Downloading and Installing SHORE

Download

Download the latest SHORE release from https://sourceforge.net/projects/shore/ or http://1001genomes.org/downloads/ or check out the git repository to compile SHORE from the very latest source:

> git clone git://shore.git.sourceforge.net/gitroot/shore/shore

Installing SHORE using the binary file

Navigate to the folder where you stored the downloaded file:

 > tar xzvf shore_<platform>_<version>.tar.gz

SHORE is now installed.

Installing SHORE using the source files

Navigate to the folder where you stored the downloaded file

> tar xzvf shore_source_<version>.tar.gz > cd shore_source_<version>

(or navigate to your shore git folder). See the file INSTALL in the SHORE directory for further installation instructions.

Download and install a mapping tool

SHORE can currently be run with five different mapping tools. The native tool of SHORE is GenomeMapper, which can be downloaded from: http://1001genomes.org/downloads/ Navigate to the folder where you stored the downloaded file:

> tar xzvf genomemapper.tar.gz
> cd genomemapper
> make

GenomeMapper is now installed. Note Mac OS users might have to change the name of the Mac OS Makefile. See the GenomeMapper manual for further details and details on parallelization of GenomeMapper.

In addtition to GenomeMapper, SHORE supports several third party mappers.

Installation of R

SHORE can optionally make use of R (http://www.r-project.org) to provide visualization, e.g. of run statistics. In order to use this feature, R has to be installed and the installation path has to be added to the $PATH environment variable. Note that it is not necessary to have R installed to run SHORE.

Environment variables

Since SHORE supports external mapping tools, it needs to know where these are located on the actual system. At least one environment variable describing the folder where the mapping tool is stored has to be set to run SHORE. Here we describe this exemplarily for the bash and show how to set up SHORE to run with GenomeMapper. Though all four mapping tools could be added at the same time. For tcsh or any other shell, users have to set the environment variables in an equivalent way. Add to your local .bashrc file ($HOME/.bashrc):

required:

export GENOMEMAPPER=/PATH/TO/GENOMEMAPPER/INSTALLATION/FOLDER/

optional:

export BWA=/PATH/TO/BWA/INSTALLATION/FOLDER/ export BOWTIE=/PATH/TO/BOWTIE/INSTALLATION/FOLDER/
export ELAND=/PATH/TO/ELAND/INSTALLATION/FOLDER/ export NOVO=/PATH/TO/NOVOCRAFT/INSTALLATION/FOLDER/

Alternatively the mapping tools may be added to your PATH variable:

export PATH=$PATH:’/PATH/TO/GENOMEMAPPER/INSTALLATION/FOLDER/’