Installing Storey's edge microarray software on Ubuntu

It takes a few steps to install this (Intrepid Ibex, Ubuntu 8.10), but here's how I got it working (we'll see if there are any bugs):

edge website

1. Install R



sudo aptitude install r-base



2. Download and unpack the source file:

linux src page

3. Install impute

Download the above link and install with something like this:


sudo R CMD INSTALL packages/impute_1.0-5.tar.gz



4. prepare the compiling environment



sudo aptitude install g++-4.2 gfortran-4.2 tetex-base
# (also might need tetex-extras ...)
sudo rm /usr/bin/g++  # just removes the soft link
sudo ln -s /usr/bin/g++4.2 /usr/bin/g++
sudo rm /bin/sh  # just a link to /bin/dash
sudo ln -s /bin/bash /bin/sh



5. Compile the sucker



cd src ; make ; make install


The make install command just copies the .so files up a directory

6. Run the software



R


Then from within R started at the base of the package:


source("edge.r")
edge()



7. Restore the original environment



sudo rm /usr/bin/g++
sudo ln -s /usr/bin/g++4.3 /usr/bin/g++
sudo rm /bin/sh
sudo ln -s /bin/dash /bin/sh