diff --git a/LifeSciences/README.md b/LifeSciences/README.md index d3aadd7a731e34a52f0676e2d2dc33797db13888..367845be4aa4e9181ab63cd49a1aa6d9bf688499 100644 --- a/LifeSciences/README.md +++ b/LifeSciences/README.md @@ -1,2 +1,3 @@ Life Sciences Software List: - repositories: xxx +- repositories: TRF-4.09.1 diff --git a/LifeSciences/TRF-4.09.1/TRF-4.09.1.sh b/LifeSciences/TRF-4.09.1/TRF-4.09.1.sh new file mode 100644 index 0000000000000000000000000000000000000000..cff0be28b7c3ddc29962d1b2844a58df55817741 --- /dev/null +++ b/LifeSciences/TRF-4.09.1/TRF-4.09.1.sh @@ -0,0 +1,36 @@ +#!/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 +if [[ "$1" == "$2" ]]; then echo "构建路径与安装路径不能相同,请输入正确的路径"; exit 1; fi + +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 + +cd $buildpath/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 \ No newline at end of file diff --git a/LifeSciences/TRF-4.09.1/build.sh b/LifeSciences/TRF-4.09.1/build.sh new file mode 100644 index 0000000000000000000000000000000000000000..3f586a703dc5dde0f685c10016cd7de0055e5f83 --- /dev/null +++ b/LifeSciences/TRF-4.09.1/build.sh @@ -0,0 +1,53 @@ +#!/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 +if [[ "$1" == "$2" ]]; then echo "构建路径与安装路径不能相同,请输入正确的路径"; exit 1; fi + +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 TRF-4.09.1.sh $buildpath $installpath + +mkdir -p pkg/TRF-4.09.1-hpc && cp -r $installpath/* pkg/TRF-4.09.1-hpc/ + +cat>"pkg/TRF-4.09.1-hpc/run.sh"<"$installpath/bisheng-compiler-2.1.0/bisheng_modulefiles"<