diff --git a/LifeSciences/README.md b/LifeSciences/README.md index cffd101b6aec3700ed6736f799b17ef9502f3b25..bb4f071e4bbea3b9bde10896fd53ec35d8d3d260 100644 --- a/LifeSciences/README.md +++ b/LifeSciences/README.md @@ -15,3 +15,5 @@ Life Sciences Software List: - repositories: 3d-dna-180922 - repositories: featureCounts-2.0.3 - repositories: ambertools-21 +- repositories: deepTools-2.0.0 + diff --git a/LifeSciences/deepTools-2.0.0/build.sh b/LifeSciences/deepTools-2.0.0/build.sh new file mode 100644 index 0000000000000000000000000000000000000000..e1f6bb723638ddce9e2d501ac9c312e8ed4ff159 --- /dev/null +++ b/LifeSciences/deepTools-2.0.0/build.sh @@ -0,0 +1,92 @@ +#!/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 +yum install zlib zlib-devel openssl openssl-devel gcc-gfortran lapack-devel xz-devel curl-devel lzo lzo-devel freetype-devel cmake bzip2-devel ncurses-devel bwa samtools -y +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 + +export CC=`which clang` +export CXX=`which clang++` +export FC=`which flang` + +bash $dep_dir/python-2.7.18.sh $buildpath $installpath +module use $installpath/python-2.7.18 +module load $installpath/python-2.7.18/python_modulefiles + +bash $dep_dir/setuptools-28.8.0.sh $buildpath $installpath + +bash $dep_dir/pip-19.3.1.sh $buildpath $installpath + +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 $installpath + +bash $dep_dir/cython-0.21.sh $buildpath $installpath + +bash $dep_dir/pysam-0.8.2.sh $buildpath $installpath + +bash $dep_dir/python-lzo-1.14.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/pyBigWig-0.2.1.sh $buildpath $installpath + +bash deeptools-2.0.0.sh $buildpath $installpath +module use $installpath/deeptools-2.0.0 +module load $installpath/deeptools-2.0.0/deeptools_modulefiles + +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 f in "\${current_dir}"/*; do + if [[ -d "\${f}" && -f "\$(ls "\${f}"/*modulefiles 2>&1)" ]]; then + module use "\${f}" && module load "\${f}"/*modulefiles + fi +done + +for file in \$(ls \$DEEPTOOLS/bin); do + sed -i "1c#!\$PWD/python-2.7.18/bin/python" \$DEEPTOOLS/bin/\$file +done + +echo -e "\033[1;32;1mdeepTools environment initialization completed.\033[0m" + +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..50e78b6f1b955dd3300c8b8bf68f12b486398cdb --- /dev/null +++ b/LifeSciences/deepTools-2.0.0/deeptools-2.0.0.sh @@ -0,0 +1,48 @@ +#!/bin/bash + +if [[ $# -ne 2 ]]; then + echo "The format is as follows:" + echo "bash deeptools-2.0.0.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" =~ ^/.* || "$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 10 -c https://github.com/deeptools/deepTools/archive/refs/tags/2.0.0.tar.gz + +tar -zxvf 2.0.0.tar.gz && rm -rf 2.0.0.tar.gz +cd $buildpath/deepTools-2.0.0 + +$installpath/python-2.7.18/bin/python setup.py install --prefix=$installpath/deeptools-2.0.0/ + +cat>"$installpath/deeptools-2.0.0/deeptools_modulefiles"<"$installpath/bisheng-compiler-2.1.0/bisheng_modulefiles"<"$installpath/python-2.7.18/python_modulefiles"<