diff --git a/templates/sambamba/0.8.2/data.sambamba.arm.cpu.bisheng.config b/templates/sambamba/0.8.2/data.sambamba.arm.cpu.bisheng.config new file mode 100644 index 0000000000000000000000000000000000000000..99f222a804f93c5bf949e78a06900f08e06c0717 --- /dev/null +++ b/templates/sambamba/0.8.2/data.sambamba.arm.cpu.bisheng.config @@ -0,0 +1,61 @@ +[SERVER] +11.11.11.11 + +[DOWNLOAD] +sambamba/0.8.2 https://github.com/biod/sambamba/archive/refs/tags/v0.8.2.tar.gz sambamba-0.8.2.tar.gz +ldc/1.29.0 https://github.com/ldc-developers/ldc/releases/download/v1.29.0/ldc2-1.29.0-linux-aarch64.tar.xz ldc2-1.29.0-linux-aarch64.tar.xz +chrom20 http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase3/data/HG00100/alignment/HG00100.chrom20.ILLUMINA.bwa.GBR.low_coverage.20130415.bam + +[DEPENDENCY] +set -e +set -x + +./jarvis -install hpckit/2024.12.30 any +module use software/utils/hpckit/2024.12.30/HPCKit/24.12.30/modulefiles +module purge +module add bisheng/compiler4.1.0/bishengmodule +export CC=`which clang` +export CXX=`which clang++` +export FC=`which flang` +sudo dnf install zlib-devel lz4-devel +tar -xzvf ${JARVIS_DOWNLOAD}/sambamba-0.8.2.tar.gz +tar xf ${JARVIS_DOWNLOAD}/ldc2-1.29.0-linux-aarch64.tar.xz +mkdir -p ldc +mkdir -p CASE +cp ${JARVIS_DOWNLOAD}/HG00100.chrom20.ILLUMINA.bwa.GBR.low_coverage.20130415.bam ./CASE +mv ldc2-1.29.0-linux-aarch64 ldc +export PATH=${JARVIS_ROOT}/ldc/ldc2-1.29.0-linux-aarch64/bin:$PATH +export LIBRARY_PATH=${JARVIS_ROOT}/ldc/ldc2-1.29.0-linux-aarch64/lib:$LIBRARY_PATH + +[ENV] +./jarvis -install hpckit/2024.12.30 any +module use software/utils/hpckit/2024.12.30/HPCKit/24.12.30/modulefiles +module purge +module add bisheng/compiler4.1.0/bishengmodule +export CC=`which clang` +export CXX=`which clang++` +export FC=`which flang` +export PATH=${JARVIS_ROOT}/ldc/ldc2-1.29.0-linux-aarch64/bin:$PATH +export LIBRARY_PATH=${JARVIS_ROOT}/ldc/ldc2-1.29.0-linux-aarch64/lib:$LIBRARY_PATH + +[APP] +app_name = sambamba +build_dir = ${JARVIS_ROOT}/sambamba-0.8.2/ +binary_dir = ${JARVIS_ROOT}/sambamba-0.8.2/bin/ +case_dir = ${JARVIS_ROOT}/CASE + +[BUILD] +make + +[CLEAN] +make clean + +[RUN] +run = time +binary = sambamba-0.8.2 sort HG00100.chrom20.ILLUMINA.bwa.GBR.low_coverage.20130415.bam +nodes = 1 + +[PERF] +perf= +nsys= +ncu=--target-processes all