diff --git a/LifeSciences/README.md b/LifeSciences/README.md index 0fbae3f8c71f4f843628c6f1469a0b5e2d7ead3a..8764c7376e152d7ef4dd6eb189aa45aafb52ea92 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: deepTools-2.0.0 \ No newline at end of file diff --git a/LifeSciences/deepTools-2.0.0/build.sh b/LifeSciences/deepTools-2.0.0/build.sh new file mode 100644 index 0000000000000000000000000000000000000000..439c3de3c1942d14c0fe1277e9fc25f2d4292ef7 --- /dev/null +++ b/LifeSciences/deepTools-2.0.0/build.sh @@ -0,0 +1,76 @@ +#!/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/numpy-1.8.0.sh $buildpath $installpath + +bash $dep_dir/scipy-0.17.0.sh $buildpath $installpath + +bash $dep_dir/matplotlib-1.4.0.sh $buildpath $installpath + +bash $dep_dir/cython-0.21.sh $buildpath $installpath + +bash $dep_dir/pysam-0.8.2.sh $buildpath $installpath + +bash $dep_dir/bx-python-0.7.4.sh $buildpath $installpath + +bash $dep_dir/numpydoc-0.5.sh $buildpath $installpath + +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/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/pyBigWig-0.2.1.sh $buildpath $installpath + +bash deeptools-2.0.0.sh $buildpath $installpath + +mkdir -p pkg/deeptools-2.0.0-hpc && cp -r $installpath/* pkg/deeptools-2.0.0-hpc/ +cat>"pkg/deeptools-2.0.0-hpc/run.sh"< /dev/null +current_dir=\$(cd "\$(dirname "\${BASH_SOURCE[0]}")" &> /dev/null && pwd) +for d in \$(ls \$current_dir) +do + [[ ! \$d =~ "deeptools" && ! \$d =~ "numpy" && ! \$d =~ "scipy" && ! \$d =~ "matplotlib" && ! \$d =~ "cython" && ! \$d =~ "pysam" && ! \$d =~ "bx-python" && ! \$d =~ "numpydoc" && ! \$d =~ "pyBigWig" && ! -f "\$current_dir/\$d" ]] && cd \$current_dir/\$d && module use \$(pwd) && module load \$(pwd)/*modulefiles +done + +EOF +cd pkg/ && tar zcvf deeptools-2.0.0-hpc.tar.gz deeptools-2.0.0-hpc + +rm -rf $buildpath $installpath diff --git a/LifeSciences/deepTools-2.0.0/deeptools-2.0.0.sh b/LifeSciences/deepTools-2.0.0/deeptools-2.0.0.sh new file mode 100644 index 0000000000000000000000000000000000000000..d67dcc330ea58091d1d1b4cd269cda249f50af9a --- /dev/null +++ b/LifeSciences/deepTools-2.0.0/deeptools-2.0.0.sh @@ -0,0 +1,34 @@ +#!/bin/bash + +if [[ $# -ne 2 ]]; then + echo "The format is as follows:" + echo "bash redundans-v0.13c.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 + +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 +yum install -y environment-modules csh time patch libatomic perl-Data-Dumper autoconf automake libtool numactl binutils systemd-devel valgrind flex wget + +set -e +yum install numpy zlib-devel git -y + +cd $buildpath +wget -t 0 -c https://github.com/deeptools/deepTools/archive/refs/tags/2.0.0.tar.gz -O $buildpath/deeptools-2.0.0.tar.gz + +tar -zxvf deeptools-2.0.0.tar.gz && rm -rf deeptools-2.0.0.tar.gz +mkdir $buildpath/deeptools-2.0.0 && cp -rf $buildpath/deepTools-2.0.0/* $buildpath/deeptools-2.0.0 + +cd $buildpath/deeptools-2.0.0 +python setup.py install +mkdir -p $installpath/deeptools-2.0.0 && cp -rf $buildpath/deeptools-2.0.0/* $installpath/deeptools-2.0.0 + +rm -rf $buildpath/deeptools-2.0.0 diff --git a/LifeSciences/deepTools-2.0.0/dependency/bisheng-compiler-2.1.0.sh b/LifeSciences/deepTools-2.0.0/dependency/bisheng-compiler-2.1.0.sh new file mode 100644 index 0000000000000000000000000000000000000000..e30d4b3fc6a847fb1323a249e0dc70d85abbf462 --- /dev/null +++ b/LifeSciences/deepTools-2.0.0/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 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"<"$installpath/bwa-0.7.17/bwa_modulefiles"<"$installpath/lzo-2.10/lzo_modulefiles"<"$installpath/samtools-1.15.1/samtools_modulefiles"<