Restore GATK3 to sequence_tools, since it is still used in limited cases

Author: bbimber

SequenceAnalysis/pipeline_code/sequence_tools_install.sh

@@ -276,6 +276,65 @@ else
     echo "Already installed"
 fi
 
+
+#
+# GATK3
+#
+echo ""
+echo ""
+echo "%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%"
+echo "Install GATK3"
+echo ""
+cd $LKSRC_DIR
+
+if [[ ! -e ${LKTOOLS_DIR}/Queue.jar || ! -z $FORCE_REINSTALL ]];
+then
+    rm -Rf ${LKTOOLS_DIR}/Queue.jar
+    rm -Rf ${LKTOOLS_DIR}/GenomeAnalysisTK.jar
+    rm -Rf ${LKSRC_DIR}/gatk
+
+    mkdir -p gatk
+    cd gatk
+
+    echo "Downloading GATK from GIT"
+    git clone git://github.com/broadgsa/gatk-protected.git
+    cd gatk-protected
+    git checkout tags/3.7
+    cd ../
+
+    #this manually increases Xss in the hope of fixing intermittent StackOverlowErrors
+    sed -i '/<groupId>org.scala-tools<\/groupId>/a <configuration><jvmArgs><jvmArg>-Xss10m<\/jvmArg><\/jvmArgs><\/configuration>' ./gatk-protected/pom.xml
+
+    #fix multithreading bug
+    sed -i 's/private final List<GenomeLoc> upstreamDeletionsLoc = new LinkedList<>();/private final ThreadLocal< List<GenomeLoc> > upstreamDeletionsLoc = ThreadLocal.withInitial(() -> new LinkedList<GenomeLoc>());/g' ./gatk-protected/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypingEngine.java
+    sed -i 's/upstreamDeletionsLoc.add(genomeLoc);/upstreamDeletionsLoc.get().add(genomeLoc);/g' ./gatk-protected/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypingEngine.java
+    sed -i 's/upstreamDeletionsLoc.iterator();/upstreamDeletionsLoc.get().iterator();/g' ./gatk-protected/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypingEngine.java
+
+    #libVectorLogless compile:
+    #see: https://gatkforums.broadinstitute.org/gatk/discussion/9947/crashes-with-segmentation-fault-in-shipped-libvectorloglesspairhmm-so
+    sed -i 's/<!--<USE_GCC>1<\/USE_GCC>-->/<USE_GCC>1<\/USE_GCC>/g' ./gatk-protected/public/VectorPairHMM/pom.xml
+    sed -i 's/<!--<C_COMPILER>\/opt\/gcc-4.8.2\/bin\/gcc<\/C_COMPILER>-->/<C_COMPILER>\/usr\/bin\/gcc<\/C_COMPILER>/g' ./gatk-protected/public/VectorPairHMM/pom.xml
+    sed -i 's/<!--<CPP_COMPILER>\/opt\/gcc-4.8.2\/bin\/g++<\/CPP_COMPILER>-->/<CPP_COMPILER>\/usr\/bin\/g++<\/CPP_COMPILER>/g' ./gatk-protected/public/VectorPairHMM/pom.xml
+    cd gatk-protected/public/VectorPairHMM/
+    mvn verify
+    cd ../../../
+    cp gatk-protected/public/VectorPairHMM/target/libVectorLoglessPairHMM.so ${LKTOOLS_DIR}
+
+    cd gatk-protected
+
+    #remove due to compilation / dependency resolution error
+    rm ./public/external-example/src/main/java/org/mycompany/app/*
+    rm ./public/external-example/src/test/java/org/mycompany/app/*
+    sed -i '/<module>external-example<\/module>/d' ./public/pom.xml
+
+    #NOTE: can add -P\!queue to skip queue in some cases
+    mvn verify -U
+    mvn package
+    cp ./protected/gatk-package-distribution/target/gatk-package-distribution-3.7.jar ${LKTOOLS_DIR}/GenomeAnalysisTK.jar
+    cp ./protected/gatk-queue-package-distribution/target/gatk-queue-package-distribution-3.7.jar ${LKTOOLS_DIR}/Queue.jar
+fi
+
+
 if [[ ! -e ${LKTOOLS_DIR}/DISCVRSeq.jar || ! -z $FORCE_REINSTALL ]];
 then
     rm -Rf DISCVRSeq*