Here is the procedure I used to build mpiblast from source
either:
wget http://mpiblast.sf.net/mpiblast-latest.tar.gz
or
cvs checkout using RestrictiveFirewallsAndSourceForge
wget ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools/old/
or
wget ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools/ncbi.tar.gz
apt-get install automake1.9
tar zxvf mpiblast-latest.tar.gz
tar zxvf ncbi.tar.gz
patch -p0 < mpiblast/ncbi_May2006_evalue.patch
ncbi/make/makedis.csh
cd mpiblast
aclocal
autoheader
automake -a
autoconf
./configure --with-ncbi=/full/path/to/ncbi
make
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