Installing dependencies

If any of the Transposome tests fail, it may be because you do not have all of the dependencies installed. If you are unsure, just try to install Transposome and see if it is successful.

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

# in the following command, omit lesstif2-dev on Ubuntu 14.04
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

# yes, this has to be run three times and it is very, very noisy
./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 mgblast
make

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 it was compiled with the NCBI Toolkit above. Just add the ncbi '/bin' directory to your PATH 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+

PORTABILITY ISSUES

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