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#!/bin/bash
CUR_DIR=`pwd`
if [ "$AUTOPKGTEST_TMP" = "" ]; then
AUTOPKGTEST_TMP=`mktemp -d /tmp/${pkg}-test.XXXX`
trap "rm -rf $AUTOPKG_TMP" 0 INT QUIT ABRT PIPE TERM
fi
mkdir -p "$AUTOPKGTEST_TMP"/tests
# Copy test dataset
cp -a "${CUR_DIR}"/debian-tests-data/* "$AUTOPKGTEST_TMP"/tests
cd "$AUTOPKGTEST_TMP"/tests/
# Extract demo dataset
tar -xvf demo.tar.gz
# Change directory to a dataset dir
cd demo/data/HEK293T-METTL3-KO-rep1/
# Run within the dataset dir
xpore dataprep --eventalign nanopolish/eventalign.txt --gtf_or_gff ../../demo.gtf --transcript_fasta ../../demo.fa --out_dir dataprep --genome
# Check output directory
if [ -d "./dataprep" ]; then
echo "Output Directory Generated"
echo "PASS"
else
echo "Output Directory Not Generated"
exit 1
fi
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