diff --git a/Life Sciences/README.md b/Life Sciences/README.md index d3aadd7a731e34a52f0676e2d2dc33797db13888..56fdae3f844e5121f435abb2c981d2efa885bcb4 100644 --- a/Life Sciences/README.md +++ b/Life Sciences/README.md @@ -1,2 +1,3 @@ Life Sciences Software List: - repositories: xxx +- repositories: TRF diff --git a/Life Sciences/TRF/TRF-4.09.1.sh b/Life Sciences/TRF/TRF-4.09.1.sh new file mode 100644 index 0000000000000000000000000000000000000000..7f54b07623d13d9d491634a90430fc962c6ffe57 --- /dev/null +++ b/Life Sciences/TRF/TRF-4.09.1.sh @@ -0,0 +1,50 @@ +#!/bin/bash +if [[ $# -ne 2 ]]; then + echo "The format is as follows:" + echo "bash TRF-4.09.1.sh buildpath installpath" + echo ":param buildpath: 应用构建绝对路径" + echo ":param installpath: 应用安装绝对路径" + exit 1 +fi + +[[ ! "$1" =~ ^/.* || ! -d "$1" || "$1" = "/" ]] && echo "请输入正确的构建路径" && exit 1 +[[ ! "$2" =~ ^/.* || ! -d "$2" || "$2" = "/" ]] && echo "请输入正确的安装路径" && exit 1 + +buildpath=$1 +installpath=$2 +[[ "$buildpath" =~ .*/$ ]] && buildpath=${buildpath%/*} +[[ "$installpath" =~ .*/$ ]] && installpath=${installpath%/*} +yum install -y environment-modules csh time patch libatomic perl-Data-Dumper autoconf automake libtool numactl binutils systemd-devel valgrind flex wget + +set -e +wget -t 0 -c -P $buildpath https://github.com/Benson-Genomics-Lab/TRF/archive/v4.09.1.tar.gz +tar -xvf $buildpath/v4.09.1.tar.gz -C $buildpath && rm -rf $buildpath/v4.09.1.tar.gz +#cp configure.defaults.patch $buildpath/TRF-4.09.1 +cd $buildpath/TRF-4.09.1 +#patch -p1 < ./configure.defaults.patch +#ln -fs /usr/lib64/libz.so.1.2.11 /usr/lib64/libz.so +#echo 4 | ./configure +#sed -i 's/derf/erf/g' ./phys/module_mp_SBM_polar_radar.F +#sed -i -e 's/gcc/clang/g' \ +# -e 's/gfortran/flang/g' \ +# -e 's/mpicc/mpicc -DMPI2_SUPPORT/g' \ +# -e 's/ -ftree-vectorize//g' \ +# -e 's/length-none/length-0/g' \ +# -e 's/-frecord-marker\=4/ /g' \ +# -e 's/\-w \-O3 \-c/-mcpu=native \-w \-O3 \-c/g' \ +# -e 's/\# \-g $(FCNOOPT) .*/\-g/g' \ +# -e 's/$(FCBASEOPTS_NO_G)/-mcpu=native $(OMP) $(FCBASEOPTS_NO_G)/g' configure.wrf + +#./compile -j $(nproc) em_real | tee compile.log +#mkdir -p $installpath/TRF-4.09.1 && cp -r $buildpath/TRF-4.09.1/* $installpath/TRF-4.09.1 +echo "make start ++++++++++++++++++++++++++++++++++++++++++++++++++++++" +mkdir -p $installpath/TRF-4.09.1 +CC=clang ./configure --prefix=$installpath/TRF-4.09.1 + +make +make install +echo "install end ++++++++++++++++++++++++++++++++++++++++++++++++++++++" +echo $buildpath +echo $installpath +cp -r $buildpath/TRF-4.09.1/test_seqs.fasta $installpath/TRF-4.09.1/bin/ +rm -rf $buildpath/TRF-4.09.1 diff --git a/Life Sciences/TRF/build.sh b/Life Sciences/TRF/build.sh new file mode 100644 index 0000000000000000000000000000000000000000..6e14bffaf70fa0b7007cdcebe62d584018901861 --- /dev/null +++ b/Life Sciences/TRF/build.sh @@ -0,0 +1,56 @@ +#!