1. Create a directory to store temporary files:

   mkdir -p $HOME/museq/
   cd $HOME/museq
   

2. Download and install Miniconda for python 2.7:

   Download miniconda

   wget https://repo.anaconda.com/miniconda/Miniconda2-latest-Linux-x86_64.sh
   

   Run

   sh Miniconda2-latest-Linux-x86_64.sh
   

   and follow the instructions. When you have finished following the instructions, you should have python installed:

   which python
   ~/miniconda2/bin/python
   

3. clone the mutationseq repo.

   git clone https://github.com/shahcompbio/mutationseq.git
   

4. create a conda environment:

   conda create --name mutationseq python=2.7 --file $HOME/museq/mutationseq/conda_packages.txt
   

5. activate the environment:

   conda activate mutationseq
   

6. Install mutationseq:

   download boost:

   wget https://sourceforge.net/projects/boost/files/boost/1.57.0/boost_1_57_0.tar.gz/download -O boost.tar.gz
   

   At the moment mutationseq only supports boost 1.57.0 or older. Newer versions will run into installation issues. extract boost:

   tar -xvf boost.tar.gz
   

   install mutationseq:

   cd $HOME/museq/mutationseq/
   python setup.py install --boost_source=$HOME/museq/boost_1_57_0
   

To call variants using MutationSeq, we use the following command:

mkdir -p museq/results; \
museq \
  normal:bam/HCC1395_exome_normal.sort.markdup.17.7MB-8MB.bam \
  tumour:bam/HCC1395_exome_tumour.sort.markdup.17.7MB-8MB.bam \
  reference:refs/GRCh37-lite.fa \
  -o museq/results/HCC1395_exome_tumour_normal_17.vcf