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DEPENDENCIES

To use Transposome, you will need Perl installed (version 5.10 or greater) and it is very simple to install Perl with a tool called perlbrew. A step-by-step set of instructions is provided for installing a recent version of Perl. That wiki page also explains the commands below.

INSTALLATION

Note that the following commands assume a fresh cloud instance with no compilers or libraries installed. There are only a couple of steps, but please be advised that it can take a little while (perhaps 20 minutes) to compile the dependencies.

For Ubuntu/Debian as the OS:

apt-get install -y build-essential lib32z1 git ncbi-blast+ curl
curl -L cpanmin.us | perl - git://github.com/sestaton/Transposome.git

For RHEL/Fedora:

yum groupinstall "Development Tools"
yum install -y glibc.i686 gcc-c++ git ncbi-blast+
curl -L cpanmin.us | perl - git://github.com/sestaton/Transposome.git

Note for CentOS users:

All of the above commands for RHEL will work on CentOS except for the ncbi-blast+ package. Please install this package separately from the NCBI downloads page copying the binaries to somewhere in your PATH (e.g., /usr/local/bin), or for regular users, just extend your PATH to the location of the BLAST+ 'bin' directory.

If you run into issues with the above steps, it is likely that you are missing a dependency. In this case, download the latest release and install manually (see the troubleshooting page for more information) with the following commands.

tar xzf Transposome.tar.gz
cd Transposome
curl -L cpanmin.us | perl - --installdeps .
perl Makefile.PL
make
make test
make install

These steps will give a clear indication of any issues. Updating your installation can be achieved by simply running the same commands. Please report any issues.