diff --git a/LifeSciences/BUSCO-5.2.2/build.sh b/LifeSciences/BUSCO-5.2.2/build.sh new file mode 100644 index 0000000000000000000000000000000000000000..5aa5c97df760bac457796912487fb452a3ae6d4d --- /dev/null +++ b/LifeSciences/BUSCO-5.2.2/build.sh @@ -0,0 +1,90 @@ +#!/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 bc time +yum install -y cmake libcurl libcurl-devel openssl openssl-devel zlib zlib-devel bzip2 bzip2-devel xz-devel boost-devel bc htslib* gsl* ncurses ncurses-base ncurses-libs ncurses-devel samtools suitesparse-devel mariadb-devel sqlite-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/ncbi-blast-2.13.0.sh $buildpath $installpath +module use $installpath/ncbi-blast-2.13.0 +module load $installpath/ncbi-blast-2.13.0/ncbi-blast_modulefiles + +bash $dep_dir/lpsolve-5.5.sh $buildpath $installpath +module use $installpath/lp_solve_5.5 +module load $installpath/lp_solve_5.5/lpsolve_modulefiles + +bash $dep_dir/mysqlpp-3.3.0.sh $buildpath $installpath +module use $installpath/mysqlpp-3.3.0 +module load $installpath/mysqlpp-3.3.0/mysqlpp_modulefiles + +bash $dep_dir/bamtools-2.5.2.sh $buildpath $installpath +module use $installpath/bamtools-2.5.2 +module load $installpath/bamtools-2.5.2/bamtools_modulefiles + +bash $dep_dir/bcftools-1.9.sh $buildpath $installpath +module use $installpath/bcftools-1.9 +module load $installpath/bcftools-1.9/bcftools_modulefiles + +bash $dep_dir/augustus-3.4.0.sh $buildpath $installpath +module use $installpath/augustus-3.4.0 +module load $installpath/augustus-3.4.0/augustus_modulefiles + +bash $dep_dir/prodigal-2.6.3.sh $buildpath $installpath +module use $installpath/prodigal-2.6.3 +module load $installpath/prodigal-2.6.3/prodigal_modulefiles + +bash $dep_dir/metaeuk-r5.sh $buildpath $installpath +module use $installpath/metaeuk-r5 +module load $installpath/metaeuk-r5/metaeuk_modulefiles + +bash $dep_dir/hmmer-h3-arm.sh $buildpath $installpath +module use $installpath/hmmer +module load $installpath/hmmer/hmmer_modulefiles + +bash busco-5.2.2.sh $buildpath $installpath + +mkdir -p pkg/BUSCO-5.2.2-hpc && cp -r $installpath/* pkg/BUSCO-5.2.2-hpc/ +cat >"pkg/BUSCO-5.2.2-hpc/run.sh" < /dev/null +current_dir=\$(cd "\$(dirname "\${BASH_SOURCE[0]}")" &> /dev/null && pwd) +for d in \$(ls \$current_dir) +do + [[ ! -f "\$current_dir/\$d" ]] && cd \$current_dir/\$d && module use \$(pwd) && module load \$(pwd)/*modulefiles +done + +EOF +chmod +x pkg/BUSCO-5.2.2-hpc/run.sh +cd pkg/ && tar zcvf BUSCO-5.2.2-hpc.tar.gz BUSCO-5.2.2-hpc + +rm -rf $buildpath $installpath diff --git a/LifeSciences/BUSCO-5.2.2/busco-5.2.2.sh b/LifeSciences/BUSCO-5.2.2/busco-5.2.2.sh new file mode 100644 index 0000000000000000000000000000000000000000..da2257bc8fa972e57b643335ec5abe3c326fede0 --- /dev/null +++ b/LifeSciences/BUSCO-5.2.2/busco-5.2.2.sh @@ -0,0 +1,44 @@ +!/bin/bash + +if [[ $# -ne 2 ]]; then + echo "The format is as follows:" + echo "bash busco-5.2.2.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 wget python3 python3-pip python3-numpy python3-devel valgrind flex libtool numactl tcsh +pip3 install pandas biopython + +set -e +wget -t 10 -c -P $buildpath https://gitlab.com/ezlab/busco/-/archive/5.2.2/busco-5.2.2.tar.gz +tar xvf $buildpath/busco-5.2.2.tar.gz -C $buildpath && rm -rf $buildpath/busco-5.2.2.tar.gz +cd $buildpath/busco-5.2.2 +python3 setup.py install --prefix=$installpath/busco-5.2.2 + +cat >"$installpath/busco-5.2.2/busco_modulefiles" <"$installpath/augustus-3.4.0/augustus_modulefiles" <"$installpath/bamtools-2.5.2/bamtools_modulefiles" <"$installpath/bcftools-1.9/bcftools_modulefiles" <"$installpath/bisheng-compiler-2.1.0/bisheng_modulefiles" <"$installpath/hmmer/hmmer_modulefiles" <"$installpath/lp_solve_5.5/lpsolve_modulefiles" <"$installpath/metaeuk-r5/metaeuk_modulefiles" <"$installpath/mysqlpp-3.3.0/mysqlpp_modulefiles" <"$installpath/ncbi-blast-2.13.0/ncbi-blast_modulefiles" <"$installpath/prodigal-2.6.3/prodigal_modulefiles" < + + + + + + Document + + + + + +
+

