#!/bin/bash
set -e
set -o pipefail

name=Test

package=package$name
seqs=sim$name.seqs.tar.gz
annots=sim$name.annots.tar.gz
ancestor=sim$name.ancestor.maf.tar.gz
burnin=sim$name.burnin.maf.tar.gz
noparalogy=sim$name.noparalogyMafs.tar.gz

curl -O "https://cgl.gi.ucsc.edu/data/alignathon/{README.txt,data/sim$name.annots.tar.gz,data/sim$name.seqs.tar.gz,data/sim$name.ancestor.maf.tar.gz,data/sim$name.burnin.maf.tar.gz,data/sim$name.examplePredictions.tar.gz,data/sim$name.noparalogyMafs.tar.gz}"
echo "78e6dc3c21f842c38d2c8359e4962208  sim$name.annots.tar.gz
579fbbfd2dfc8b07667eb0047d8a90da  sim$name.seqs.tar.gz
5c73438007aef3cd255403e5ad4f5483  sim$name.ancestor.maf.tar.gz
3fc9ff8328c3ed856a59a8235ccf0f5c  sim$name.burnin.maf.tar.gz
30f05c4868a530d1aa38824574a09e9d  sim$name.examplePredictions.tar.gz
28fcdd2181ca095b66a73d674d355ae9  simTest.noparalogyMafs.tar.gz" > md5sum.txt
md5sum --check md5sum.txt
rm md5sum.txt
mkdir -p $package/annotations $package/predictions $package/sequences $package/truths $package/regions
mv README.txt $package/

mv $seqs $package/sequences
pushd $package/sequences
tar -xvzf $seqs
rm $seqs
popd

mv $annots $package/annotations
pushd $package/annotations
tar -xvzf $annots
rm $annots
popd

mv $ancestor $package/truths
mv $burnin $package/truths
mv $noparalogy $package/truths
pushd $package/truths
tar -xvzf $ancestor
tar -xvzf $burnin
tar -xvzf $noparalogy
rm $ancestor $burnin $noparalogy
popd

mv sim$name.examplePredictions.tar.gz $package/predictions
pushd $package/predictions
tar -xvzf sim$name.examplePredictions.tar.gz
rm sim$name.examplePredictions.tar.gz
popd