Installing dependencies

Evan Staton edited this page Apr 21, 2017 · 22 revisions

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.

Linux

To use Transposome, it must be possible to execute 32-bit binaries and a C++ compiler is required.

On Ubuntu, the following command will install the required libraries:

sudo apt-get install -y build-essential lib32z1

The final thing to do is install NCBI BLAST+ if it is not already installed (you can test your installation by typing makeblastdb and blastn to see if these programs are available). The installation can be done with the following command (assuming Ubuntu as the OS):

sudo apt-get -y install ncbi-blast+

On RHEL/Fedora, the same steps are listed below:

sudo yum groupinstall "Development Tools"
sudo yum install -y glibc.i686 gcc-c++

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 

Installing Perl

It is likely that Perl is already installed on your machine however, I recommend using the following approach to make installation easier and to avoid messing with the system Perl. This can be set up very easily using perlbrew. Just copy the commands below in a terminal window (one at a time).

\curl -L http://install.perlbrew.pl | bash
echo "source ~/perl5/perlbrew/etc/bashrc" >> ~/.bashrc
source ~/.bashrc
perlbrew --force install perl-5.20.3 -Dusethreads
perlbrew switch perl-5.20.3
perlbrew install-cpanm

This will set up Perl in your home directory under the "perl5" directory and will ensure that you don't use the system Perl. The last command installs cpanminus, a friendly package manager for Perl. At this point you can install Transposome with one command (assuming you followed the steps above to install the dependencies):

cpanm git://github.com/sestaton/Transposome.git

If you run into any issues with this command please follow the instructions under the "INSTALLATION" section of the README file, and see below.

RESOLVING ISSUES

Note that these instructions may have to be modified slightly depending on your operating system. If you run into any issues please let me know and I'll be happy to help.

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