Install Miniconda 3 with:
wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
sh Miniconda3-latest-Linux-x86_64.sh
After setting up Miniconda, install dependencies from the kantorlab channel with:
conda create -n hiv-profile-sampling -c kantorlab biopython=1.73 mafft=7.313 raxml=8.2.12 scons=3.0.1.1 pandas=1.0.3
To activate the environment, use:
source activate hiv-profile-sampling
Setup your scratch directory on Oscar:
mkdir -p /gpfs/scratch/$USER/hiv-profile-sampling
ln -s /gpfs/scratch/$USER/hiv-profile-sampling scratch
To download the singularity container for OMM-MACSE, run:
cd scratch && singularity pull library://vranwez/default/omm_macse:sha256.096cd4607b78cd6aaf0d8af1e232e43824405320d155c5343f9c0a713595976c
The run order and dependencies of the scripts are specified in the SConstruct
file. The entire analysis can be run by executing the scons command from the
root directory of the repo.