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#!/bin/bash
set -e
set -u
# I can't ship all the reference data in the DEB package. This script
# will help you install it.
# Hopefully soon I'll be able to deal with this by integrating with BioMaj3
enterkey() {
if tty -s ; then
read -p "Press ENTER to continue, Ctrl+C to exit..." -r ignored
echo
fi
}
datadir=rRNA_databases
if echo "$*" | grep -wq -- --here ; then
echo "Downloading to ./$datadir as --here was specified."
# No prompt needed here.
mkdir -p $datadir
cd $datadir
elif [ "`id -u`" = 0 ] ; then
datadir=/usr/share/sortmerna/rRNA_databases
echo "Data will be downloaded to $datadir"
cd $datadir
umask 022
enterkey
else
datadir="$HOME/sortmerna/rRNA_databases"
echo "Data will be downloaded to $datadir"
enterkey
mkdir -p "$datadir"
cd "$datadir"
fi
#Let us fetch! Thankfully no funny processing like we had to do with RDP-Classifier
#tag=master
tag=2.0
for db in rfam-{5s,5.8s}-database-id98 \
silva-arc-{16s-id95,23s-id98} \
silva-bac-{16s-id90,23s-id98} \
silva-euk-{18s-id95,28s-id98} ; do
wget -c "https://github.com/biocore/sortmerna/raw/$tag/rRNA_databases/${db}.fasta"
done
echo DONE
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