Overview

As we have seen though several points in the course, controlling for different versions of different programs can cause headaches. In this tutorial you will install your own copy of the breseq analysis pipeline. Additionally (and more importantly), you will install an updated version of bowtie2 which will address a bug in bowtie2 that prevents breseq from being able to run on multiple threads.

Learning objectives

1. Check versions of bowtie2 and breseq to verify this tutorial is necessary
2. upgrade bowtie2 
3. clone your own copy of breseq

Checking installations and versions

which -a bowtie2
bowtie2 --version

I expect the which command gives 1 line of data listing '/opt/apps/intel18/bowtie/2.3.4/bin/bowtie2' and the 2nd command gives several lines of output that includes 'version 2.3.4' in the first line, you will need to upgrade bowtie2 to a different version. This tutorial will go over installing bowtie 2.3.5.1 as this is version is known to address the error while more recent versions are unchecked.

which -a breseq 
breseq --version

I expect the which command gives 1 line of data listing '/corral-repl/utexas/BioITeam/breseq/bin/breseq' and the 2nd command gives 'breseq 0.35.1', if so you do not have to clone your own copy of breseq, but it is still encouraged particularly if you envision using breseq in your own work outside of this course.

Upgrading bowtie2

mkdir $WORK/src
cd $WORK/src
wget https://github.com/BenLangmead/bowtie2/releases/download/v2.3.5.1/bowtie2-2.3.5.1-linux-x86_64.zip
unzip bowtie2-2.3.5.1-linux-x86_64.zip

Next we need to make sure that that version of bowtie2 is in your path variable. Do one of the following:

1. Make 2 changes to your .bashrc file using nano

   modify your your .bashrc file in your $HOME directory

   # comment out the line in the module system listing module load bowtie/2.3.4
   # add the following line in the section dealing with the path variable
   export PATH=$PATH:$WORK/src/bowtie2-2.3.5.1-linux-x86_64  #temp bowtie2 executables

2. Copy the updated version of the .bashrc file from $BI/scripts

   Preferred solution

   cp /corral-repl/utexas/BioITeam/scripts/GVA2020.bashrc.updated_bowtie2 $HOME/.bashrc
   chmod 700 .bashrc

Finally, log out of tacc and log back in using ssh. 

which -a bowtie2
bowtie2 --version

should now return 1 line similar to '/work/01821/ded/lonestar/src/bowtie2-2.3.5.1-linux-x86_64/bowtie2' and the first line of the 2nd command end with "version 2.3.5.1". If not get my attention on zoom.

Cloning breseq

Compiling breseq

Testing breseq