diff --git a/LifeSciences/README.md b/LifeSciences/README.md index 0fbae3f8c71f4f843628c6f1469a0b5e2d7ead3a..d34b463ecc6e1e9de2351acb32c148eea054004c 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: RepeatModeler-2.0.3 diff --git a/LifeSciences/RepeatModeler-2.0.3/RepeatModeler-2.0.3.sh b/LifeSciences/RepeatModeler-2.0.3/RepeatModeler-2.0.3.sh new file mode 100644 index 0000000000000000000000000000000000000000..43384c0e520e493ef6b37bac7cbf6236c1ba24ba --- /dev/null +++ b/LifeSciences/RepeatModeler-2.0.3/RepeatModeler-2.0.3.sh @@ -0,0 +1,31 @@ +#!/bin/bash + +if [[ $# -ne 2 ]]; then + echo "The format is as follows:" + echo "./RepeatModeler-2.0.3.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 + +if [[ ! "$1" =~ ^/.* || ! -d "$1" || "$1" = "/" ]]; then echo "请输入正确的构建路径"; exit 1; fi +if [[ ! "$2" =~ ^/.* || ! -d "$2" || "$2" = "/" ]]; then echo "请输入正确的安装路径"; exit 1; fi +[[ "$1" = "$2" ]] && echo "构建路径与安装路径不能相同" && exit 1 +buildpath=$1 +installpath=$2 +if [[ "$1" =~ .*/$ ]]; then buildpath=${buildpath%/*}; fi +if [[ "$2" =~ .*/$ ]]; then installpath=${installpath%/*}; fi +wget -t 0 -c https://github.com/Dfam-consortium/RepeatModeler/archive/2.0.3.tar.gz -O $buildpath/RepeatModeler-2.0.3.tar.gz +cd $installpath +tar xf $buildpath/RepeatModeler-2.0.3.tar.gz +mv RepeatModeler-2.0.3 RepeatModeler +cd RepeatModeler + +perl configure \ + -cdhit_dir=$installpath/cd-hit -genometools_dir=$installpath/genometools/bin \ + -ltr_retriever_dir=$installpath/LTR_retriever -mafft_dir=$installpath/mafft/bin \ + -ninja_dir=$installpath/NINJA/NINJA -recon_dir=$installpath/RECON/bin \ + -repeatmasker_dir=$installpath/RepeatMasker \ + -rmblast_dir=$installpath/rmblast/bin -rscout_dir=$installpath/RepeatScout \ + -trf_dir=$installpath \ + -ucsctools_dir=$installpath/ucsc_tools diff --git a/LifeSciences/RepeatModeler-2.0.3/build.sh b/LifeSciences/RepeatModeler-2.0.3/build.sh new file mode 100644 index 0000000000000000000000000000000000000000..b082fae79b122729bba1410f693876f80329b4ff --- /dev/null +++ b/LifeSciences/RepeatModeler-2.0.3/build.sh @@ -0,0 +1,102 @@ +#!/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 perl-JSON perl-File-Which perl-Devel-Size perl-LWP-Protocol-https sudo tar wget python3 bc libtool numactl systemd-devel valgrind flex patch mysql environment-modules zlib-devel +pip3 install h5py -i https://mirrors.aliyun.com/pypi/simple/ +source /etc/profile + +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/rmblast-2.10.0.sh $buildpath $installpath +#bisheng +bash $dep_dir/hmmer-3.3.2.sh $buildpath $installpath +#use sse2neon +bash $dep_dir/trf-4.09.1.sh $buildpath $installpath +#bisheng +bash $dep_dir/RepeatScout-1.0.6.sh $buildpath $installpath +#bisheng +bash $dep_dir/RECON-1.08.sh $buildpath $installpath +#bisheng +bash $dep_dir/cd-hit-4.8.1.sh $buildpath $installpath +#bisheng +bash $dep_dir/genometools-1.6.0.sh $buildpath $installpath +#bisheng +bash $dep_dir/LTR_retriever-2.9.0.sh $buildpath $installpath +#binary file(do not need to be compiled) +bash $dep_dir/mafft-7.471.sh $buildpath $installpath +#bisheng +bash $dep_dir/NINJA-0.97.sh $buildpath $installpath +#bisheng sse2neon +bash $dep_dir/ucsc_tools.sh $buildpath $installpath +#bisheng +bash $dep_dir/RepeatMasker-4.1.2.sh $buildpath $installpath +#use sse2neon +bash $dep_dir/coseg-0.2.2.sh $buildpath $installpath +#bisheng +bash RepeatModeler-2.0.3.sh $buildpath $installpath << EOF + + +y +EOF +#file(do not need to be compiled) + +mkdir -p pkg/RepeatModeler-2.0.3-hpc && cp -r $installpath/* pkg/RepeatModeler-2.0.3-hpc/ +cat > "pkg/RepeatModeler-2.0.3-hpc/run.sh" < /dev/null +ln -fs \$basepath/RepeatModeler/RepeatModeler /usr/local/bin/RepeatModeler +ln -fs \$basepath/RepeatModeler/BuildDatabase /usr/local/bin/BuildDatabase +EOF +cd pkg/ && tar zcvf RepeatModeler-2.0.3-hpc.tar.gz RepeatModeler-2.0.3-hpc + +rm -rf $buildpath $installpath diff --git a/LifeSciences/RepeatModeler-2.0.3/dependency/LTR_retriever-2.9.0.sh b/LifeSciences/RepeatModeler-2.0.3/dependency/LTR_retriever-2.9.0.sh new file mode 100644 index 0000000000000000000000000000000000000000..5a9d71be284841d64033429f970137893c5fefd3 --- /dev/null +++ b/LifeSciences/RepeatModeler-2.0.3/dependency/LTR_retriever-2.9.0.sh @@ -0,0 +1,30 @@ +#!/bin/bash + +if [[ $# -ne 2 ]]; then + echo "The format is as follows:" + echo "./LTR_retriever-2.9.0.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 + +if [[ ! "$1" =~ ^/.* || ! -d "$1" || "$1" = "/" ]]; then echo "请输入正确的构建路径"; exit 1; fi +if [[ ! "$2" =~ ^/.* || ! -d "$2" || "$2" = "/" ]]; then echo "请输入正确的安装路径"; exit 1; fi +[[ "$1" = "$2" ]] && echo "构建路径与安装路径不能相同" && exit 1 +buildpath=$1 +installpath=$2 +if [[ "$1" =~ .*/$ ]]; then buildpath=${buildpath%/*}; fi +if [[ "$2" =~ .*/$ ]]; then installpath=${installpath%/*}; fi + +wget -t 0 -c -P $installpath https://github.com/oushujun/LTR_retriever/archive/v2.9.0.tar.gz -O $installpath/LTR_retriever-2.9.0.tar.gz +cd $installpath +tar xf LTR_retriever-2.9.0.tar.gz +mv LTR_retriever-2.9.0 LTR_retriever \ +&& cd LTR_retriever \ +&& sed -i \ + -e "s#BLAST+=#BLAST+=$installpath/rmblast/bin#" \ + -e "s#RepeatMasker=#RepeatMasker=$installpath/RepeatMasker#" \ + -e "s#HMMER=#HMMER=$installpath/hmmer/bin#" \ + -e "s#CDHIT=#CDHIT=$installpath/cd-hit#" \ + paths +rm -rf $installpath/LTR_retriever-2.9.0.tar.gz diff --git a/LifeSciences/RepeatModeler-2.0.3/dependency/NINJA-0.97.sh b/LifeSciences/RepeatModeler-2.0.3/dependency/NINJA-0.97.sh new file mode 100644 index 0000000000000000000000000000000000000000..47bdc759c4bd05142b45caf8f33e21f0e12f5595 --- /dev/null +++ b/LifeSciences/RepeatModeler-2.0.3/dependency/NINJA-0.97.sh @@ -0,0 +1,33 @@ +#!/bin/bash +set -e +if [[ $# -ne 2 ]]; then + echo "The format is as follows:" + echo "./NINJA-0.97.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 + +if [[ ! "$1" =~ ^/.* || ! -d "$1" || "$1" = "/" ]]; then echo "请输入正确的构建路径"; exit 1; fi +if [[ ! "$2" =~ ^/.* || ! -d "$2" || "$2" = "/" ]]; then echo "请输入正确的安装路径"; exit 1; fi +[[ "$1" = "$2" ]] && echo "构建路径与安装路径不能相同" && exit 1 +buildpath=$1 +installpath=$2 +if [[ "$1" =~ .*/$ ]]; then buildpath=${buildpath%/*}; fi +if [[ "$2" =~ .