diff --git a/LifeSciences/README.md b/LifeSciences/README.md index 90e4d8d71015b85bb1e3a03c5091ea1911a184da..2fd359dd05ab9f7badc27e23c5994e7fc89541eb 100644 --- a/LifeSciences/README.md +++ b/LifeSciences/README.md @@ -3,3 +3,4 @@ Life Sciences Software List: - repositories: TRF-4.09.1 - repositories: genewise-2.4.1 - repositories: trimmomatic-0.40 +- repositories: RepeatMasker-4.1.2 diff --git a/LifeSciences/RepeatMasker-4.1.2/RepeatMasker-4.1.2.sh b/LifeSciences/RepeatMasker-4.1.2/RepeatMasker-4.1.2.sh new file mode 100644 index 0000000000000000000000000000000000000000..b0f58972b8aa6efb8441945280702ba2588b4427 --- /dev/null +++ b/LifeSciences/RepeatMasker-4.1.2/RepeatMasker-4.1.2.sh @@ -0,0 +1,43 @@ +#!/bin/bash + +if [[ $# -ne 2 ]]; then + echo "The format is as follows:" + echo "bash wrf-4.2.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 +#download src +wget -t 0 -c -P $buildpath http://www.repeatmasker.org/RepeatMasker/RepeatMasker-4.1.2-p1.tar.gz +tar -xvf $buildpath/RepeatMasker-4.1.2-p1.tar.gz -C $buildpath && rm -rf $buildpath/RepeatMasker-4.1.2-p1.tar.gz +#install +mkdir -p $installpath/RepeatMasker-4.1.2-p1 && cp -r $buildpath/RepeatMasker/* $installpath/RepeatMasker-4.1.2-p1 + +cat>"$installpath/RepeatMasker-4.1.2-p1/RepeatMasker_modulefiles"<"pkg/RepeatMasker-4.1.2/run.sh"< /dev/null +current_dir=\$(cd "\$(dirname "\${BASH_SOURCE[0]}")" &> /dev/null && pwd) +for d in \$(ls \$current_dir) +do + [[ ! \$d =~ "RepeatMasker" && ! -f "\$current_dir/\$d" ]] && cd \$current_dir/\$d && module use \$(pwd) && module load \$(pwd)/*modulefiles +done +cd \$current_dir/RepeatMasker-4.1.2-p1 +perl ./configure -libdir \$current_dir/RepeatMasker-4.1.2-p1/Libraries \ + -rmblast_dir \$current_dir/rmblast-2.13.0/bin \ + -trf_prgm \$current_dir/trf-4.09.1/bin/trf \ + -default_search_engine rmblast +cd \$current_dir +EOF +cd pkg/ && tar zcvf RepeatMasker-4.1.2.tar.gz RepeatMasker-4.1.2 + +rm -rf $buildpath $installpath + diff --git a/LifeSciences/RepeatMasker-4.1.2/dependency/bisheng-compiler-2.1.0.sh b/LifeSciences/RepeatMasker-4.1.2/dependency/bisheng-compiler-2.1.0.sh new file mode 100644 index 0000000000000000000000000000000000000000..a53069995751e081370ff3e2559fbc3b2dfd3f4c --- /dev/null +++ b/LifeSciences/RepeatMasker-4.1.2/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"<"$installpath/rmblast-2.13.0/rmblast_modulefiles"<"$installpath/trf-4.09.1/trf_modulefiles"<