diff --git a/LifeSciences/README.md b/LifeSciences/README.md index 0fbae3f8c71f4f843628c6f1469a0b5e2d7ead3a..e33049be9bd2b76c525125ba1cdc6807eeeea9a3 100644 --- a/LifeSciences/README.md +++ b/LifeSciences/README.md @@ -6,4 +6,5 @@ Life Sciences Software List: - repositories: RepeatMasker-4.1.2 - repositories: eigensoft-7.2.1 - repositories: redundans-v0.13c -- repositories: bamtools-2.5.2 \ No newline at end of file +- repositories: bamtools-2.5.2 +- repositories: gridss-2.13.2 \ No newline at end of file diff --git a/LifeSciences/gridss-2.13.2/build.sh b/LifeSciences/gridss-2.13.2/build.sh new file mode 100644 index 0000000000000000000000000000000000000000..afb33b48ac7d2eea39b5dd16023f8e51525a8d86 --- /dev/null +++ b/LifeSciences/gridss-2.13.2/build.sh @@ -0,0 +1,68 @@ +#!/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 + +bash $dep_dir/bisheng-jdk-8u322.sh $buildpath $installpath +module use $installpath/bisheng-jdk-8u322 +module load $installpath/bisheng-jdk-8u322/jdk_modulefiles + +bash $dep_dir/bwa-0.7.17.sh $buildpath $installpath +module use $installpath/bwa-0.7.17 +module load $installpath/bwa-0.7.17/bwa_modulefiles + +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/R-4.1.0.sh $buildpath $installpath +module use $installpath/R-4.1.0 +module load $installpath/R-4.1.0/R_modulefiles + +bash gridss-2.13.2.sh $buildpath $installpath + +mkdir -p pkg/gridss-2.13.2-hpc && cp -r $installpath/* pkg/gridss-2.13.2-hpc/ +cat>"pkg/gridss-2.13.2-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 + +EOF +cd pkg/ && tar zcvf gridss-2.13.2-hpc.tar.gz gridss-2.13.2-hpc + +rm -rf $buildpath $installpath diff --git a/LifeSciences/gridss-2.13.2/dependency/R-4.1.0.sh b/LifeSciences/gridss-2.13.2/dependency/R-4.1.0.sh new file mode 100644 index 0000000000000000000000000000000000000000..e3577c28f9c4ee752db14291e5debaa67d34f167 --- /dev/null +++ b/LifeSciences/gridss-2.13.2/dependency/R-4.1.0.sh @@ -0,0 +1,46 @@ +#!/bin/bash + +if [[ $# -ne 2 ]]; then + echo "The format is as follows:" + echo "bash R-4.1.0.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 \ +zlib zlib-devel gcc-gfortran readline-devel libXt-devel openssl openssl-devel pcre pcre-devel bzip2-devel curl-devel + +wget -t 0 -c -P $buildpath https://mirror.lzu.edu.cn/CRAN/src/base/R-4/R-4.1.0.tar.gz +tar xf $buildpath/R-4.1.0.tar.gz -C $buildpath && rm -rf $buildpath/R-4.1.0.tar.gz +cd $buildpath/R-4.1.0 + +./configure --prefix=$installpath/R-4.1.0 CC=clang +make -j$(nproc) +make install + +cat>"$installpath/R-4.1.0/R_modulefiles"<"$installpath/bisheng-compiler-2.1.0/bisheng_modulefiles"<"$installpath/bisheng-jdk-8u322/jdk_modulefiles"<"$installpath/bwa-0.7.17/bwa_modulefiles"<"$installpath/samtools-1.15.1/samtools_modulefiles"<"$installpath/gridss-2.13.2/gridss_modulefiles"<