humann2_interactive

#!/bin/bash

# Set defaults
LOCAL_BASE=''
IMAGE_VERSION='1.0.0'

while getopts :l:c: opt; do
  case $opt in
    l)
      LOCAL_BASE=$OPTARG
      ;;
    \?)
      echo "Invalid option: -$OPTARG" >&2
      exit 1
      ;;
    :)
      echo "Option -$OPTARG requires an argument." >&2
      exit 1
      ;;
  esac
done

if [[ "$(docker images -q umigs/chiron-humann2:${IMAGE_VERSION} 2> /dev/null)" == "" ]]; then
  echo "Docker image v${IMAGE_VERSION} for HUMAnN2 not found.  Downloading first ..."
fi

if [ -z $LOCAL_BASE ]; then
    if [ -w "/opt/chiron" ]; then
        LOCAL_BASE="/opt/chiron/humann2"
    else
        LOCAL_BASE="${HOME}/chiron/humann2"
    fi
fi

if [ ! -d ${LOCAL_BASE} ]; then
    echo "Creating local output directory: ${LOCAL_BASE}"
    mkdir -p ${LOCAL_BASE}
fi

echo "Saving files to /output in this Docker image will make them available in ${LOCAL_BASE} outside of it."
docker run --rm -v ${LOCAL_BASE}:/output -i -t umigs/chiron-humann2:${IMAGE_VERSION} /bin/bash