Download and building

Prerequisites

To build the HPG Aligner application you need to install in your system:

• the libraries:

  • zlib
  • curl
  • xml
  • curse
  • gsl
  • check
  • tcmalloc (only for MPI)

• and the applications:

  • gcc
  • scons
  • mvapich2 or openMPI (only for MPI)

For Ubuntu and Debian, you can install them using the following commands:

apt-get install gcc
apt-get install scons   
apt-get install zlib1g-dev libcurl4-gnutls-dev libxml2-dev libncurses5-dev libgsl0-dev check

And for Centos and Fedora:

yum install gcc
yum install scons
yum install zlib-devel libcurl-devel libxml2-devel ncurses-devel gsl-devel check-devel

Download

In order to download the project from the GitHub repository, you need to install git in your system.

• To install git in Ubuntu and Debian systems, run: apt-get install git

• To install git in Centos and Fedora systems, run: yum install git

Once git installed, you download the project by by invoking the following git commands:

git clone https://github.com/opencb/hpg-aligner.git
cd hpg-aligner
git submodule update --init

Building

For a HPG Aligner's stable version, choose the git branch master, both for hpg-aligner and hpg-libs. The branch develop contains the most recent HPG Alinger version.

cd lib/hpg-libs
git checkout master
cd ../..
git checkout master

For MPI HPG Aligner (only available for RNA) choose the git branch develop-mpi

cd lib/hpg-libs
git checkout develop-mpi
cd ../..
git checkout develop-mpi

Finally, use Scons to build the HPG Aligner application:

scons

or for MPI HPG Aligner:

scons compiler=mpicc

If the compliation succeeds, the binary hpg-aligner will be created in the folder bin:

bin/hpg-aligner