[Bioclusters] NCBI rpm?

[Dan Bolser]

On Wed, 18 Feb 2004, Joe Landman wrote:

> 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
> 
> 	/usr/local/bin/formatdb

Hmmm, something went wrong...

Nothing new is under /usr/local/bin/

> 
> > 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

I usually do this (more from habit than anything else).

Should the above command build from source, or should I make a binary RPM
as you describe below? Anyway...

> /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.

Both files are missing, nothing new under either location. Sorry if this
is my ignorance of RPM showing up...

> 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.

OK

uname -a

Linux beagle 2.4.20-28.9 #1 Thu Dec 18 13:46:42 EST 2003 i686 athlon i386
GNU/Linux

Is this the right one?

Thanks very much,
Dan.

> 
> Joe
> 
>  
>