INSTALLATION

Three different ways to install FusionCatcher are presented below.


1. Installation using FusionCatcher's own installation script (RECOMMENDED)
===========================================================================

```
wget http://sf.net/projects/fusioncatcher/files/bootstrap.py -O bootstrap.py && python bootstrap.py -y -t --download
```

NOTE: In case that the above command gives and erro it might be that some 
dependencies are missing and in this case the missin dependencies could be 
installed on Ubuntu Linux by running this:
```
sudo apt-get install wget gawk gcc g++ make cmake automake curl unzip zip bzip2 tar gzip pigz parallel build-essential libncurses5-dev libc6-dev zlib1g zlib1g-dev libtbb-dev libtbb2 python python-dev python-numpy python-biopython python-xlrd python-openpyxl default-jdk
```


2. Installation using CONDA
===========================

conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge
conda create -n fusioncatcher fusioncatcher
source activate fusioncatcher
download-human-db.sh



3. Installation from GITHUB
===========================

git clone https://github.com/ndaniel/fusioncatcher
cd fusioncatcher/tools/
./install_tools.sh
cd ../data
./download-human-db.sh

NOTE: Here it is assumed that Python 2.7.x, BioPython (>v1.5), and Java Runtime Environment 1.8 are already installed.