.com/downloads/ncbi/NCBI-2.2.7-6.i686.rpm and use this if you don't need to recompile.  Please do let me know if there are any issues with the build.


Joseph Landman, Ph.D
Scalable Informatics LLC
email: landman@scalableinformatics.com
  web: http://scalableinformatics.com
phone: +1 734 612 4615