diff --git a/LifeSciences/Lumpy-0.3.1/build.sh b/LifeSciences/Lumpy-0.3.1/build.sh new file mode 100644 index 0000000000000000000000000000000000000000..4547526a38e7532cf06a4a5ac5ef6407fe271430 --- /dev/null +++ b/LifeSciences/Lumpy-0.3.1/build.sh @@ -0,0 +1,81 @@ +#!/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 \ +xz-devel ncurses-devel numpy zlib-devel bzip2-devel lz4-devel Cython autoconf automake libcurl-devel openssl-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 + +export CC=clang +export CXX=clang++ +export FC=flang + +bash $dep_dir/samtools-1.15.1.sh $buildpath $installpath +module use $installpath/samtools-1.15.1 +module load $installpath/samtools-1.15.1/samtools_modulefiles + +bash $dep_dir/samblaster-0.1.26.sh $buildpath $installpath +module use $installpath/samblaster-0.1.26 +module load $installpath/samblaster-0.1.26/samblaster_modulefiles + +bash $dep_dir/ldc2-1.15.0.sh $buildpath $installpath +module use $installpath/ldc2-1.15.0 +module load $installpath/ldc2-1.15.0/ldc2_modulefiles + +bash $dep_dir/sambamba-0.8.2.sh $buildpath $installpath +module use $installpath/sambamba-0.8.2 +module load $installpath/sambamba-0.8.2/sambamba_modulefiles + +bash $dep_dir/pysam-0.19.0.sh $buildpath $installpath +module use $installpath/pysam-0.19.0 +module load $installpath/pysam-0.19.0/pysam_modulefiles + +bash lumpy-0.3.1.sh $buildpath $installpath + +mkdir -p pkg/lumpy-0.3.1-hpc && cp -r $installpath/* pkg/lumpy-0.3.1-hpc/ +cat>"pkg/lumpy-0.3.1-hpc/run.sh"< /dev/null +current_dir="\$(cd "\$(dirname "\${BASH_SOURCE[0]}")" && pwd -P)" +for f in "\${current_dir}"/*; do + if [[ -d "\${f}" && -f "\$(ls "\${f}"/*modulefiles 2>&1)" ]]; then + module use "\${f}" && module load "\${f}"/*modulefiles + fi +done +echo -e "\033[1;32;1mLumpy environment initialization completed.\033[0m" + +EOF +cd pkg/ && tar zcvf lumpy-0.3.1-hpc.tar.gz lumpy-0.3.1-hpc + +rm -rf $buildpath $installpath diff --git a/LifeSciences/Lumpy-0.3.1/dependency/bisheng-compiler-2.1.0.sh b/LifeSciences/Lumpy-0.3.1/dependency/bisheng-compiler-2.1.0.sh new file mode 100644 index 0000000000000000000000000000000000000000..a9f267c24cff4c3d2b8084cdc19684cfc8b0ec0b --- /dev/null +++ b/LifeSciences/Lumpy-0.3.1/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=${installpath%/*} +[[ "$buildpath" == "$installpath" ]] && echo "构建路径与安装路径需为不同路径" && exit 1 +set -e +yum install -y wget tar environment-modules libatomic + +wget -t 10 -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"<"$installpath/ldc2-1.15.0/ldc2_modulefiles"<"$installpath/pysam-0.19.0/pysam_modulefiles"<"$installpath/sambamba-0.8.2/sambamba_modulefiles"<"$installpath/samblaster-0.1.26/samblaster_modulefiles"<"$installpath/samtools-1.15.1/samtools_modulefiles"<"$installpath/lumpy-0.3.1/lumpy_modulefiles"<