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 > > >