Download

ncbi.tar.gz

latest patch version

Example multiseed with corresponding alphabet, for 7tm_1 family

Installation

First, download the package ncbi.tar.gz and the latest patch version.
Unzip inside a temporary folder
 
 zcat ncbi.tar.gz | tar xv
 cd ncbi
 
Apply the patch
 
 zcat ../seedfa-ncbi-blast2.2.22-0.77.patch.gz | patch -p1
 
Setup
Edit compilation settings if you want to:
 
  vim platform/linux-x86.ncbi.mk
  
You can adjust important flags like optimization, libraries, includes, etc.

If another platform than x86 is needed you will have to check all makefile files which
 
 grep -e 'include ../platform/linux-x86.ncbi.mk' -R ./
 
and change the include directives appropriately.

Before compiling you have to make sure you have libboost-program-options-dev installed. On Ubuntu simply do:
 
  sudo apt-get libboost-program-options-dev
 
Compilation:
  
 cd make
 csh ./copy-essential.seed.csh
 cd ../build
 make LCL=lnx -f makefile.seed blast  
 # if this stops early because of an error, try running again 
 # on some systems WAIT doesn't work well and files are still
 # being copied when make tries to find them
 make LCL=lnx -f makefile.seed formatdb
 
Done!
Now you can copy the essential binaries and example config file to a directory of your choice:
  
 cd ..
 cp build/blast build/formatdb seedfa/seedfa.cfg  destination/dir/