File: run-tests

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berkeley-express 1.5.3%2Bdfsg-1
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file content (12 lines) | stat: -rwxr-xr-x 414 bytes parent folder | download | duplicates (3) 
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#!/bin/sh -ex
pkg=berkeley-express
if [ "$AUTOPKGTEST_TMP" = "" ] ; then
  AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
fi

cd "${AUTOPKGTEST_TMP}"
cp /usr/share/doc/${pkg}/sample_data/* .
gunzip *
bowtie-build --offrate 1 transcripts.fasta transcripts
bowtie -aS -X 800 --offrate 1 transcripts -1 reads_1.fastq -2 reads_2.fastq | samtools view -Sb - > hits.bam
berkeley-express transcripts.fasta hits.bam