diff --git a/example/example_pipeline.sh b/example/example_pipeline.sh index cbaf9ce53..bbe5abec9 100644 --- a/example/example_pipeline.sh +++ b/example/example_pipeline.sh @@ -19,7 +19,7 @@ REFERENCE=~/reference_genomes/human/hg19.fa INPUT=pipelined.example.input.bam OUTPUT=pipelined.example.sv.vcf RAW_GRIDSS_ASSEMBLY=${OUTPUT/.sv.vcf/.gridss.assembly.bam} -GRIDSS_JAR=~/bin/gridss-1.8.0-SNAPSHOT-jar-with-dependencies.jar +GRIDSS_JAR=~/bin/gridss-1.8.1-jar-with-dependencies.jar GRIDSS_JVM_ARGS=" -Dsamjdk.use_async_io_read_samtools=true -Dsamjdk.use_async_io_write_samtools=true diff --git a/example/gridss.sh b/example/gridss.sh index 40a45391a..1096d3e97 100644 --- a/example/gridss.sh +++ b/example/gridss.sh @@ -7,7 +7,7 @@ BLACKLIST=wgEncodeDacMapabilityConsensusExcludable.bed REFERENCE=hg19.fa OUTPUT=${INPUT/.bam/.sv.vcf} ASSEMBLY=${OUTPUT/.sv.vcf/.gridss.assembly.bam} -GRIDSS_JAR=../target/gridss-1.8.0-gridss-jar-with-dependencies.jar +GRIDSS_JAR=../target/gridss-1.8.1-gridss-jar-with-dependencies.jar if [[ ! -f "$INPUT" ]] ; then echo "Missing $INPUT input file." diff --git a/example/somatic.sh b/example/somatic.sh index 9813ee410..892c9abd7 100644 --- a/example/somatic.sh +++ b/example/somatic.sh @@ -8,7 +8,7 @@ BLACKLIST=wgEncodeDacMapabilityConsensusExcludable.bed REFERENCE=~/reference_genomes/human/hg19.fa OUTPUT=somatic.sv.vcf ASSEMBLY=${OUTPUT/.sv.vcf/.gridss.assembly.bam} -GRIDSS_JAR=~/bin/gridss-1.8.0-jar-with-dependencies.jar +GRIDSS_JAR=~/bin/gridss-1.8.1-jar-with-dependencies.jar if [[ ! -f "$NORMAL" ]] ; then echo "Missing $NORMAL input file."