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a few tweaks to scripts/jenkins-test #459

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merged 2 commits into from
Nov 4, 2014
Merged

a few tweaks to scripts/jenkins-test #459

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3836744
quote bash vars in scripts/jenkins-test
ryan-williams Nov 3, 2014
2f8fb91
CYA: pre-remove output files in jenkins-test
ryan-williams Nov 4, 2014
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36 changes: 20 additions & 16 deletions scripts/jenkins-test
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Original file line number Diff line number Diff line change
Expand Up @@ -5,26 +5,26 @@ set -e -x
DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
PROJECT_ROOT="$DIR/.."

VERSION=$(grep "<version>" "$PROJECT_ROOT/pom.xml" | head -2 | tail -1 | sed 's/ *<version>//g' | sed 's/<\/version>//g')
HADOOP_VERSION=$(grep "<hadoop.version>" "$PROJECT_ROOT/pom.xml" | head -2 | tail -1 | sed 's/ *<hadoop.version>//g' | sed 's/<\/hadoop.version>//g')
VERSION="$(grep "<version>" "$PROJECT_ROOT/pom.xml" | head -2 | tail -1 | sed 's/ *<version>//g' | sed 's/<\/version>//g')"
HADOOP_VERSION="$(grep "<hadoop.version>" "$PROJECT_ROOT/pom.xml" | head -2 | tail -1 | sed 's/ *<hadoop.version>//g' | sed 's/<\/hadoop.version>//g')"
echo "Testing ADAM version ${VERSION} on Hadoop ${HADOOP_VERSION}"

export MAVEN_OPTS="-Xmx1536m -XX:MaxPermSize=1g"
mvn test -Dnetworkconnected -Dhadoop.version="${HADOOP_VERSION}"

ADAM_TMP_DIR=$(mktemp -d -t "adamTestXXXXXXX")
ADAM_TMP_DIR="$(mktemp -d -t "adamTestXXXXXXX")"
# Just to be paranoid.. use a directory internal to the ADAM_TMP_DIR
ADAM_TMP_DIR="$ADAM_TMP_DIR/deleteMePleaseThisIsNoLongerNeeded"
mkdir $ADAM_TMP_DIR
mkdir "$ADAM_TMP_DIR"

pushd "$PROJECT_ROOT"
# Copy the jar into our temp space for testing
cp -r . $ADAM_TMP_DIR
cp -r . "$ADAM_TMP_DIR"
popd

export SPARK_DRIVER_MEMORY=8g

pushd $ADAM_TMP_DIR
pushd "$ADAM_TMP_DIR"

if [[ $HADOOP_VERSION == "1.0.4" ]]; then
wget http://d3kbcqa49mib13.cloudfront.net/spark-1.1.0-bin-hadoop1.tgz
Expand All @@ -36,23 +36,27 @@ else
export SPARK_HOME="${ADAM_TMP_DIR}/spark-1.1.0-bin-hadoop2.3"
fi

ADAM="./bin/adam-submit "
ADAM="./bin/adam-submit"

echo "Fetching BAM file"
BAM=mouse_chrM.bam
READS=$BAM.reads
PILEUPS=$BAM.pileup
wget https://s3.amazonaws.com/bdgenomics-test/$BAM
READS="$BAM".reads
PILEUPS="$BAM".pileup
rm -rf "$BAM"
wget https://s3.amazonaws.com/bdgenomics-test/"$BAM"
echo "Converting BAM to ADAM read format"
$ADAM bam2adam -samtools_validation lenient $BAM $READS
rm -rf "$READS"
"$ADAM" bam2adam -samtools_validation lenient "$BAM" "$READS"
echo "Converting BAM to ADAM read format with sorting"
$ADAM transform -sort_reads $READS $READS.sorted
rm -rf "$READS".sorted
"$ADAM" transform -sort_reads "$READS" "$READS".sorted
echo "Converting read file to pileup format"
$ADAM reads2ref $READS $PILEUPS
rm -rf "$PILEUPS"
"$ADAM" reads2ref "$READS" "$PILEUPS"
echo "Reading reads"
$ADAM print $READS 1>/dev/null 2>/dev/null
$ADAM flagstat $READS
rm -rf $ADAM_TMP_DIR
"$ADAM" print "$READS" 1>/dev/null 2>/dev/null
"$ADAM" flagstat "$READS"
rm -rf "$ADAM_TMP_DIR"
popd

pushd "$PROJECT_ROOT"
Expand Down