QUAST INSTALLATION README

1. SYSTEM REQUIREMENTS

QUAST can be run on Linux or Mac OS.

2. SOFTWARE REQUIREMENTS

For the main pipeline:
python 2 (2.5 or higher)
perl 5.6.0 or higher
g++
make
sh
csh
sed
awk
ar

In addition, several submodules require:
Java JDK (tested with OpenJDK 6) for GAGE
Time::HiRes perl module for GeneMark-ES
Boost (tested with v1.56.0) for Manta and E-MEM
cmake (tested with v2.8.12) for Manta

All those tools are usually preinstalled on Linux.
Mac OS, however, initially misses make, g++ and ar, 
so you will have to install Xcode (or only Command Line Tools for Xcode) 
to make them available. 

It is also highly recommended to install the Matplotlib Python library for drawing plots. 
We recommend to use Matplotlib version 1.1 or higher. Tested with Matplotlib v.1.3.1.
Installation can be done with Python pip-installer:
    pip install matplotlib
Or with the Easy Install Python module:
    easy_install matplotlib
Or on Ubuntu by typing:
    sudo apt-get install python-matplotlib

3. INSTALLATION

To download the QUAST source code tarball and extract it, type:
    wget https://downloads.sourceforge.net/project/quast/quast-4.1.tar.gz
    tar -xzf quast-4.1.tar.gz
    cd quast-4.1

QUAST automatically compiles all its sub-parts when needed (on the first use). 
Thus, there is no special installation command for QUAST.
However, we recommend you to run:
    python quast.py --test (if you plan to use quast.py)
or/and
    python quast.py --test-sv  (if you plan to use quast.py or metaquast.py with SV calling)
or/and 
    python metaquast.py --test  (if you plan to use metaquast.py with references)
or/and
    python metaquast.py --test-no-ref  (if you plan to use metaquast.py without references) 
These commands run all QUAST and metaQUAST modules and check correctness
of their work on your platform.

We also provide ./install.sh and ./install_full.sh scripts. The former runs two simple --test 
commands, the latter runs all four mentioned above commands.

NOTE: You should place quast-4.1 directory in the final destination before
the first use (e.g. before run with --test). If you want to move QUAST to 
some new place after several usages you should use a clean copy of quast-4.1.
This limitation is caused by auto-generation of absolute paths in compiled 
modules of QUAST.
