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#!/bin/sh -e
export VERSION=5.2
# Separate version-subversion by '_'
# E.g.: '4_1' (instead of '4.1')
export VERSION_UND=`echo $VERSION | tr '.' '_'`
#---
# Build SnpEff
#---
cd $HOME/workspace/SnpEff/
mvn clean compile assembly:single jar:jar
cp target/SnpEff-$VERSION-jar-with-dependencies.jar $HOME/snpEff/snpEff.jar
# Install JAR file in local Maven repo
mvn install:install-file \
-Dfile=target/SnpEff-$VERSION.jar \
-DgroupId=org.snpeff \
-DartifactId=SnpEff \
-Dversion=$VERSION \
-Dpackaging=jar \
-DgeneratePom=true \
--quiet
cd -
#---
# Build SnpSift
#---
cd $HOME/workspace/SnpSift/
mvn clean compile assembly:single jar:jar
cp target/SnpSift-$VERSION-jar-with-dependencies.jar $HOME/snpEff/SnpSift.jar
# Install JAR file in local Maven repo
mvn install:install-file \
-Dfile=target/SnpSift-$VERSION.jar \
-DgroupId=org.snpsift \
-DartifactId=SnpSift \
-Dversion=$VERSION \
-Dpackaging=jar \
-DgeneratePom=true \
--quiet
cd -
#---
# Update galaxy databases
#---
./scripts_build/galaxy.sh
echo "Build done!"
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