Shell script to download and transfrom ENCODE files to ADAM format

transfer.sh

# Files.txt contains URLs for the files
# Make sure you set SPARK_HOME

while read line; do
  url=$line
  filename=$(basename "$url")
  wget "$url"
  hadoop fs -put $filename /user/mapr/encoded/
  ./../adam/bin/adam-submit transform /user/mapr/encoded/$filename /user/mapr/encoded/"${filename/.bam/.adam}"
  hadoop fs -rm /user/mapr/encoded/$filename
  rm $filename
done < files.txt