aws-speed-notes.txt

- Ubuntu 18.04 like vg does for the same BWA.
- Give it vg-k8s cluster role so we can use that bucket. Make root volume 20 GB

sudo mdadm --create --verbose --auto=yes /dev/md0 --level=0 --raid-devices=4 /dev/nvme0n1 /dev/nvme1n1 /dev/nvme2n1 /dev/nvme3n1
sudo mkfs.ext4  /dev/md0
sudo mkdir /mnt/scratch
sudo mount /dev/md0 /mnt/scratch

sudo apt-get update -q && sudo bash -c "DEBIAN_FRONTEND=noninteractive apt-get install git build-essential libz-dev libtbb-dev bwa hisat2 awscli -q -y --force-yes"

git clone https://github.com/lh3/minimap2
cd minimap2 && git checkout 2c52364527268358448e6552923bb12d6f994025 && make
sudo cp minimap2 /bin
cd ..
git clone https://github.com/BenLangmead/bowtie2.git
cd bowtie2 && git checkout v2.4.1 && make
sudo cp bowtie2 bowtie2-align-s bowtie2-align-l bowtie2-build bowtie2-build-s bowtie2-build-l bowtie2-inspect bowtie2-inspect-s bowtie2-inspect-l /bin
cd ..
wget https://github.com/vgteam/vg/releases/download/v1.27.1/vg
chmod +x vg
sudo mv vg /bin

cd /mnt/scratch
sudo mkdir work
sudo chown $USER:$USER work
cd work
mkdir tmp

screen

export TMPDIR=$(pwd)/tmp

git clone https://github.com/vgteam/giraffe-sv-paper.git
cd giraffe-sv-paper
git checkout a912a457d19efb3177aa75ddc5f9206135cb9563
cat scripts/linear_mappers/speed_linear.sh | sed 's/xhchang/adamnovak/g' | bash && \
cat scripts/graph_mappers/speed_map.sh | sed 's/xhchang/adamnovak/g' | bash && \
cat scripts/giraffe/speed_giraffe.sh | sed 's/xhchang/adamnovak/g' | bash