*/$ ]]; then installpath=${installpath%/*}; fi + +wget -t 0 -c -P $installpath https://github.com/TravisWheelerLab/NINJA/archive/0.97-cluster_only.tar.gz -O $installpath/NINJA-cluster.tar.gz +cd $installpath +mkdir -p NINJA +tar -xf NINJA-cluster.tar.gz -C NINJA --strip-components 1 +cd NINJA/NINJA +sed -i -e 's/g++/clang++/g' \ + -e 's/-mssse3/-march=armv8-a+fp+simd+crc -fsigned-char/g' Makefile + +#use sse2neon to adapt arm +wget -t 0 -c https://github.com/DLTcollab/sse2neon/archive/refs/tags/v1.5.1.tar.gz +tar xf v1.5.1.tar.gz +mv sse2neon-1.5.1 sse2neon +sed -i '15,17c #include "sse2neon/sse2neon.h"' DistanceCalculator.hpp +make clean && make -j$(nproc) all CXX=clang++ +rm -rf $installpath/NINJA-cluster.tar.gz diff --git a/LifeSciences/RepeatModeler-2.0.3/dependency/RECON-1.08.sh b/LifeSciences/RepeatModeler-2.0.3/dependency/RECON-1.08.sh new file mode 100644 index 0000000000000000000000000000000000000000..23b6f130a8dfda94495351d7054f1bdfa38845ed --- /dev/null +++ b/LifeSciences/RepeatModeler-2.0.3/dependency/RECON-1.08.sh @@ -0,0 +1,27 @@ +#!/bin/bash +set -e +if [[ $# -ne 2 ]]; then + echo "The format is as follows:" + echo "./RECON-1.08.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 + +if [[ ! "$1" =~ ^/.* || ! -d "$1" || "$1" = "/" ]]; then echo "请输入正确的构建路径"; exit 1; fi +if [[ ! "$2" =~ ^/.* || ! -d "$2" || "$2" = "/" ]]; then echo "请输入正确的安装路径"; exit 1; fi +[[ "$1" = "$2" ]] && echo "构建路径与安装路径不能相同" && exit 1 +buildpath=$1 +installpath=$2 +if [[ "$1" =~ .*/$ ]]; then buildpath=${buildpath%/*}; fi +if [[ "$2" =~ .*/$ ]]; then installpath=${installpath%/*}; fi + +wget -t 0 -c -P $installpath https://www.repeatmasker.org/RepeatModeler/RECON-1.08.tar.gz +cd $installpath +tar xf RECON-1.08.tar.gz +mv RECON-1.08 RECON && cd RECON +sed -i -e 's/gcc/clang/g' src/Makefile +make -j$(nproc) -C src && sudo make -j$(nproc) -C src install +cp 00README bin +sed -i "s#^\$path =.*#\$path = \"$installpath/RECON/bin\";#" scripts/recon.pl +rm -rf $installpath/RECON-1.08.tar.gz diff --git a/LifeSciences/RepeatModeler-2.0.3/dependency/RepeatMasker-4.1.2.sh b/LifeSciences/RepeatModeler-2.0.3/dependency/RepeatMasker-4.1.2.sh new file mode 100644 index 0000000000000000000000000000000000000000..023a70b6d2662324eee7a7ea849aa7d6c0257e88 --- /dev/null +++ b/LifeSciences/RepeatModeler-2.0.3/dependency/RepeatMasker-4.1.2.sh @@ -0,0 +1,29 @@ +#!/bin/bash + +if [[ $# -ne 2 ]]; then + echo "The format is as follows:" + echo "./RepeatMasker-4.1.2.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 + +if [[ ! "$1" =~ ^/.* || ! -d "$1" || "$1" = "/" ]]; then echo "请输入正确的构建路径"; exit 1; fi +if [[ ! "$2" =~ ^/.* || ! -d "$2" || "$2" = "/" ]]; then echo "请输入正确的安装路径"; exit 1; fi +[[ "$1" = "$2" ]] && echo "构建路径与安装路径不能相同" && exit 1 +buildpath=$1 +installpath=$2 +if [[ "$1" =~ .*/$ ]]; then buildpath=${buildpath%/*}; fi +if [[ "$2" =~ .*/$ ]]; then installpath=${installpath%/*}; fi + +wget -t 0 -c -P $buildpath https://www.repeatmasker.org/RepeatMasker/RepeatMasker-4.1.2-p1.tar.gz +cd $installpath +tar xf $buildpath/RepeatMasker-4.1.2-p1.tar.gz +chmod a+w RepeatMasker/Libraries +cd RepeatMasker +perl configure \ + -hmmer_dir=$installpath/hmmer/bin \ + -rmblast_dir=$installpath/rmblast/bin \ + -libdir=$installpath/RepeatMasker/Libraries \ + -trf_prgm=$installpath/trf \ + -default_search_engine=rmblast diff --git a/LifeSciences/RepeatModeler-2.0.3/dependency/RepeatScout-1.0.6.sh b/LifeSciences/RepeatModeler-2.0.3/dependency/RepeatScout-1.0.6.sh new file mode 100644 index 0000000000000000000000000000000000000000..8f3532e5329858108b3d32469c71643e9ff43825 --- /dev/null +++ b/LifeSciences/RepeatModeler-2.0.3/dependency/RepeatScout-1.0.6.sh @@ -0,0 +1,23 @@ +#!