diff --git a/LifeSciences/README.md b/LifeSciences/README.md index 3be3521b50e9d7cae92fe80b0372874a8b5549df..9d0034c0063a9f2ad0a25759b6e8111622a45ca6 100644 --- a/LifeSciences/README.md +++ b/LifeSciences/README.md @@ -5,3 +5,4 @@ Life Sciences Software List: - repositories: trimmomatic-0.40 - repositories: RepeatMasker-4.1.2 - repositories: eigensoft-7.2.1 +- repositories: bamtools-2.5.2 diff --git a/LifeSciences/bamtools-2.5.2/bamtools-2.5.2.sh b/LifeSciences/bamtools-2.5.2/bamtools-2.5.2.sh new file mode 100644 index 0000000000000000000000000000000000000000..9bd7014e36ef94cc95044d8ff58f8e00d2c6eb46 --- /dev/null +++ b/LifeSciences/bamtools-2.5.2/bamtools-2.5.2.sh @@ -0,0 +1,48 @@ +#!/bin/bash + +if [[ $# -ne 2 ]]; then + echo "The format is as follows:" + echo "bash bamtools-2.5.2.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 +wget -t 0 -c -P $buildpath https://github.com/pezmaster31/bamtools/archive/refs/tags/v2.5.2.tar.gz + +tar -xvf $buildpath/v2.5.2.tar.gz -C $buildpath && rm -rf $buildpath/v2.5.2.tar.gz + +cd $buildpath/bamtools-2.5.2 + +export CC=clang +export CXX=clang++ + +mkdir -p $installpath/bamtools-2.5.2 +cmake -DCMAKE_INSTALL_PREFIX=$installpath/bamtools-2.5.2 +make +make install +cat>"$installpath/bamtools-2.5.2/bamtools_modulefiles"<"pkg/bamtools-2.5.2-hpc/run.sh"< /dev/null +current_dir=\$(cd "\$(dirname "\${BASH_SOURCE[0]}")" &> /dev/null && pwd) +for d in \$(ls \$current_dir) +do + [[ ! -f "\$current_dir/\$d" ]] && cd \$current_dir/\$d && module use \$(pwd) && module load \$(pwd)/*modulefiles +done +cd \$current_dir +EOF +cd pkg/ && tar zcvf bamtools-2.5.2-hpc.tar.gz bamtools-2.5.2-hpc +rm -rf $buildpath $installpath diff --git a/LifeSciences/bamtools-2.5.2/dependency/bisheng-compiler-2.1.0.sh b/LifeSciences/bamtools-2.5.2/dependency/bisheng-compiler-2.1.0.sh new file mode 100644 index 0000000000000000000000000000000000000000..a53069995751e081370ff3e2559fbc3b2dfd3f4c --- /dev/null +++ b/LifeSciences/bamtools-2.5.2/dependency/bisheng-compiler-2.1.0.sh @@ -0,0 +1,43 @@ +#!/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 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"<