Installation

Installing BAD_Mutations

To install BAD_Mutations, simply clone the GitHub respository:

git clone https://github.com/MorrellLAB/BAD_Mutations.git

dev Functionality

To access experimental functionality in the dev branch of BAD_Mutations, "checkout" the dev branch of the repository:

cd BAD_Mutations/
git checkout dev

Installing Dependencies

BAD_Mutations requires the following packages:

• Python 3.x
• PASTA
• HyPhy 2.3
• BLAST+
• MAFFT
• FastTree
• BioPython
• Clustal-omega

The YAML file provided in Supporting/bad_mutations.yml defines a Conda environment for BAD_Mutations. To install the Conda environment, run the following commands. Note if you are running on MSI systems, then you must run module load python3 before using conda:

conda env create -f /path/to/BAD_Mutations/Supporting/bad_mutations.yml
conda activate bad_mutations

The PASTA aligner requires that you set a path to the MAFFT alignment program. This requires some manual editing of the Conda environment startup scripts:

mkdir -p \
    ${CONDA_PREFIX}/etc/conda/activate.d \
    ${CONDA_PREFIX}/etc/conda/deactivate.d

touch \
    ${CONDA_PREFIX}/etc/conda/activate.d/env_vars.sh \
    ${CONDA_PREFIX}/etc/conda/deactivate.d/env_vars.sh

Edit ${CONDA_PREFIX}/etc/conda/activate.d/env_vars.sh to look like the following:

#!/bin/sh
export PASTA_TOOLS_DEVDIR="${CONDA_PREFIX}/bin"

Edit ${CONDA_PREFIX}/etc/conda/deactivate.d/env_vars.sh to look like the following:

#!/bin/sh
unset PASTA_TOOLS_DEVDIR

Deactivate and re-activate the Conda environment to set the environment variable. You should now be able to run BAD_Mutations with all its dependencies. This uses the commands below:

conda deactivate
conda activate bad_mutations

If you cannot use Conda, then these packages are available in most package managers for Linux. They are also available via Homebrew for MacOS.