dl_from_bs.sh

#!/bin/bash

if [ $# -eq 0 ]; then
    echo "This script can be used to transfer all files from a BaseSpace project "
    echo "Usage: $0 BaseSpaceProjectName DNAnexusProjectName"
    echo "       Before running, be sure to log in to BaseSpace"
    echo "          bs auth"
    echo "       The CLI toolkits for bs and dx can be found here and must be installed first:"
    echo "          https://developer.basespace.illumina.com/docs/content/documentation/cli/cli-overview"
    exit 1
fi

bsproject="$1"

for fileinfo in $(bs contents run --name "$bsproject" --template='{{.Id}},{{.FilePath}}'); do
    fileid=$(echo "$fileinfo" | cut -d, -f1)
    filename=$(echo "$fileinfo" | cut -d, -f2)
    echo "Starting job to transfer file: $filename"
    bslink=$(bs file link --id "$fileid")

    containing_dir=$(dirname "${filename}")
    mkdir -p "${containing_dir}"

    wget $bslink -O $filename
done