Create a new conda environment covid-v1 with python 3.7:
conda create -n covid-v1 python==3.7.10
conda activate covid-v1
pip install snakemake
Install the desired version of pangolin and pangolin-data with the update_pangolin.sh script, for example:
bash update_pangolin.sh 4.0.6 1.9
In the future, you could update the pangolin version using this script.
Install nextclade and nextalign in the bin subdirectory:
mkdir -p bin
curl -fsSL "https://github.com/nextstrain/nextclade/releases/latest/download/nextclade-Linux-x86_64" -o "bin/nextclade" && chmod +x bin/nextclade
curl -fsSL "https://github.com/nextstrain/nextclade/releases/latest/download/nextalign-Linux-x86_64" -o "bin/nextalign" && chmod +x bin/nextalign
The input file of sequences in FASTA format should be named ri_sequence.fa (edit the run.sh script to use a different input filename).
The pipeline is designed to be submitted as a batch job to a SLURM cluster:
sbatch run.sh
If you are running locally instead of on a cluster, simply execute the script in bash:
bash run.sh
Results are written to the results subdirectory.
The pipeline is freely available for non-commercial use under the license provided in LICENSE.txt.