How to make a GATB Compiler VM? - GATB/gatb-core-tuto GitHub Wiki

Here is the simple process to setup a GATB-core environment.

Prerequisite: we start from a fresh installation of Linux Debian 7.

Then:

# we prepare the Debian distribution with GATB dependencies
apt-get update
apt-get install cmake
apt-get install zlib1g-dev

# we install GATB-Core (official release v1.2.2; update as needed)
cd /opt
git clone https://github.com/GATB/gatb-core.git
git checkout v1.2.2
cd gatb-core
mkdir build ; cd build ; cmake ..
make -j4 package

# we copy the GATB-Core binary library to a production place    
cp gatb-core-1.2.2-bin-Linux.tar.gz /opt
cd /opt
gunzip gatb-core-1.2.2-bin-Linux.tar.gz
tar -xf gatb-core-1.2.2-bin-Linux.tar

# setup the GATB compiling env
export GATB_HOME=/opt/gatb-core-1.2.2-bin-Linux

# here is how to compile a GATB code
g++ $GATB_HOME/examples/debruijn/debruijn1.cpp -I$GATB_HOME/include \
    -L$GATB_HOME/lib -Llib -lgatbcore -lhdf5 -ldl -lz -lpthread -std=c++0x -O3 -o db

# run the produced binary
./db
# you should have the inline help message...

# from here, you have a ready-to-use GATB compiling environment

This is the exact procedure we used to apply on the A||GO platform (through Docker) to setup our GATB-Compiler Linux-based VM.