diff --git a/LifeSciences/Pilon-1.24/build.sh b/LifeSciences/Pilon-1.24/build.sh new file mode 100644 index 0000000000000000000000000000000000000000..a816f31d46fddf4d3cb8e095eddb3592bd5ab1c7 --- /dev/null +++ b/LifeSciences/Pilon-1.24/build.sh @@ -0,0 +1,74 @@ +#!/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/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/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/ldc2-1.29.0.sh $buildpath $installpath +module use $installpath/ldc2-1.29.0-linux-aarch64 +module load $installpath/ldc2-1.29.0-linux-aarch64/ldc2_modulefiles + +bash $dep_dir/sambamba-0.8.2.sh $buildpath $installpath +module use $installpath/sambamba-0.8.2 +module load $installpath/sambamba-0.8.2/sambamba_modulefiles + +bash $dep_dir/bisheng-jdk1.8.0.sh $buildpath $installpath +module use $installpath/bisheng-jdk1.8.0_322 +module load $installpath/bisheng-jdk1.8.0_322/bisheng_jdk_modulefiles + +bash pilon-1.24.sh $buildpath $installpath + +mkdir -p pkg/pilon-1.24-hpc && cp -r $installpath/* pkg/pilon-1.24-hpc/ +cat>"pkg/pilon-1.24-hpc/run.sh"< /dev/null +current_dir="\$(cd "\$(dirname "\${BASH_SOURCE[0]}")" && pwd -P)" +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 +echo -e "\033[1;32;1mpilon environment initialization completed.\033[0m" +EOF + +cd pkg/ && tar zcvf pilon-1.24-hpc.tar.gz pilon-1.24-hpc +rm -rf $buildpath $installpath diff --git a/LifeSciences/Pilon-1.24/dependency/bisheng-compiler-2.1.0.sh b/LifeSciences/Pilon-1.24/dependency/bisheng-compiler-2.1.0.sh new file mode 100644 index 0000000000000000000000000000000000000000..e30d4b3fc6a847fb1323a249e0dc70d85abbf462 --- /dev/null +++ b/LifeSciences/Pilon-1.24/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"<$installpath/bisheng-jdk1.8.0_322/bisheng_jdk_modulefiles<"$installpath/bwa-0.7.17/bwa_modulefiles"<"$installpath/ldc2-1.29.0-linux-aarch64/ldc2_modulefiles"<"$installpath/sambamba-0.8.2/sambamba_modulefiles"<"$installpath/samtools-1.15.1/samtools_modulefiles"< + + + + + + Document + + + +
+

+ 2022/08/11 06:15:21

+
+ +

+ 配置信息

+
+
+ 软件安装包存放路径或软件包名称 + /opt/portadv/portadmin/package/pilon-1.24.jar +
+ +
+ 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:您指定的分析路径/分析包中没有需要评估的内容 +

+
+ +
+
+ +
+

可兼容替换

+

0

+
+ +
+

待验证替换

+

0

+
+ +
+

依赖文件总数

+

0

+
+ +
+ +
+
+ +
+
+ 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
+
+
+ + + + + + + + + + + + + + + + + + + +
+
+
+ 未发现与架构相关的依赖文件
+
+
+
+ + +
+
+ + + + \ No newline at end of file diff --git "a/LifeSciences/Pilon-1.24/doc/Devkit\346\212\245\345\221\212/Pilon.html" "b/LifeSciences/Pilon-1.24/doc/Devkit\346\212\245\345\221\212/Pilon.html" new file mode 100644 index 0000000000000000000000000000000000000000..9c822d3b99fdfbe01329110b565a660ed2596456 --- /dev/null +++ "b/LifeSciences/Pilon-1.24/doc/Devkit\346\212\245\345\221\212/Pilon.html" @@ -0,0 +1,506 @@ + + + + + + + + Document + + + + + +
+

