diff --git a/templates/cactus/2.9.2/data.cactus.arm.cpu.config b/templates/cactus/2.9.2/data.cactus.arm.cpu.config new file mode 100644 index 0000000000000000000000000000000000000000..4e7bd93745d0beab393772d36f7fe9251e13e1f3 --- /dev/null +++ b/templates/cactus/2.9.2/data.cactus.arm.cpu.config @@ -0,0 +1,91 @@ +[SERVER] +11.11.11.11 + +[DOWNLOAD] +cactus/2.9.2 https://github.com/ComparativeGenomicsToolkit/cactus/releases/download/v2.9.2/cactus-v2.9.2.tar.gz +SSE2NONE.h/1.0 https://raw.githubusercontent.com/jratcliff63367/sse2neon/refs/heads/master/SSE2NEON.h +case1 https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactusTestData/master/T2T_primate_PAR/mPanTro3_XY_1_5000000.fa +case2 https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactusTestData/master/T2T_primate_PAR/mPanPan1_XY_1_5000000.fa +case3 https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/refs/heads/master/examples/par1_cb.txt + +[DEPENDENCY] +set -e +set -x +module purge +./jarvis -install package/anaconda3/2023.3 any +source ${JARVIS_ROOT}/software/utils/anaconda3/2023.3/etc/profile.d/conda.sh + +[ENV] +module purge +source ${JARVIS_ROOT}/software/utils/anaconda3/2023.3/etc/profile.d/conda.sh +mkdir -p ${JARVIS_ROOT}/case + +[APP] +app_name = cactus +build_dir = ${JARVIS_ROOT} +binary_dir = +case_dir = ${JARVIS_ROOT}/case + +[BUILD] +rm -rf ${JARVIS_ROOT}/software/utils/anaconda3/2023.3/envs/cactus +conda create -n cactus -y +conda activate cactus +conda install python=3.8 -c conda-forge -y +cd ${JARVIS_TMP} +rm -rf cactus-v2.9.2 +tar -xf ${JARVIS_DOWNLOAD}/cactus-v2.9.2.tar.gz +cd cactus-v2.9.2 +git config --global --add safe.directory `pwd` +export C_INCLUDE_PATH=/usr/include +python3 -m pip install -U -r ./toil-requirement.txt --trusted-host mirrors.huaweicloud.com -i https://mirrors.huaweicloud.com/repository/pypi/simple +python3 -m pip install -U . --trusted-host mirrors.huaweicloud.com -i https://mirrors.huaweicloud.com/repository/pypi/simple +conda install libxml2 zlib hdf5 hdf5-static gxx_linux-aarch64=10.3.0 gcc_linux-aarch64=10.3.0 gfortran_linux-aarch64=10.3.0 libgomp=10.3.0 -c conda-forge -y +export C_INCLUDE_PATH=$CONDA_PREFIX/include:$CONDA_PREFIX/include/libxml2:$C_INCLUDE_PATH +export LIBRARY_PATH=$CONDA_PREFIX/lib:/usr/lib64 +cp ${JARVIS_DOWNLOAD}/SSE2NEON.h submodules/abPOA/include +make +cp -a bin/* $CONDA_PREFIX/bin +cp -a lib/* $CONDA_PREFIX/lib +cp -a include/* $CONDA_PREFIX/include +conda deactivate +rm -rf ${JARVIS_TMP}/cactus-v2.9.2 + +[RUN] +run = +binary = +nodes = 1 + +[BATCH] +#定义日志文件 +LOG_FILE="cactus-performance.log" + +#清空日志文件 +> "$LOG_FILE" + +#执行命令并统计性能 +#待补充 + +[JOB] +#!/bin/sh +#DSUB -n cactus_test +#DSUB --mpi hmpi +#DSUB -q default +#DSUB -N 1 +#DSUB -R cpu =128 +#DSUB -oo cactus_$J.out +#DSUB -eo cactus.$J.err + +conda activate cactus + +#生成算例 +cd ${JARVIS_ROOT}/case +if [ ! -f "par1_cb.txt" ];then + cp ${JARVIS_DOWNLOAD}/mPanTro3_XY_1_5000000.fa . + cp ${JARVIS_DOWNLOAD}/mPanPan1_XY_1_5000000.fa . + cp ${JARVIS_DOWNLOAD}/par1_cb.txt . + sed -i "s%https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactusTestData/master/T2T_primate_PAR/%%g" par1_cb.txt +fi + +#运行 +#待补充 +#cactus ./output ./par1_cb.txt ./par1_cb.hal