diff --git a/templates/bwa/0.7.17/data.bwa.arm.cpu.config b/templates/bwa/0.7.17/data.bwa.arm.cpu.config index c21dc541c414cf9a759ce46cc4092ed1815499dc..414a291c3fe2758150a7476053ec61b4c88516b2 100644 --- a/templates/bwa/0.7.17/data.bwa.arm.cpu.config +++ b/templates/bwa/0.7.17/data.bwa.arm.cpu.config @@ -3,46 +3,83 @@ [DOWNLOAD] bwa/0.7.17 https://sourceforge.net/projects/bio-bwa/files/bwa-0.7.17.tar.bz2 -sse2nenon/master https://www.github.com/jratcliff63367/sse2neon/archive/refs/heads/master.zip sse2neon.zip +SSE2NONE.h/1.0 https://raw.githubusercontent.com/jratcliff63367/sse2neon/refs/heads/master/SSE2NEON.h +case1 https://ftp.sra.ebi.ac.uk/vol1/fastq/ERR104/008/ERR1044518/ERR1044518_1.fastq.gz +case2 https://ftp.sra.ebi.ac.uk/vol1/fastq/ERR104/008/ERR1044518/ERR1044518_2.fastq.gz +case3 https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/001/405/GCA_000001405.15_GRCh38/seqs_for_alignment_pipelines.ucsc_ids/GCA_000001405.15_GRCh38_full_analysis_set.fna.gz [DEPENDENCY] -module use ./software/modulefiles +set -e +set -x module purge -./jarvis -install bisheng/2.1.0 com - +./jarvis -install package/hpckit/2024.12.30 any +module use software/utils/hpckit/2024.12.30/HPCKit/latest/modulefiles +module add bisheng/compiler4.1.0/bishengmodule [ENV] module purge -module use ${JARVIS_ROOT}/software/modulefiles -module add bisheng/2.1.0 -export CC=clang CXX=clang++ FC=flang +module use software/utils/hpckit/2024.12.30/HPCKit/latest/modulefiles +module add bisheng/compiler4.1.0/bishengmodule +export PATH=$JARVIS_ROOT/software/apps/bisheng/bwa/0.7.17:$PATH +mkdir -p ${JARVIS_ROOT}/case [APP] app_name = bwa build_dir = ${JARVIS_ROOT} binary_dir = -case_dir = +case_dir = ${JARVIS_ROOT}/case [BUILD] -#./jarvis -install bwa/0.7.17/clang clang cd ${JARVIS_TMP} -rm -rf bwa-0.7.17 sse2neon-master +rm -rf bwa-0.7.17 tar -xvf ${JARVIS_DOWNLOAD}/bwa-0.7.17.tar.bz2 -unzip ${JARVIS_DOWNLOAD}/sse2neon.zip cd bwa-0.7.17 -bisheng_includedir=`which clang` -bisheng_includedir=${bisheng_includedir%/*/*}/include -cp ${JARVIS_TMP}/sse2neon-master/SSE2NEON.h ${bisheng_includedir} +cp ${JARVIS_DOWNLOAD}/SSE2NEON.h . sed -i "1s/gcc/clang/g" Makefile -sed -i "14s%$%-I${bisheng_includedir}%g" Makefile +sed -i "3s/$/ -Xlinker -zmuldefs/g" Makefile +sed -i "14s%$%-I.%g" Makefile sed -i "29s///g" ksw.c -sed -i "33s%^%//%g" rle.h make +rm -rf $JARVIS_ROOT/software/apps/bisheng/bwa/0.7.17 mkdir -p $JARVIS_ROOT/software/apps/bisheng/bwa/0.7.17 -cp -r ../bwa-0.7.17/* $JARVIS_ROOT/software/apps/bisheng/bwa/0.7.17 -rm -rf ${bisheng_includedir}/SSE2NEON.h +cp -r *.pl bwa $JARVIS_ROOT/software/apps/bisheng/bwa/0.7.17 +rm -rf ${JARVIS_TMP}/bwa-0.7.17 [RUN] run = binary = nodes = 1 + +[BATCH] +#定义日志文件 +LOG_FILE="bwa-performance.log" + +#清空日志文件 +> "$LOG_FILE" + +#执行命令并统计性能 +#待补充 + +[JOB] +#!/bin/sh +#DSUB -n bwa_test +#DSUB --mpi hmpi +#DSUB -q default +#DSUB -N 1 +#DSUB -R cpu =128 +#DSUB -oo bwa_$J.out +#DSUB -eo bwa.$J.err + +#生成算例 +cd ${JARVIS_ROOT}/case +if [ ! -f "ERR1044518_1.fastq" ];then + gzip -d ${JARVIS_DOWNLOAD}/ERR1044518_1.fastq.gz + gzip -d ${JARVIS_DOWNLOAD}/ERR1044518_1.fastq.gz + gzip -d ${JARVIS_DOWNLOAD}/GCA_000001405.15_GRCh38_full_analysis_set.fna.gz + mv GCA_000001405.15_GRCh38_full_analysis_set.fna hs38DH.fasta +fi + +#运行 +#待补充 +#bwa index -a bwtsw hs38DH.fasta +#bwa mem -t 128 hs38DH.fasta ERR1044518_1.fastq ERR1044518_2.fastq > bwa.sam 2>&1 |tee bwa_log