mq.sh

#!/bin/bash
# This script sets up a benchmarking harness for MaxQuant on a c5ad ubuntu EC2 instance
sudo apt update && \
sudo apt install -y \
    tmux \
    htop \
    awscli \
    unzip \
    mono-complete \
    gdb

# Setup NVME mount for EC2
sudo mkfs.ext4 /dev/nvme1n1
sudo mkdir /data
sudo mount /dev/nvme1n1 /data
sudo chown -R ubuntu:ubuntu /data

cd /data

# Download data
aws s3 cp s3://BUCKET/MaxQuant_2.4.2.0.zip .
aws s3 sync s3://BUCKET/PXD003881/params .
aws s3 sync s3://BUCKET/PXD003881/raw .

unzip MaxQuant_2.4.2.0.zip
mv "MaxQuant 2.4.2.0" "MaxQuant"

/usr/bin/time -o mq.log -v \
    mono MaxQuant/bin/MaxQuantCmd.exe mqpar.xml