Installing dependencies

A modified version of megablast called mgblast is required for doing the all vs. all BLAST prior to clustering. This program is used because it is very memory efficient, making it possible to execute many threads with very little resource usage. Below is an example script (assuming Ubuntu as the OS) to download and install mgblast.

#!/bin/bash

wget sourceforge.net/projects/gicl/files/mgblast.tar.gz && tar xzf mgblast.tar.gz
cd mgblast
dir=`pwd`
sed "s,NCBIDIR = .*,NCBIDIR = $dir/ncbi," Makefile > Makefile.bak
mv Makefile.bak Makefile

sudo apt-get -y install csh xorg-dev openbox lesstif2-dev
wget ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools/old/20060507/ncbi.tar.gz && tar xzf ncbi.tar.gz

./ncbi/make/makedis.csh 2>&1 > /dev/null
./ncbi/make/makedis.csh 2>&1 > /dev/null
./ncbi/make/makedis.csh 2>&1 > /dev/null

## Compile and install mgblast
make
make install

The last command is optional. You may want to keep this program in a custom location, but it must be in your PATH variable.

The program formatdb is also required, and if it is not installed on your system in can be done with the following commands:

wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/release/2.2.14/blast-2.2.14-x64-linux.tar.gz
tar xzf blast-2.2.14-x64-linux.tar.gz

It is important to add the path to the above executables to your PATH variable so the programs can be found by Transposome.

The final thing to do is install BerkeleyDB and NCBI BLAST+, which can be done with the following command:

sudo apt-get -y install libdb-dev libdb++-dev ncbi-blast+

Note that these instructions will have to modified slightly depending on your operating system. If you work the method for installing these programs on another system, please let me know and I'll update this page.