From 28fe17558774d7e5b5d874df5b485062ed0a4bb4 Mon Sep 17 00:00:00 2001 From: limingyang Date: Wed, 27 Aug 2025 17:08:01 +0800 Subject: [PATCH] Update augustus template. --- .../3.3.3/data.augustus.arm.cpu.config | 154 +++++++++--------- 1 file changed, 77 insertions(+), 77 deletions(-) diff --git a/templates/augustus/3.3.3/data.augustus.arm.cpu.config b/templates/augustus/3.3.3/data.augustus.arm.cpu.config index 11253660..849c06e8 100644 --- a/templates/augustus/3.3.3/data.augustus.arm.cpu.config +++ b/templates/augustus/3.3.3/data.augustus.arm.cpu.config @@ -1,77 +1,77 @@ -[SERVER] -11.11.11.11 - -[DOWNLOAD] -augustus/3.3.3 $JARVIS_PROXY/Gaius-Augustus/Augustus/archive/refs/tags/v3.3.3.tar.gz Augustus-3.3.3.tar.gz - -[DEPENDENCY] -set -x -set -e -yum install gsl* mysql-devel sqlite* suitesparse* bzip2-devel -y -pip3 install parallel_augustus -i https://mirrors.aliyun.com/pypi/simple --trusted-host mirrors.aliyun.com -. ${DOWNLOAD_TOOL} -u https://rpmfind.net/linux/mageia/distrib/9/aarch64/media/core/release/lpsolve-5.5.2.5-5.mga9.aarch64.rpm -. ${DOWNLOAD_TOOL} -u https://www.rpmfind.net/linux/mageia/distrib/9/aarch64/media/core/release/lpsolve-devel-5.5.2.5-5.mga9.aarch64.rpm -. ${DOWNLOAD_TOOL} -u http://bioinf.uni-greifswald.de/augustus/datasets/sag178.fa.gz -rpm -q lpsolve-5.5.2.5-5.mga9.aarch64 &> /dev/null || rpm -ivh ${JARVIS_DOWNLOAD}/lpsolve-5.5.2.5-5.mga9.aarch64.rpm -rpm -q lpsolve-devel-5.5.2.5-5.mga9.aarch64 &> /dev/null || rpm -ivh ${JARVIS_DOWNLOAD}/lpsolve-devel-5.5.2.5-5.mga9.aarch64.rpm - -module purge -module use ./software/modulefiles - -./jarvis -install bisheng/4.1.0 com -module load bisheng/4.1.0 -export CC=clang CXX=clang++ FC=flang -./jarvis -install mysql/3.3.0 clang -./jarvis -install boost/1.72.0/clang clang -./jarvis -install htslib/1.11 clang -./jarvis -install samtools/1.11 clang -./jarvis -install bamtools/2.5.0 clang - -tar -zxvf $JARVIS_DOWNLOAD/Augustus-3.3.3.tar.gz - -[ENV] -module purge -module use ./software/modulefiles -module load bisheng/4.1.0 -module load mysql/3.3.0 -module load boost-clang/1.72.0 -module load htslib/1.11 -module load samtools/1.11 -module load bamtools/2.5.0 - -[APP] -app_name = Augustus -build_dir = ${JARVIS_ROOT} -binary_dir = -case_dir = ${JARVIS_ROOT}/Augustus-3.3.3/run - -[BUILD] -rm -rf Augustus-3.3.3 -tar -zxvf ${JARVIS_DOWNLOAD}/Augustus-3.3.3.tar.gz -cd Augustus-3.3.3 - -AUGUSTUS_PATH=$(realpath ./install) -sed -i "s|\/opt\/augustus|$AUGUSTUS_PATH|g" Makefile -sed -i -e "18s|.*|SAMTOOLS=${SAMTOOLS_PATH}/lib|" \ - -e "19s|.*|HTSLIB=${HTSLIB_PATH}/lib|" \ - ./auxprogs/bam2wig/Makefile -sed -i "s/g++/clang++/g" ./auxprogs/joingenes/Makefile ./auxprogs/utrrnaseq/Debug/makefile ./auxprogs/utrrnaseq/Debug/src/subdir.mk ./auxprogs/bam2hints/Makefile ./auxprogs/homGeneMapping/src/Makefile ./src/Makefile ./src/unittests/Makefile -sed -i "s?\/usr\/include\/boost?${BOOST_CLANG_PATH}\/include?g" ./auxprogs/utrrnaseq/Debug/src/subdir.mk - -make -j VERBOSE=1 CC=clang CXX=clang++ \ - CFLAGS="-g -lstdc++ -I${SAMTOOLS_PATH}/include -I${BAMTOOLS_PATH}/include/bamtools -I${BOOST_CLANG_PATH}/include -I${HTSLIB_PATH}/include -I${HTSLIB_PATH}/include/htslib -I${MYSQL_PATH}/include/mysql++ -L${BAMTOOLS_PATH}/lib64 -L${BOOST_CLANG_PATH}/lib -L${HTSLIB_PATH}/lib -L${MYSQL_PATH}/lib -L/usr/lib64/mysql" \ - CXXFLAGS="-g -std=c++17 -lstdc++ -I${SAMTOOLS_PATH}/include -I${BAMTOOLS_PATH}/include/bamtools -I${BOOST_CLANG_PATH}/include -I${HTSLIB_PATH}/include -I${HTSLIB_PATH}/include/htslib -I${MYSQL_PATH}/include/mysql++ -L${BAMTOOLS_PATH}/lib64 -L${BOOST_CLANG_PATH}/lib -L${HTSLIB_PATH}/lib -L${MYSQL_PATH}/lib -L/usr/lib64/mysql" -make install - -mkdir run -cd ./run -cp ${JARVIS_DOWNLOAD}/sag178.fa.gz . -gzip -d sag178.fa.gz - -[CLEAN] -make clean - -[RUN] -run = time -p -binary = parallel_augustus -g sag178.fa -o sag178.res -c 1024 -p 128 --extra '--species=human -UTR=on' -nodes = 1 +[SERVER] +11.11.11.11 + +[DOWNLOAD] +augustus/3.3.3 $JARVIS_PROXY/Gaius-Augustus/Augustus/archive/refs/tags/v3.3.3.tar.gz Augustus-3.3.3.tar.gz + +[DEPENDENCY] +set -x +set -e +yum install gsl* mysql-devel sqlite* suitesparse* bzip2-devel lzma xz xz-devel -y +pip3 install parallel_augustus -i https://mirrors.aliyun.com/pypi/simple --trusted-host mirrors.aliyun.com +. ${DOWNLOAD_TOOL} -u https://rpmfind.net/linux/mageia/distrib/9/aarch64/media/core/release/lpsolve-5.5.2.5-5.mga9.aarch64.rpm +. ${DOWNLOAD_TOOL} -u https://www.rpmfind.net/linux/mageia/distrib/9/aarch64/media/core/release/lpsolve-devel-5.5.2.5-5.mga9.aarch64.rpm +. ${DOWNLOAD_TOOL} -u http://bioinf.uni-greifswald.de/augustus/datasets/sag178.fa.gz +rpm -q lpsolve-5.5.2.5-5.mga9.aarch64 &> /dev/null || rpm -ivh ${JARVIS_DOWNLOAD}/lpsolve-5.5.2.5-5.mga9.aarch64.rpm +rpm -q lpsolve-devel-5.5.2.5-5.mga9.aarch64 &> /dev/null || rpm -ivh ${JARVIS_DOWNLOAD}/lpsolve-devel-5.5.2.5-5.mga9.aarch64.rpm + +module purge +module use ./software/modulefiles + +./jarvis -install bisheng/4.1.0 com +module load bisheng/4.1.0 +export CC=clang CXX=clang++ FC=flang +./jarvis -install mysql/3.3.0 clang +./jarvis -install boost/1.72.0/clang clang +./jarvis -install htslib/1.11 clang +./jarvis -install samtools/1.11 clang +./jarvis -install bamtools/2.5.0 clang + +tar -zxvf $JARVIS_DOWNLOAD/Augustus-3.3.3.tar.gz + +[ENV] +module purge +module use ./software/modulefiles +module load bisheng/4.1.0 +module load mysql/3.3.0 +module load boost-clang/1.72.0 +module load htslib/1.11 +module load samtools/1.11 +module load bamtools/2.5.0 + +[APP] +app_name = Augustus +build_dir = ${JARVIS_ROOT} +binary_dir = +case_dir = ${JARVIS_ROOT}/Augustus-3.3.3/run + +[BUILD] +rm -rf Augustus-3.3.3 +tar -zxvf ${JARVIS_DOWNLOAD}/Augustus-3.3.3.tar.gz +cd Augustus-3.3.3 + +AUGUSTUS_PATH=$(realpath ./install) +sed -i "s|\/opt\/augustus|$AUGUSTUS_PATH|g" Makefile +sed -i -e "18s|.*|SAMTOOLS=${SAMTOOLS_PATH}/lib|" \ + -e "19s|.*|HTSLIB=${HTSLIB_PATH}/lib|" \ + ./auxprogs/bam2wig/Makefile +sed -i "s/g++/clang++/g" ./auxprogs/joingenes/Makefile ./auxprogs/utrrnaseq/Debug/makefile ./auxprogs/utrrnaseq/Debug/src/subdir.mk ./auxprogs/bam2hints/Makefile ./auxprogs/homGeneMapping/src/Makefile ./src/Makefile ./src/unittests/Makefile +sed -i "s?\/usr\/include\/boost?${BOOST_CLANG_PATH}\/include?g" ./auxprogs/utrrnaseq/Debug/src/subdir.mk + +make -j VERBOSE=1 CC=clang CXX=clang++ \ + CFLAGS="-g -lstdc++ -I${SAMTOOLS_PATH}/include -I${BAMTOOLS_PATH}/include/bamtools -I${BOOST_CLANG_PATH}/include -I${HTSLIB_PATH}/include -I${HTSLIB_PATH}/include/htslib -I${MYSQL_PATH}/include/mysql++ -L${BAMTOOLS_PATH}/lib64 -L${BOOST_CLANG_PATH}/lib -L${HTSLIB_PATH}/lib -L${MYSQL_PATH}/lib -L/usr/lib64/mysql" \ + CXXFLAGS="-g -std=c++17 -lstdc++ -I${SAMTOOLS_PATH}/include -I${BAMTOOLS_PATH}/include/bamtools -I${BOOST_CLANG_PATH}/include -I${HTSLIB_PATH}/include -I${HTSLIB_PATH}/include/htslib -I${MYSQL_PATH}/include/mysql++ -L${BAMTOOLS_PATH}/lib64 -L${BOOST_CLANG_PATH}/lib -L${HTSLIB_PATH}/lib -L${MYSQL_PATH}/lib -L/usr/lib64/mysql" +make install + +mkdir run +cd ./run +cp ${JARVIS_DOWNLOAD}/sag178.fa.gz . +gzip -d sag178.fa.gz + +[CLEAN] +make clean + +[RUN] +run = time -p +binary = parallel_augustus -g sag178.fa -o sag178.res -c 1024 -p 128 --extra '--species=human -UTR=on' +nodes = 1 -- Gitee