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This tutorial assumes that you have created the paths $WORK/src and $HOME/local/bin and added $HOME/local/bin to your $PATH. FreeBayes uses a git repository and requires the cmake build system to compile. You can install it with these commands:

login1$ module load git
login1$ mkdir -p $WORK/src && cd $WORK/src
login1$ git clone --recursive git://github.com/ekg/freebayes.git
login1$ cd freebayes
login1$ module load cmake
login1$ module load gcc
login1$ make
login1$ mv bin/* $HOME/local/bin

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This won't work on Lonestar! (You aren't an admin.) However, the make command created the executables inside of the source tree, so we find and move them to our standard $HOME/local/bin directory with the last command.

Installation for deepSNV

Requires The newest R module on lonestar is version 2.14, but deep SNV requires R 2.15.

You can install your own version of R 2.15 using the instructions below, but this takes a while to compile, so you can also just add this location to your path by adding this line to your ~/.profile_user file.

export PATH="/corral-repl/utexas/BioITeam/ngs_course/local/bin"

If you want to go through installing R 2.15 and deep SNV for yourself, here's how:

login1$ wget http://cran.wustl.edu/src/base/R-2/R-2.15.0.tar.gz
login1$ tar -xvzf R-2.15.0.tar.gz
login1$ cd R-2.15.0
login1$ ./configure --prefix=$HOME/local
login1$ make
login1$ make install

Once you have access to R 2.15, you can install deepSNV using these commands.

login1$ R
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> source("http://bioconductor.org/biocLite.R")
> biocLite("deepSNV")

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A mixed population of E. coli from an evolution experiment was sequenced at several different time points (PMID: 19838166 , PMID:19776167). At generation 0 it consisted of a clone (cells grown from a colony with essentially no genetic variation), then additional samples were taken at 20K and 40K generations after which mutations arose and swept through the (asexual) population.

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/corral-repl/utexas/BioITeam/ngs_course/FreeBayes/ecoli_mixed

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