diff --git a/LifeSciences/README.md b/LifeSciences/README.md index 11f1002e5faf8780ba6e0143e8d738f4cde02f7b..a900e830b3360b78ed8e635e5d75c0ca3744b147 100644 --- a/LifeSciences/README.md +++ b/LifeSciences/README.md @@ -29,3 +29,4 @@ Life Sciences Software List: - repositories: fsl-6.0.5.2 - repositories: freesurfer-7.2 - repositories: BUSCO-5.2.2 +- repositories: gridss-2.13.2 diff --git a/LifeSciences/gridss-2.13.2/build.sh b/LifeSciences/gridss-2.13.2/build.sh new file mode 100644 index 0000000000000000000000000000000000000000..d1b6e17498bd13dda190cde314be9e77bbee5fba --- /dev/null +++ b/LifeSciences/gridss-2.13.2/build.sh @@ -0,0 +1,103 @@ +#!/bin/bash +# 此脚本用来编译安装gridss-2.13.2软件 +# gridss-2.13.2软件介绍 +# GRIDSS是一个模块软件套件，其中包含可用于检测基因组重排的工具。 +# Usage: +# bash /path/to/build.sh /path/to/build /path/to/install +# 使用build.sh 脚本样例 bash /path/to/build.sh /path/to/build /path/to/install +# 使用build.sh 需要root权限或者sudo权限,否则无法安装依赖 +# +############################################################## + +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 bc zlib-devel zlib 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/R-4.2.0.sh $buildpath $installpath + module use $installpath/R-4.2.0 + module load $installpath/R-4.2.0/R-4.2.0_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 gridss-2.13.2.sh $buildpath $installpath + mkdir -p pkg/gridss-2.13.2-hpc && cp -r $installpath/* pkg/gridss-2.13.2-hpc/ + + rm -rf pkg/gridss-2.13.2-hpc/R-4.2.0 + cp $dep_dir/R-4.2.0.sh 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 + [[ ! \$d =~ "scripts" && ! -f "\$current_dir/\$d" ]] && cd \$current_dir/\$d && module use \$(pwd) && module load \$(pwd)/*modulefiles +done + +# 编译 R 并初始化其环境变量 +mkdir "\${current_dir}"/build +bash "\${current_dir}"/R-4.2.0.sh "\${current_dir}"/build "\${current_dir}" +module use "\${current_dir}"/R-4.2.0 +module load "\${current_dir}"/R-4.2.0/R-4.2.0_modulefiles +rm -rf "\${current_dir}"/build + +echo -e "\033[1;32;1mgridss environment initialization completed.\033[0m" + +EOF + + chmod +x pkg/gridss-2.13.2-hpc/run.sh + + echo "# 正在打包 gridss 文件 路径为$1" + cd pkg && tar -zcf gridss-2.13.2-hpc.tar.gz gridss-2.13.2-hpc + echo -e "\033[1;32;1m# gridss 已经打包成功 文件路径为$1/gridss-2.13.2-hpc.tar.gz\033[0m" + + echo " # ------------------------------------------------------------------------" + echo "# 运行软件前请执行以下命令" + echo -e "\033[1;32;1m# source pkg/gridss-2.13.2-hpc/run.sh\033[0m" + echo "# 来加载 gridss 运行时环境变量" + echo "# ------------------------------------------------------------------------" + rm -rf "$buildpath" "$installpath" diff --git a/LifeSciences/gridss-2.13.2/dependency/R-4.2.0.sh b/LifeSciences/gridss-2.13.2/dependency/R-4.2.0.sh new file mode 100644 index 0000000000000000000000000000000000000000..bbb2e49b0b7162ed1507d87d5f827bfdf8915f2b --- /dev/null +++ b/LifeSciences/gridss-2.13.2/dependency/R-4.2.0.sh @@ -0,0 +1,58 @@ +#!/bin/bash + +if [[ $# -ne 2 ]]; then + echo "The format is as follows:" + echo "bash bwa-0.7.17.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 +sudo yum install -y wget tar environment-modules libatomic readline-devel libXt-devel \ + bzip2-devel xz-devel libcurl-devel glibc-headers gcc-c++ pcre* + source /etc/profile + + echo "# R正在下载" + wget -t 0 -T 20 -c -P $buildpath http://mirror.bjtu.edu.cn/cran/src/base/R-4/R-4.2.0.tar.gz + if [[ $? -eq 0 ]]; then + echo -e "\033[1;32;1m# R已经下载成功\033[0m" + else + echo -e "\033[31m# R下载失败,请重新执行脚本\033[0m" + exit 1 + fi + + echo "# R 正在安装" + tar -xzf $buildpath/R-4.2.0.tar.gz -C $buildpath && rm -rf $buildpath/R-4.2.0.tar.gz + cd $buildpath/R-4.2.0 + FC=flang CC=clang CXX=clang++ ./configure --enable-R-shlib=yes --with-tcltk --prefix=$installpath/R-4.2.0 + make -j"$(nproc)" && make install + echo -e "\033[1;32;1m# R 已经安装完毕\033[0m" + + cat >"$installpath/R-4.2.0/R-4.2.0_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" < + + + + + + Document + + + +
+

