diff --git a/docker/docker-build.sh b/docker/docker-build.sh index e352c41..f219cd3 100644 --- a/docker/docker-build.sh +++ b/docker/docker-build.sh @@ -95,6 +95,9 @@ chmod +x /usr/local/bin/duphold wget -qO /usr/bin/gsort https://github.com/brentp/gsort/releases/download/v0.0.6/gsort_linux_amd64 chmod +x /usr/bin/gsort +wget -qO /usr/bin/bpbio https://github.com/brentp/bpbio/releases/download/v0.1.1/bpbio +chmod +x /usr/bin/bpbio + wget -qO /usr/bin/gargs https://github.com/brentp/gargs/releases/download/v0.3.9/gargs_linux chmod +x /usr/bin/gargs diff --git a/scripts/evaluation.sh b/scripts/evaluation.sh index c9c7f16..b3ac3a6 100644 --- a/scripts/evaluation.sh +++ b/scripts/evaluation.sh @@ -31,11 +31,9 @@ tabix HG002_SVs_Tier1_v0.6.DEL.vcf.gz #smoove_cmd=go run cmd/smoove/smoove.go version=dev -smoove_cmd=./smoove_022 -version=v0.2.2 rm -rf evaluation-$version -$smoove_cmd call --genotype -o evaluation-$version/ -x -p 4 -f $fasta -n testing $cram +go run cmd/smoove/smoove.go call --genotype -o evaluation-$version/ -x -p 4 -f $fasta -n testing $cram bcftools view -i 'SVTYPE="DEL"' evaluation-$version/testing-smoove.genotyped.vcf.gz -O z -o evaluation-$version/testing-smoove.genotyped.DEL.vcf.gz tabix evaluation-$version/testing-smoove.genotyped.DEL.vcf.gz