install_rnasik_aws.sh

#!/bin/bash -i
sudo apt-get update < "/dev/null"
sudo apt-get install python-pip -y < "/dev/null"
sudo pip install awscli < "/dev/null"

# 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"

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

sudo mkfs -t ext4 /dev/xvdb
sudo mkdir -p /mnt/data
sudo mount /dev/xvdb /mnt/data

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

sudo mkdir ~/data/gtf
sudo mkdir ~/data/fq
sudo mkdir ~/data/fa
sudo mkdir ~/data/refFiles
sudo mkdir ~/data/run
sudo chown -R ubuntu /mnt/data

aws s3 cp s3://mus-musculus-grcm38 ~/data --recursive --region ap-southeast-2
aws s3 cp s3://mus-musculus-grcm38-fa/Mus_musculus.GRCm38.dna_sm.primary_assembly.fa ~/data/fa --region ap-southeast-2
aws s3 cp s3://rnasik-test-data/gtf/Mus_musculus.GRCm38.82-geneFeatureLinesRemoved.gtf ~/data/gtf
aws s3 cp s3://rnasik-test-data/fq/ ~/data/fq --recursive

sudo docker pull monashbioinformaticsplatform/rnasik:0.2.1 < "/dev/null"

sudo docker run -v ~/data:/root/data -i monashbioinformaticsplatform/rnasik:0.2.1 /bin/bash -c "source /etc/environment; cd ~/data/run; RNAsik-pipe -star \
                            -fqRegex A \
                            -fqDirs ~/data/fq \
                            -count \
                            -gtfFile ~/data/gtf/Mus_musculus.GRCm38.82-geneFeatureLinesRemoved.gtf \
                            -genomeIndex ~/data/refFiles/Mus_musculus.GRCm38.dna_sm.primary_assembly-starIndex \
                            -threads 36" >> ~/data/run/run.log

aws s3 mb s3://rnasik-run2-results
aws s3 cp --recursive ~/data/run s3://rnasik-run2-results