/bin/bash +if [[ $# -ne 2 ]]; then + echo "The format is as follows:" + echo "bash build.sh buildpath installpath" + echo ":param buildpath: 应用构建绝对路径" + echo ":param installpath: 应用安装绝对路径" + exit 1 +fi + +[[ ! "$1" =~ ^/.* || "$1" = "/" ]] && echo "请输入正确的构建路径" && exit 1 +[[ ! "$2" =~ ^/.* || "$2" = "/" ]] && echo "请输入正确的安装路径" && exit 1 + +create_dir() +{ + local path=$1 + [[ "$path" =~ .*/$ ]] && path=${path%/*} + if [[ ! -d "$path" && ! -f "$path" ]]; then mkdir -p $path; else path=$path`date "+%y%m%d%H%M%S"` && mkdir -p $path; fi + echo $path +} + +buildpath=$(create_dir $1) +installpath=$(create_dir $2) + +yum install -y m4 environment-modules systemd-devel +source /etc/profile +module purge + +set -e +dep_dir="dependency" +bash $dep_dir/bisheng-compiler-2.1.0.sh $buildpath $installpath +module use $installpath/bisheng-compiler-2.1.0 +module load $installpath/bisheng-compiler-2.1.0/bisheng_modulefiles + +echo "aaaaaaa" + +bash TRF-4.09.1.sh $buildpath $installpath + +mkdir -p pkg/TRF-4.09.1 && cp -r $installpath/* pkg/TRF-4.09.1/ +ls +cat>"pkg/TRF-4.09.1/env.sh"< /dev/null +current_dir=\$(cd "\$(dirname "\${BASH_SOURCE[0]}")" &> /dev/null && pwd) +for d in \$(ls \$current_dir) +do + [[ ! \$d =~ "TRF" && ! -f "\$current_dir/\$d" ]] && cd \$current_dir/\$d && module use \$(pwd) && module load \$(pwd)/*modulefiles +done +cd \$current_dir + +EOF +rm -rf pkg/TRF-4.09.1/bisheng-compiler-2.1.0 +cd pkg/ && tar zcvf TRF-4.09.1.tar.gz TRF-4.09.1 + +rm -rf $buildpath $installpath diff --git a/Life Sciences/TRF/dependency/bisheng-compiler-2.1.0.sh b/Life Sciences/TRF/dependency/bisheng-compiler-2.1.0.sh new file mode 100644 index 0000000000000000000000000000000000000000..5d46084f8395a233419c091eec9aadfeaa014429 --- /dev/null +++ b/Life Sciences/TRF/dependency/bisheng-compiler-2.1.0.sh @@ -0,0 +1,42 @@ +#!/bin/bash + +if [[ $# -ne 2 ]]; then + echo "The format is as follows:" + echo "bash bisheng-compiler-2.1.0.sh buildpath installpath" + echo ":param buildpath: 应用构建绝对路径" + echo ":param installpath: 应用安装绝对路径" + exit 1 +fi + +[[ ! "$1" =~ ^/.* || ! -d "$1" || "$1" = "/" ]] && echo "请输入正确的构建路径" && exit 1 +[[ ! "$2" =~ ^/.* || ! -d "$2" || "$2" = "/" ]] && echo "请输入正确的安装路径" && exit 1 + +buildpath=$1 +installpath=$2 +[[ "$buildpath" =~ .*/$ ]] && buildpath=${buildpath%/*} +[[ "$installpath" =~ .*/$ ]] && installpath=${installpath%/*} +set -e +yum install -y wget tar environment-modules libatomic + +wget -t 0 -c -P $buildpath https://mirrors.huaweicloud.com/kunpeng/archive/compiler/bisheng_compiler/bisheng-compiler-2.1.0-aarch64-linux.tar.gz +tar xf $buildpath/bisheng-compiler-2.1.0-aarch64-linux.tar.gz -C $buildpath && rm -rf $buildpath/bisheng-compiler-2.1.0-aarch64-linux.tar.gz +mkdir -p $installpath/bisheng-compiler-2.1.0 && cp -r $buildpath/bisheng-compiler-2.1.0-aarch64-linux/* $installpath/bisheng-compiler-2.1.0/ + +cat>"$installpath/bisheng-compiler-2.1.0/bisheng_modulefiles"<