Difference between revisions of "Downloading and Installing SHORE"

Revision as of 17:36, 5 April 2011

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/’

TMP directory

Some files need to be sorted before SHORE can use them. Before using these input files SHORE checks if they are sorted in the appropriate way and in case of inconsistencies SHORE will start to sort them. E.g., initially alignments are sorted by read ids, but to analyze them they need to be sorted by the alignment location. Therefore sorting is required. SHORE implements its own sorting program. By default this program uses /tmp if the files to be sorted are large (which is usually the case). Therefore, it can happen that the disc space in /tmp is not sufficient. We recommend at least 200GB. This can be achieved by setting the TMPDIR environment variable to a file system with sufficient space.

 export TMPDIR=/PATH/TO/A/FOLDER/