+ 2022/08/10 12:52:09

+
+ +

+ 配置信息

+
+
+ 软件安装包存放路径或软件包名称 + /home/portadv/portadmin/package/gridss-2.13.2.tar.gz +
+ +
+ 目标操作系统 + openEuler 20.03 SP3 +
+
+ 目标系统内核版本 +

+ 4.19.90 +

+
+ +
+ 评估结果 +

+ + 软件迁移评估成功 +

+
+ +
+
+ +
+

可兼容替换

+

0

+
+ +
+

待验证替换

+

2

+
+ +
+

依赖文件总数

+

2

+
+ +
+ +
+
+ +
+
+ 与架构相关的依赖文件 +
+
+ +
+
+ + + + + + + + + + + + + + + +
序号依赖文件名文件类型软件包存放路径待下载软件包名称分析结果处理建议
+
+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ 1 + + gridsstools + + 可执行文件 + + /package/gridss-2.13.2.tar.gz/gridsstools + + -- + + 待验证替换 + + 请先在鲲鹏平台上验证。若不兼容，请联系供应方获取鲲鹏兼容版本，或获取源码并编译成鲲鹏兼容版本 +
+ + + 2 + + gridss-2.13.2-gridss-jar-with-dependencies.jar + + Jar包 + + /package/gridss-2.13.2.tar.gz/gridss-2.13.2-gridss-jar-with-dependencies.jar + + -- + + 待验证替换 + + 请先在鲲鹏平台上验证。若不兼容，请联系供应方获取鲲鹏兼容版本，或获取源码并编译成鲲鹏兼容版本 +
+
+
+ + +
+
+ + + + \ No newline at end of file diff --git "a/LifeSciences/gridss-2.13.2/doc/Devkit\346\212\245\345\221\212/gridss.html" "b/LifeSciences/gridss-2.13.2/doc/Devkit\346\212\245\345\221\212/gridss.html" new file mode 100644 index 0000000000000000000000000000000000000000..8e42f327730e910b9f042074f7f703c3a44e49f9 --- /dev/null +++ "b/LifeSciences/gridss-2.13.2/doc/Devkit\346\212\245\345\221\212/gridss.html" @@ -0,0 +1,506 @@ + + + + + + + + Document + + + + + +
+

+ 2022/08/10 13:02:27 +

+
+ +

配置信息

+ +
+
+ 源码文件存放路径 + + /home/portadv/portadmin/sourcecode/gridss-2.13.2 + +
+
+ 目标操作系统 + + openEuler 20.03 SP3 + +
+
+ 目标系统内核版本 + + 4.19.90 + +
+
+ 编译器版本 + + -- + +
+
+ 构建工具 + + -- + +
+
+ 编译命令 + + -- + +
+
+ 迁移结果 + + + + 源码迁移分析成功：您指定的分析路径/分析包中没有需要迁移的内容 + +
+
+ +
+
+
+

