Installing PEER executable peertool

John Lees included in bioinformatics linux

2016-01-19 143 words One minute

Contents

PEER (probabilistic estimation of expression residuals) is a tool to determine hidden factors from expression data, for use in genetic association studies such as eQTL mapping.

The method is first discussed in a 2010 PLOS Comp Bio paper: http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1000770 and a guide to its applications and use in a 2012 Nature Protocols paper: http://www.nature.com/nprot/journal/v7/n3/pdf/nprot.2011.457.pdf

To install a command line version of the tool, you can clone it from the github page

git clone https://github.com/PMBio/peer

When installing, it won’t install the executable binary peertool by default, nor will it use a user directory as the install location (though the latter is addressed at the end of documentation). To install these, use the following commands:

cd peer && mkdir build && cd build cmake -D CMAKE_INSTALL_PREFIX=~/software -D BUILD_PEERTOOL=1 ./.. make make install

Which will install peertool to ~/software/bin, which you can put on your path.