Tuesday, April 14, 2009

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

  2. sudo aptitude install r-base

  3. Download and unpack the source file:

  4. linux src page
  5. Install impute

  6. Download the above link and install with something like this:
    sudo R CMD INSTALL packages/impute_1.0-5.tar.gz

  7. prepare the compiling environment

  8. 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

  9. Compile the sucker

  10. cd src ; make ; make install

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

  12. R

    Then from within R started at the base of the package:
    source("edge.r")
    edge()

  13. Restore the original environment

  14. 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

3 comments:

EGP said...

If you use g++-4.3 or above it will not compile, so stick to g++4.2

stewchang said...

Conveniently, g++-4.2 has been removed from the latest version of Ubuntu (Lucid). I'm trying some backdoor routes to try to get a version of g++-4.2 installed on my box.

Jeremiah said...

Compiled on RHEL 5 using R 2.4.1 (exception when trying to run 2.12). Needed to specify --with-tcltk option.