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Setting up R packages for CBM of genome-scale metabolic models on Ubuntu 13.10

Long ago, I posted here the steps involved in setting up R packages for performing constraint based modelling (CBM) of genome scale metabolic models. It was Ubuntu 10.04 LTS back then. Now, I am trying to reproduce the same set-up on Ubuntu 13.10.

As a quick summary, we need the following R packages: "sybil", "sybilSBML", and "glpkAPI". The "sybilSBML" R package requires the Bioconductor package "rsbml" which requires "libsbml" library, which in turn depends on "swig". The "glpkAPI" is an R wrapper for glpk library which is the optimization engine.

I have been able to install all these packages by executing the following steps.

1. Install swig from ubuntu repositories.


sudo apt-get install swig

2. Install python-dev from ubuntu repositories.


sudo apt-get install python-dev


3. Install openjdk from ubuntu repositories.


sudo apt-get install openjdk-7-jdk


4. Install libxml2 and libxml2-dev from ubuntu repositories.

sudo apt-get install libxml2 libxml2-dev

5. Install libsbml 5.9.0 from sources. I downloaded the source file libsbml-5.9.0-core-plus-packages-src.tar.gz, extracted the contents and ran the following


sudo su
./configure --with-libxml=/usr --with-java --with-python --with-matlab=/usr/local/MATLAB/R2013a/
make
make install
ldconfig


6. Install the Bioconductor package "rsbml". I ran the following commands in R.


source("http://bioconductor.org/biocLite.R")
biocLite("rsbml")


7. Install the R packages "sybil" and "sybilSBML". I ran the following commands in R.


install.packages(c("sybil", "sybilSBML"))



8. Install glpk from ubuntu repositories.


sudo apt-get install glpk


9. Install R package glpkAPI. I downloaded the source of the R package, namely gplkAPI_1.2.9.tar.gz and ran the following command at the linux console.

sudo R CMD INSTALL glpkAPI_1.2.9.tar.gz --configure-args="--with-glpk-lib=/usr/local/lib --with-glpk-include=/usr/local/include --enable-gmp=no"

Comments

Gopal said…
I recently tried to install glpkmex for MATLAB (to call GLPK functions from MATLAB) on this same machine which has R setup for metabolic modelling. The glpk version that came from the ubuntu repositories was not good for glpkmex apparently. I noticed from the release notes that glpkmex likes glpk 4.36 the best. But it turned out that glpkAPI in R did not like this 4.36 version. According to glpkAPI release notes, it needs version >=4.42. I however wanted to have both MATLAB/glpkmex and R/glpkAPI work. By trial and error I found that glpk version 4.45 is good for both. The installation was of glpk 4.45 was pretty straightforward:

wget ftp://ftp.gnu.org/gnu/glpk/glpk-4.45.tar.gz
tar -xvzf glpk-4.45.tar.gz
cd glpk-4.45
./configure
make
make install

So, please use this as step 8 if you are interested in using both MATLAB (e.g. openCOBRA) and R (e.g. sybil) for metabolic modelling on the same machine.

Finally, I believe that many other GLPK versions might work with glpkmex as well as glpkAPI. But I just tried a couple of versions and as soon as I hit upon 4.45 which worked, I didn't try other versions.
14 February 2014 at 09:12
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