Bash script for lauching VSCode on a GenomeDK compute node

gdk-code.sh

#!/usr/bin/env bash

usage=$(cat <<-END

Use like this:

    gdk-code <memory> <walltime> <environment> <projectdir> <> ~/some/dir/on/genomedk

The following needs to be part of your .ssh/config file:

Host gdk
    HostName        login.genome.au.dk
    User            your_user_name_on_the_genomedk

Host cn-* gn-* s21n* s22n*
    HostName %h
    ProxyJump gdk
    User your_user_name_on_the_genomedk
END
)

while getopts ":m:t:e:a:d:" opt; do
  case $opt in
    m) mem="$OPTARG"
    ;;
    t) walltime="$OPTARG"
    ;;
    e) environment="$OPTARG"
    ;;
    a) account="$OPTARG"
    ;;
    d) open_dir="$OPTARG"
    ;;
    h) usage
    exit 0;;
    *) usage
    exit 1;;
  esac
done

if [ -z "$mem" ]; then mem="8g"; fi
if [ -z "$walltime" ]; then walltime="08:00:00"; fi
# if [ -z "$environment" ]; then environment="base"; fi

# mem=$1
# walltime=$2
# environment=$3
# account=$4
# open_dir=$5

if [ "$1" = "-h" ] || [ -z "$1" ]; then
    echo "$USAGE"
    exit
fi

if [ "$HOSTNAME" = "fe-ipsych-01" ]; then
    jobid=$(sbatch --mem-per-cpu=${mem} --cores=1 --time=${walltime} --account=${account}  --wrap='sleep 6d' | awk '{print $4}')
    echo "Submitted job with id: ${jobid}"
    while [ -z "${is_running}" ]; do
        sleep 5
        is_running=$(jobinfo ${jobid} | grep RUNNING)
    done
    node=$(jobinfo $jobid | grep Nodes | awk '{print $3}')
    echo "Job allocated core on node ${node}"
    conda run -n $environment ~/ChrXh2/VSCode-linux-x64/bin/code --folder-uri "vscode-remote://ssh-remote+${node}${open_dir}"
else
    jobid=$(ssh gdk "sbatch --mem-per-cpu=${mem} --cores=1 --time=${walltime} --account=${account}  --wrap='sleep 6d'" | awk '{print $4}')
    echo "Submitted job with id: ${jobid}"
    while [ -z "${is_running}" ]; do
        sleep 5
        is_running=$(ssh gdk "jobinfo ${jobid}" | grep RUNNING)
    done
    node=$(ssh gdk "jobinfo $jobid" | grep Nodes | awk '{print $3}')
    echo "Job allocated core on node ${node}"
    conda run -n $environment code --folder-uri "vscode-remote://ssh-remote+${node}${open_dir}" 
fi