Run `msconvert` on Linux/MacOS. A bash script to parse standard arguments to an `msconvert` Docker container. #docker

docker-msconvert.sh

#!/bin/bash

# Script to run Proteowizard `msconvert` installed through Docker on Linux/MacOS systems.
# Parses standard command line arguments for `msconvert`. e.g.
# `docker-msconvert data.RAW --zlib --filter "zeroSamples removeExtra" --mz5`
# Requires `msconvert` Docker-container installed as on https://hub.docker.com/r/chambm/pwiz-skyline-i-agree-to-the-vendor-licenses
# Assumes `msconvert` is installed in an environment named 'default', replace this with the appropriate environment name.
# 2019 Jedd Bellamy-Carter

# Modify path strings for docker environment
newargs+=("/data/$1")
for ((i = 2; i <= $#; i++ )); do
    if [[ "${!i}" = "-o" ]]; then
        newargs+=("${!i}")
        ((i+=1))
        newargs+=("/data/${!i}")
    else
        newargs+=("${!i}")
    fi
done

# Check directory
if [ ${1:0:1} = "/" ]; then
    dir="/"
else
    dir="$PWD/"
fi

# Check status of docker-machine and start it if necessary
if docker-machine status default | grep -q "Stopped"; then
    echo "Docker not running"
    echo "Starting docker-machine"
    eval $(docker-machine start default)
    echo "Docker now running"
else
    echo "Docker already running"
fi

# Evaluate docker-machine environment
eval $(docker-machine env default)

# Run msconvert through docker
docker run -it --rm -e WINEDEBUG=-all -v $dir:/data chambm/pwiz-skyline-i-agree-to-the-vendor-licenses wine msconvert "${newargs[@]}"