#!/bin/bash

BINARY_HOME=$PREFIX/bin
PACKAGE_HOME=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM

mkdir -p $BINARY_HOME
mkdir -p $PACKAGE_HOME

cp -R * $PACKAGE_HOME

ln -s $PACKAGE_HOME/bin/dsh-bio $BINARY_HOME
ln -s $PACKAGE_HOME/bin/dsh-disinterleave-fastq $BINARY_HOME
ln -s $PACKAGE_HOME/bin/dsh-downsample-fastq $BINARY_HOME
ln -s $PACKAGE_HOME/bin/dsh-downsample-interleaved-fastq $BINARY_HOME
ln -s $PACKAGE_HOME/bin/dsh-extract-fastq $BINARY_HOME
ln -s $PACKAGE_HOME/bin/dsh-fasta-to-fastq $BINARY_HOME
ln -s $PACKAGE_HOME/bin/dsh-fastq-description $BINARY_HOME
ln -s $PACKAGE_HOME/bin/dsh-fastq-to-fasta $BINARY_HOME
ln -s $PACKAGE_HOME/bin/dsh-filter-vcf $BINARY_HOME
ln -s $PACKAGE_HOME/bin/dsh-gfa1-to-gfa2 $BINARY_HOME
ln -s $PACKAGE_HOME/bin/dsh-interleave-fastq $BINARY_HOME
ln -s $PACKAGE_HOME/bin/dsh-intersect-bed $BINARY_HOME
ln -s $PACKAGE_HOME/bin/dsh-remap-phase-set $BINARY_HOME
ln -s $PACKAGE_HOME/bin/dsh-rename-references $BINARY_HOME
ln -s $PACKAGE_HOME/bin/dsh-split-bed $BINARY_HOME
ln -s $PACKAGE_HOME/bin/dsh-split-fasta $BINARY_HOME
ln -s $PACKAGE_HOME/bin/dsh-split-fastq $BINARY_HOME
ln -s $PACKAGE_HOME/bin/dsh-split-gff3 $BINARY_HOME
ln -s $PACKAGE_HOME/bin/dsh-split-interleaved-fastq $BINARY_HOME
ln -s $PACKAGE_HOME/bin/dsh-split-vcf $BINARY_HOME
ln -s $PACKAGE_HOME/bin/dsh-variant-table-to-vcf $BINARY_HOME
ln -s $PACKAGE_HOME/bin/dsh-vcf-header $BINARY_HOME
ln -s $PACKAGE_HOME/bin/dsh-vcf-pedigree $BINARY_HOME
ln -s $PACKAGE_HOME/bin/dsh-vcf-samples $BINARY_HOME
