Update versions and remove old software

Author: bbimber

SequenceAnalysis/pipeline_code/sequence_tools_install.sh

@@ -276,107 +276,13 @@ else
     echo "Already installed"
 fi
 
-#
-# GATK
-#
-echo ""
-echo ""
-echo "%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%"
-echo "Install GATK"
-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}
-
-    #this is a custom extension: https://github.com/biodev/HTCondor_drivers
-    #git clone https://github.com/biodev/HTCondor_drivers.git
-    #mkdir ./gatk-protected/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/condor
-    #cp ./HTCondor_drivers/Queue/CondorJob* ./gatk-protected/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/condor/
-
-    #another, for MV checking
-    mkdir -p ${LK_HOME}/svn/trunk/pipeline_code/
-    svn co --no-auth-cache https://github.com/BimberLab/DiscvrLabkeyModules/trunk/SequenceAnalysis/pipeline_code/gatk ${LK_HOME}/svn/trunk/pipeline_code/gatk/
-
-    mv ${LK_HOME}/svn/trunk/pipeline_code/gatk/MendelianViolationCount.java ./gatk-protected/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/
-    mv ${LK_HOME}/svn/trunk/pipeline_code/gatk/MendelianViolationBySample.java ./gatk-protected/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/
-    mv ${LK_HOME}/svn/trunk/pipeline_code/gatk/GenotypeConcordance.java ./gatk-protected/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/
-    mv ${LK_HOME}/svn/trunk/pipeline_code/gatk/GenotypeConcordanceBySite.java ./gatk-protected/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/
-    mv ${LK_HOME}/svn/trunk/pipeline_code/gatk/MinorAlleleFrequency.java ./gatk-protected/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/
-
-    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*
     rm -Rf ${LKTOOLS_DIR}/DISCVRSeq.jar
 
-    wget $WGET_OPTS https://github.com/BimberLab/DISCVRSeq/releases/download/1.0/DISCVRSeq-1.0.jar
-    cp DISCVRSeq-1.0.jar ${LKTOOLS_DIR}/DISCVRSeq.jar
-fi
-
-if [[ ! -e ${LKTOOLS_DIR}/GenomeAnalysisTK-discvr.jar || ! -z $FORCE_REINSTALL ]];
-then
-    rm -Rf ${LKTOOLS_DIR}/GenomeAnalysisTK-discvr.jar
-    rm -Rf ${LKSRC_DIR}/gatk-discvr
-
-    mkdir -p gatk-discvr
-    cd gatk-discvr
-
-    echo "Downloading GATK from GIT"
-    git clone git://github.com/bbimber/gatk-protected.git
-    cd gatk-protected
-
-    #remove due to compilation error
-    rm ./public/external-example/src/main/java/org/mycompany/app/*
-    rm ./public/external-example/src/test/java/org/mycompany/app/*
-
-    mvn verify -U -P\!queue
-    mvn package -P\!queue
-
-    cp ./protected/gatk-package-distribution/target/gatk-package-distribution-3.7.jar ${LKTOOLS_DIR}/GenomeAnalysisTK-discvr.jar
+    wget $WGET_OPTS https://github.com/BimberLab/DISCVRSeq/releases/download/1.29/DISCVRSeq-1.29.jar
+    cp DISCVRSeq-1.29.jar ${LKTOOLS_DIR}/DISCVRSeq.jar
 fi
 
 
@@ -1336,7 +1242,7 @@ fi
 echo ""
 echo ""
 echo "%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%"
-echo "Installing Trimmomatic"
+echo "Installing lofreq"
 echo ""
 cd $LKSRC_DIR
 
@@ -1355,29 +1261,6 @@ else
 fi
 
 
-#
-#CITE-seq-count
-#
-#
-#echo ""
-#echo ""
-#echo "%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%"
-#echo "Installing CITE-seq-count"
-#echo ""
-#cd $LKSRC_DIR
-#
-#if [[ ! -e ${LKTOOLS_DIR}/CITE-seq-Count || ! -z $FORCE_REINSTALL ]];
-#then
-#    rm -Rf ${LKTOOLS_DIR}/CITE-seq*
-#    mkdir -p ${LKTOOLS_DIR}/CITE-seq-count-base
-#
-#    pip install CITE-seq-Count --upgrade --install-option="--prefix=${LKTOOLS_DIR}/CITE-seq-count-base"
-#    mv ${LKTOOLS_DIR}/CITE-seq-count-base/bin/* ${LKTOOLS_DIR}
-#
-#else
-#    echo "Already installed"
-#fi
-
 if [ ! -z $LK_USER ];
 then
     echo "Setting owner of files to: ${LK_USER}"