可兼容替换

+

0

+
+
+

待验证替换

+

0

+
+
+

依赖文件总数

+

0

+
+
+
+
+

源文件数

+

0

+
+
+

代码行数

+

0

+
+
+

源码迁移人力

+

0人月

+
+
+

+ 预估标准：1人月迁移工作量 = 500行 C/C++/Fortran/Go/构建文件等源码，或250行汇编代码 +

+
+
+
+ +
+
+ 与架构相关的依赖文件 +
+ +
+ +
+
+ + + + + + + + + + + +
序号依赖文件名文件类型 + 待下载软件包名称 + 分析结果处理建议
+
+
+ + + + + + + + + + + + + + + +
+
+
+ 未发现与架构相关的依赖文件 +
+
+
+
+ + +
+
+ 需要迁移的源码文件 +
+ +
+ +
+
+ + + + + + + + + + + +
序号文件名路径文件类型需修改的代码行
+
+
+ + + + + + + + + + + + + + +
+
+
+ 未发现需要迁移的源码文件 +
+
+
+
+ + +
+
+ 需要迁移的代码行数 +
+ +
+ +
+
+ + + + + + + + + +
文件名行号（起始行，结束行）关键字建议
+
+
+ + + + + + + + + + + + + +
+
+
+ 无数据 +
+
+
+
+ + +
+
+ + + + + + \ No newline at end of file diff --git "a/LifeSciences/gridss-2.13.2/doc/gridss-2.13.2\345\272\224\347\224\250\346\265\213\350\257\225\346\212\245\345\221\212.docx" "b/LifeSciences/gridss-2.13.2/doc/gridss-2.13.2\345\272\224\347\224\250\346\265\213\350\257\225\346\212\245\345\221\212.docx" new file mode 100644 index 0000000000000000000000000000000000000000..c89d41d16948515bb0192e1d9f758a80e69c207e Binary files /dev/null and "b/LifeSciences/gridss-2.13.2/doc/gridss-2.13.2\345\272\224\347\224\250\346\265\213\350\257\225\346\212\245\345\221\212.docx" differ diff --git "a/LifeSciences/gridss-2.13.2/doc/gridss-2.13.2\345\272\224\347\224\250\347\247\273\346\244\215\346\214\207\345\215\227.docx" "b/LifeSciences/gridss-2.13.2/doc/gridss-2.13.2\345\272\224\347\224\250\347\247\273\346\244\215\346\214\207\345\215\227.docx" new file mode 100644 index 0000000000000000000000000000000000000000..95f6761958613767b648ec5557d7eea94094750e Binary files /dev/null and "b/LifeSciences/gridss-2.13.2/doc/gridss-2.13.2\345\272\224\347\224\250\347\247\273\346\244\215\346\214\207\345\215\227.docx" differ diff --git "a/LifeSciences/gridss-2.13.2/doc/\351\262\262\351\271\217\345\237\272\345\272\247\350\275\257\344\273\266\346\220\255\345\273\272\346\214\207\345\215\227.docx" "b/LifeSciences/gridss-2.13.2/doc/\351\262\262\351\271\217\345\237\272\345\272\247\350\275\257\344\273\266\346\220\255\345\273\272\346\214\207\345\215\227.docx" new file mode 100644 index 0000000000000000000000000000000000000000..7b36b4638c730fa3d3c3edcc3764ad24f613acca Binary files /dev/null and "b/LifeSciences/gridss-2.13.2/doc/\351\262\262\351\271\217\345\237\272\345\272\247\350\275\257\344\273\266\346\220\255\345\273\272\346\214\207\345\215\227.docx" differ diff --git a/LifeSciences/gridss-2.13.2/gridss-2.13.2.sh b/LifeSciences/gridss-2.13.2/gridss-2.13.2.sh new file mode 100644 index 0000000000000000000000000000000000000000..931c99f1981d924afd632fc6b5c6119a6380b95c --- /dev/null +++ b/LifeSciences/gridss-2.13.2/gridss-2.13.2.sh @@ -0,0 +1,65 @@ +#!/bin/bash + +if [[ $# -ne 2 ]]; then + echo "The format is as follows:" + echo "bash juicer-1.6.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 +sudo yum install -y tar Cython cmake git time +source /etc/profile + +cd $buildpath + echo "# gridss正在下载" + +wget -t 10 -T 20 -c -O $buildpath/gridss-2.13.2.tar.gz \ + https://github.com/PapenfussLab/gridss/archive/refs/tags/v2.13.2.tar.gz + + if [[ $? -eq 0 ]]; then + echo -e "\033[1;32;1m# gridss已经下载成功\033[0m" + else + echo -e "\033[31m# gridss下载失败,请重新执行脚本\033[0m" + exit 1 + fi + + echo "# gridss正在安装" + tar -xzf $buildpath/gridss-2.13.2.tar.gz -C $buildpath && rm -rf $buildpath/gridss-2.13.2.tar.gz + wget -t 40 -c -P $buildpath https://github.com/PapenfussLab/gridss/releases/download/v2.13.2/gridss-2.13.2-gridss-jar-with-dependencies.jar + + cp -r $buildpath/gridss-2.13.2-gridss-jar-with-dependencies.jar $buildpath/gridss-2.13.2/scripts + cd $buildpath/gridss-2.13.2/scripts + chmod 777 gridss + sed -i '1205,1207d' gridss + echo -e "\033[1;32;1m# gridss已经安装完毕\033[0m" + + mkdir -p $installpath/gridss-2.13.2 && cp -r $buildpath/gridss-2.13.2/* $installpath/gridss-2.13.2 + + cat >"$installpath/gridss-2.13.2/gridss_modulefiles" <