From f5dfe7c2872e71aec0bf55d5618080ca5ae57090 Mon Sep 17 00:00:00 2001 From: Jonathan Crabtree Date: Tue, 18 Jun 2019 14:39:03 -0400 Subject: [PATCH] Update compilation command for Ubuntu 16.04LTS and samtools-1.7 --- util/samtools/make.sh | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/util/samtools/make.sh b/util/samtools/make.sh index 6aa2f4f..f69f594 100755 --- a/util/samtools/make.sh +++ b/util/samtools/make.sh @@ -1,6 +1,7 @@ #!/bin/bash -# compilation command for Ubuntu Linux +# compilation command for Ubuntu 16.04LTS export CFLAGS=`pkg-config --cflags --libs glib-2.0` -export SAMTOOLS=../samtools-0.1.19 -gcc bam_hmp_util.c bam_get_coverage.c $CFLAGS -L$SAMTOOLS -I$SAMTOOLS -lbam -o bam_get_coverage -lz -lgobject-2.0 -lgmodule-2.0 -lpthread +export SAMTOOLS=/opt/samtools-1.7 +export HTSLIB=/opt/samtools-1.7/htslib-1.7 +gcc bam_hmp_util.c bam_get_coverage.c $CFLAGS -L$SAMTOOLS -L$HTSLIB -I$SAMTOOLS -I$HTSLIB -lst -lhts -lbam -o bam_get_coverage -llzma -lbz2 -lz -lgobject-2.0 -lgmodule-2.0 -lpthread