+ 2022/08/11 06:04:42 +

+
+ +

配置信息

+ +
+
+ 源码文件存放路径 + + /opt/portadv/portadmin/sourcecode/pilon-1.24 + +
+
+ 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/Pilon-1.24/doc/Devkit\346\212\245\345\221\212/pilon-2.5.RC1.tar" "b/LifeSciences/Pilon-1.24/doc/Devkit\346\212\245\345\221\212/pilon-2.5.RC1.tar" new file mode 100644 index 0000000000000000000000000000000000000000..9f9289376ea6f579f3dae1a75d3807bae637997d Binary files /dev/null and "b/LifeSciences/Pilon-1.24/doc/Devkit\346\212\245\345\221\212/pilon-2.5.RC1.tar" differ diff --git "a/LifeSciences/Pilon-1.24/doc/Pilon-1.24\345\272\224\347\224\250\346\265\213\350\257\225\346\212\245\345\221\212.docx" "b/LifeSciences/Pilon-1.24/doc/Pilon-1.24\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..4a52681eaeb640de3ea1b0131481fbd52607de6c Binary files /dev/null and "b/LifeSciences/Pilon-1.24/doc/Pilon-1.24\345\272\224\347\224\250\346\265\213\350\257\225\346\212\245\345\221\212.docx" differ diff --git "a/LifeSciences/Pilon-1.24/doc/Pilon-1.24\345\272\224\347\224\250\347\247\273\346\244\215\346\214\207\345\215\227.docx" "b/LifeSciences/Pilon-1.24/doc/Pilon-1.24\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..933ee317ff960257af6c19213d3fb46a9c0c6a4b Binary files /dev/null and "b/LifeSciences/Pilon-1.24/doc/Pilon-1.24\345\272\224\347\224\250\347\247\273\346\244\215\346\214\207\345\215\227.docx" differ diff --git "a/LifeSciences/Pilon-1.24/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/Pilon-1.24/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..0d83971bcf83e85b110e1d77a43b8ce4e863dbd1 Binary files /dev/null and "b/LifeSciences/Pilon-1.24/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/Pilon-1.24/pilon-1.24.sh b/LifeSciences/Pilon-1.24/pilon-1.24.sh new file mode 100644 index 0000000000000000000000000000000000000000..d6d84cded9a8c7843a214da65effb0497eb1597a --- /dev/null +++ b/LifeSciences/Pilon-1.24/pilon-1.24.sh @@ -0,0 +1,25 @@ +#!/bin/bash + +if [[ $# -ne 2 ]]; then + echo "The format is as follows:" + echo "bash zlib-1.12.11.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 +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 -y xz-devel ncurses-devel bzip2-devel curl-devel + +wget -t 0 -c -P $buildpath https://github.com/broadinstitute/pilon/releases/download/v1.24/pilon-1.24.jar +mkdir -p $installpath/ && cp -r $buildpath/pilon-1.24.jar $installpath/ +rm -rf $buildpath/pilon-1.24.jar diff --git a/LifeSciences/README.md b/LifeSciences/README.md index 477bac193c5672fa4b470a8d1102286688d7c944..a3c52a22242c585f642db9447c9e036179391d02 100644 --- a/LifeSciences/README.md +++ b/LifeSciences/README.md @@ -28,3 +28,4 @@ Life Sciences Software List: - repositories: fsl-6.0.5.2 - repositories: freesurfer-7.2 - repositories: BUSCO-5.2.2 +- repositories: Pilon-1.24 \ No newline at end of file diff --git a/README.md b/README.md index e78b8d5b986a378242db5f72e54d9b6384b009d5..7127f951cf8dad83cea8c0369e16edfd763df345 100644 --- a/README.md +++ b/README.md @@ -32,3 +32,4 @@ HPC Software List: - repositories: LifeSciences/FSL-6.0.5.2 - repositories: LifeSciences/freesurfer-7.2 - repositories: LifeSciences/BUSCO-5.2.2 +- repositories: LifeSciences/Pilon-1.24 \ No newline at end of file