install_rnasik.sh

# use eg. curl -s https://myurl.com/script.sh | bash /dev/stdin
# only run on an empty cloud server with blank vdb volume attached!
sudo apt-get update < "/dev/null"
sudo apt-get install curl -y < "/dev/null"
sudo true

# Install kernel extra's to enable docker aufs support
sudo apt-get -y install linux-image-extra-$(uname -r) < "/dev/null"

# Add Docker PPA and install latest version
sudo apt-key adv --keyserver hkp://keyserver.ubuntu.com:80 --recv-keys 36A1D7869245C8950F966E92D8576A8BA88D21E9
sudo sh -c "echo deb https://get.docker.io/ubuntu docker main > /etc/apt/sources.list.d/docker.list"
sudo apt-get update < "/dev/null"
sudo apt-get install lxc-docker -y < "/dev/null"

sudo groupadd docker
sudo gpasswd -a ${USER} docker
sudo service docker restart

sudo sh -c "newgrp docker"

#mkdir /home/ubuntu/data
#sudo chown ubuntu:docker ~/data
#sudo chmod 775 ~/data

sudo mkfs.ext4 /dev/vdb
sudo mount /dev/vdb /mnt -t auto

sudo mkdir /mnt/data
sudo chown ubuntu:docker /mnt/data
sudo chmod 775 /mnt/data
sudo ln -s /mnt/data /home/ubuntu/data

sudo docker pull monashbioinformaticsplatform/rnasik:0.2.1
echo "docker image installed! log out of this terminal and in again then open the README file"
echo "docker run -v /mnt/data:/root/data -it monashbioinformaticsplatform/rnasik:0.2.1 bash" >> "/home/ubuntu/README"
echo "and once inside: source /etc/environment" >> "/home/ubuntu/README"
echo "The RNAsik-pipe command and its tools should work (put input and output data in ~/data) or it will be lost!" >> "/home/ubuntu/README"