+ 2022/07/14 04:53:45 +

+
+ +

配置信息

+ +
+
+ 源码文件存放路径 + + /home/poradv/portadv/portadmin/sourcecode/busco-5.2.2 + +
+
+ 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/BUSCO-5.2.2/doc/Devkit\346\212\245\345\221\212/BUSCO\350\275\257\344\273\266\350\277\201\347\247\273\350\257\204\344\274\260.html" "b/LifeSciences/BUSCO-5.2.2/doc/Devkit\346\212\245\345\221\212/BUSCO\350\275\257\344\273\266\350\277\201\347\247\273\350\257\204\344\274\260.html" new file mode 100644 index 0000000000000000000000000000000000000000..831c9ea9d52a4f035609b6dd3297427583ccef31 --- /dev/null +++ "b/LifeSciences/BUSCO-5.2.2/doc/Devkit\346\212\245\345\221\212/BUSCO\350\275\257\344\273\266\350\277\201\347\247\273\350\257\204\344\274\260.html" @@ -0,0 +1,499 @@ + + + + + + + + Document + + + +
+

+ 2022/07/14 04:55:44

+
+ +

+ 配置信息

+
+
+ 软件安装包存放路径或软件包名称 + /home/poradv/portadv/portadmin/package/busco-5.2.2.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: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/BUSCO-5.2.2/doc/Devkit\346\212\245\345\221\212/busco-process_20220722_162348-2.5.RC1.tar" "b/LifeSciences/BUSCO-5.2.2/doc/Devkit\346\212\245\345\221\212/busco-process_20220722_162348-2.5.RC1.tar" new file mode 100644 index 0000000000000000000000000000000000000000..fc384d63c59ffd2e64ffce3816e759365ea74340 Binary files /dev/null and "b/LifeSciences/BUSCO-5.2.2/doc/Devkit\346\212\245\345\221\212/busco-process_20220722_162348-2.5.RC1.tar" differ diff --git "a/LifeSciences/BUSCO-5.2.2/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/BUSCO-5.2.2/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..cb4a3386f2e2d9f38c36cc6555d3cabd28f8dc6f Binary files /dev/null and "b/LifeSciences/BUSCO-5.2.2/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/README.md b/LifeSciences/README.md index e7a176dae29f70667ccf393405288dbe8b771959..11f1002e5faf8780ba6e0143e8d738f4cde02f7b 100644 --- a/LifeSciences/README.md +++ b/LifeSciences/README.md @@ -28,3 +28,4 @@ Life Sciences Software List: - repositories: rMATs-4.1.2 - repositories: fsl-6.0.5.2 - repositories: freesurfer-7.2 +- repositories: BUSCO-5.2.2 diff --git a/README.md b/README.md index 8a5c14e8c27d197c78f1b05c3a711977cc04ac66..df732667603253ae138a20a403c88d199d39134a 100644 --- a/README.md +++ b/README.md @@ -31,3 +31,4 @@ HPC Software List: - repositories: LifeSciences/rMATs-4.1.2 - repositories: LifeSciences/FSL-6.0.5.2 - repositories: LifeSciences/freesurfer-7.2 +- repositories: LifeSciences/BUSCO-5.2.2