diff --git a/templates/hisat/2.1.0/data.hisat.arm.cpu.bisheng.config b/templates/hisat/2.1.0/data.hisat.arm.cpu.bisheng.config new file mode 100644 index 0000000000000000000000000000000000000000..2d8528ce627a7083d73245e26c27778e933cd1bb --- /dev/null +++ b/templates/hisat/2.1.0/data.hisat.arm.cpu.bisheng.config @@ -0,0 +1,81 @@ +[SERVER] +11.11.11.11 + +[DOWNLOAD] +hisat2/2.1.0 $JARVIS_PROXY/infphilo/hisat2/archive/refs/tags/v2.1.0.tar.gz hisat2-2.1.0.tar.gz +R1.fq http://opengene.org/data/R1.fq.gz +R2.fq http://opengene.org/data/R2.fq.gz +Drosophila_melanogaster.BDGP6.dna.toplevel.fa http://ftp.ensembl.org/pub/release-84/fasta/drosophila_melanogaster/dna/Drosophila_melanogaster.BDGP6.dna.toplevel.fa.gz + + +[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 +tar -vzxf ${JARVIS_DOWNLOAD}/hisat2-2.1.0.tar.gz +mkdir -p TESTCASE +cp ${JARVIS_DOWNLOAD}/Drosophila_melanogaster.BDGP6.dna.toplevel.fa.gz TESTCASE +cp ${JARVIS_DOWNLOAD}/R1.fq.gz TESTCASE +cp ${JARVIS_DOWNLOAD}/R2.fq.gz TESTCASE +cd TESTCASE +gzip -d Drosophila_melanogaster.BDGP6.dna.toplevel.fa.gz +gzip -d R1.fq.gz +gzip -d R2.fq.gz +mv Drosophila_melanogaster.BDGP6.dna.toplevel.fa genome.fa + + + + +[ENV] +module use software/utils/hpckit/2024.12.30/HPCKit/24.12.30/modulefiles +module purge +module add bisheng/compiler4.1.0/bishengmodule + +[APP] +app_name = hisat2 +build_dir = ${JARVIS_ROOT}/hisat2-2.1.0/ +binary_dir = ${JARVIS_ROOT}/hisat2-2.1.0/ +case_dir = ${JARVIS_ROOT}/TESTCASE/ + +[BUILD] +sed -i '140a\ +ifeq (aarch64,$(shell uname -m))\ +BITS=64\ +endif +' Makefile +# 使用sed在159行后插入条件判断 +sed -i '160a\ +ifeq (aarch64,$(shell uname -m))\ + BITS_FLAG =\ + SSE_FLAG =\ +endif +' Makefile +sed -i '/^EXTRA_FLAGS\s*+=\s*/s/-DPOPCNT_CAPABILITY//g' Makefile +sed -i.bak '165s/$/ -funroll-loops -std=c++98/' Makefile +sed -i.bak '167s/$/ -std=c++98 -Xlinker --allow-multiple-definition/' Makefile +sed -i.bak '23s/$/ -I./' Makefile + +sed -i.bak 's|#include |#include |g' aligner_sw.h +sed -i.bak 's|#include |#include |g' sse_util.h +export NO_TBB=1 +export POPCNT_CAPABILITY=0 +wget https://raw.githubusercontent.com/DLTcollab/sse2neon/master/sse2neon.h +make -j $(nproc) + + +[CLEAN] +make clean + +[RUN] +run = +binary = hisat2-build genome.fa genome && ${JARVIS_ROOT}/hisat2-2.1.0/hisat2 -t -x genome -p 96 -1 R1.fq -2 R2.fq -S result.sam +nodes = 1 + +[PERF] +perf= +nsys= +ncu=--target-processes all