Install.sh

#!/bin/bash

# Installation script for the assembly pipeline
echo "###########################"
echo "# Starting installation ..."
wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
echo -e "\nyes\n\nyes\n" | bash Miniconda3-latest-Linux-x86_64.sh
export PATH=~/miniconda3/bin:$PATH
conda update -y -n base conda
conda config --add channels defaults
conda config --add channels conda-forge
conda config --add channels bioconda

echo "########################"
echo "# Installing udocker ..."
conda install -y -p ~/miniconda3 udocker==1.1.1
rm -f udocker.py
wget https://raw.githubusercontent.com/indigo-dc/udocker/7f6975c19c63c3d65ec6256c7cf5b2369d5c115d/udocker.py
sed 's/proot_killonexit = True/proot_killonexit = False/1' udocker.py > ~/miniconda3/bin/udocker.py
rm -f udocker.py
chmod uog+x ~/miniconda3/bin/udocker.py
sed 's/#!\/bin\/bash/#!\/bin\/bash\nexport CONDA_PREFIX=~\/miniconda3/1' ~/miniconda3/bin/udocker > udocker
chmod uog+x udocker
mv udocker ~/miniconda3/bin
wget https://github.com/proot-me/proot-static-build/raw/master/static/proot-x86_64 -P ~/miniconda3/bin
wget https://github.com/proot-me/proot-static-build/raw/master/static/proot-x86 -P ~/miniconda3/bin
chmod uog+x ~/miniconda3/bin/proot*

echo "###########################"
echo "# Installing containers ..."
udocker pull walkbay3000/hpgap:latest
udocker create --name=HPGAP_c1 walkbay3000/hpgap:latest

echo "###########################"
echo "# Finished installation ..."

udocker run -v /home/darcy/PopGen_WorkFlow/Pipeline/:/home/darcy/PopGen_WorkFlow/Pipeline/ --env="PATH=/home/darcy/PopGen_WorkFlow/Pipeline/" HPGAP_c1 /bin/bash -c 'HPGAP.pl'