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#!/bin/sh -e
# http://dep.debian.net/deps/dep8/
# Autopkgtest: Test if (bio-)eagle run analysis correctly
# Author: Dylan Aïssi <bob.dybian@gmail.com>
# Last-Update: 2016-10-30
pkg=bio-eagle
if [ "$AUTOPKGTEST_TMP" = "" ] ; then
AUTOPKGTEST_TMP=`mktemp -d /tmp/${pkg}-test.XXXXXX`
fi
cd $AUTOPKGTEST_TMP
cp -a /usr/share/doc/${pkg}/examples/* $AUTOPKGTEST_TMP
gunzip EUR_test.bed.gz
gunzip EUR_test.bim.gz
gunzip EUR_test.fam.gz
gunzip phased.sample.gz
gunzip ref.bcf.gz
# From upstream run_example.sh
bio-eagle \
--bfile=EUR_test \
--geneticMapFile=USE_BIM \
--chrom=21 \
--outPrefix=phased \
--numThreads=4
bio-eagle \
--bfile=EUR_test \
--geneticMapFile=USE_BIM \
--chrom=21 \
--outPrefix=phased \
--numThreads=4 \
--v1
bio-eagle \
--bfile=EUR_test \
--geneticMapFile=USE_BIM \
--chrom=21 \
--outPrefix=phased \
--numThreads=4 \
--v1fast
rm -rf $AUTOPKGTEST_TMP/*
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