install_pangolin.sh

#!/bin/bash

set -e

cd /software
yum -y install libffi-devel
## sudo apt install libffi-dev
wget https://www.python.org/ftp/python/3.7.4/Python-3.7.4.tgz
tar -xf Python-3.7.4.tgz
cd Python-3.7.4
./configure --enable-optimizations
make -j 8
make altinstall
## release space
cd ..
rm -rf Python-3.7.4*
## python3.7 --version

## pangolin virtual env
virtualenv pangolin --python=python3.7 --prompt "(pangolin) "
. pangolin/bin/activate
cd pangolin
pip3 install biopython==1.74 pandas==1.0.1 snakemake
pip3 install git+https://github.com/cov-lineages/pangolin.git

## external software
mkdir minimap2; cd minimap2
wget https://github.com/lh3/minimap2/releases/download/v2.18/minimap2-2.18_x64-linux.tar.bz2
tar -jxvf minimap2-2.18_x64-linux.tar.bz2; rm minimap2-2.18_x64-linux.tar.bz2
cd ..; mkdir gofasta; cd gofasta
wget https://github.com/cov-ert/gofasta/releases/download/v0.0.3/gofasta-linux-amd64
chmod a+x gofasta-linux-amd64

## make links
cd ../bin
ln -s ../minimap2/minimap2-2.18_x64-linux/minimap2 minimap2
ln -s ../minimap2/minimap2-2.18_x64-linux/k8 k8
ln -s ../gofasta/gofasta-linux-amd64 gofasta

pip3 install git+https://github.com/cov-lineages/pangoLEARN.git --upgrade

## done