/bin/bash +set -e +if [[ $# -ne 2 ]]; then + echo "The format is as follows:" + echo "./RepeatScout-1.0.6.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 + +if [[ ! "$1" =~ ^/.* || ! -d "$1" || "$1" = "/" ]]; then echo "请输入正确的构建路径"; exit 1; fi +if [[ ! "$2" =~ ^/.* || ! -d "$2" || "$2" = "/" ]]; then echo "请输入正确的安装路径"; exit 1; fi +[[ "$1" = "$2" ]] && echo "构建路径与安装路径不能相同" && exit 1 +buildpath=$1 +installpath=$2 +if [[ "$1" =~ .*/$ ]]; then buildpath=${buildpath%/*}; fi +if [[ "$2" =~ .*/$ ]]; then installpath=${installpath%/*}; fi + +wget -t 0 -c -P $buildpath http://www.repeatmasker.org/RepeatScout-1.0.6.tar.gz +cd $buildpath +tar xf RepeatScout-1.0.6.tar.gz +cd RepeatScout-1.0.6 && sed -i "s#^INSTDIR =.*#INSTDIR = ${installpath}/RepeatScout#" Makefile +make -j$(nproc) CC=clang CFLAGS="-O3 -Wall -march=armv8.2-a -fsigned-char" && sudo make -j$(nproc) install && make clean diff --git a/LifeSciences/RepeatModeler-2.0.3/dependency/bisheng-compiler-2.1.0.sh b/LifeSciences/RepeatModeler-2.0.3/dependency/bisheng-compiler-2.1.0.sh new file mode 100644 index 0000000000000000000000000000000000000000..36e2602f5ea9e333f1fd3bf801a4f1c2d642c018 --- /dev/null +++ b/LifeSciences/RepeatModeler-2.0.3/dependency/bisheng-compiler-2.1.0.sh @@ -0,0 +1,41 @@ +#!/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 +[[ "$1" = "$2" ]] && echo "构建路径与安装路径不能相同" && exit 1 +buildpath=$1 +installpath=$2 +[[ "$buildpath" =~ .*/$ ]] && buildpath=${buildpath%/*} +[[ "$installpath" =~ .*/$ ]] && installpath=${installpath%/*} +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"</d' easel/*.c +sed -i -e 's/#include /#include "..\/sse2neon\/sse2neon.h"/' easel/*.h +sed -i -e '41c #include "../sse2neon/sse2neon.h"' src/hmmer.h +sed -i -e '/#include /d' \ +-e '/#include /d' \ +-e '/#include /d' \ +src/impl_sse/*.h +sed -i -e '/#include /d' \ +-e '/#include /d' \ +-e '/#include /d' \ +src/impl_sse/*.c +sed -i -e '/#include /d' \ +-e '/#include /d' \ +src/*.h +sed -i -e '/#include /d' \ +-e '/#include /d' \ +src/*.c +make -j$(nproc) && sudo make -j$(nproc) install && make clean diff --git a/LifeSciences/RepeatModeler-2.0.3/dependency/mafft-7.471.sh b/LifeSciences/RepeatModeler-2.0.3/dependency/mafft-7.471.sh new file mode 100644 index 0000000000000000000000000000000000000000..ac0e7049b4bd081e3d69f9c35b52bea70cd0723f --- /dev/null +++ b/LifeSciences/RepeatModeler-2.0.3/dependency/mafft-7.471.sh @@ -0,0 +1,25 @@ +#!/bin/bash + +if [[ $# -ne 2 ]]; then + echo "The format is as follows:" + echo "./mafft-7.471.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 + +if [[ ! "$1" =~ ^/.* || ! -d "$1" || "$1" = "/" ]]; then echo "请输入正确的构建路径"; exit 1; fi +if [[ ! "$2" =~ ^/.* || ! -d "$2" || "$2" = "/" ]]; then echo "请输入正确的安装路径"; exit 1; fi +[[ "$1" = "$2" ]] && echo "构建路径与安装路径不能相同" && exit 1 +buildpath=$1 +installpath=$2 +if [[ "$1" =~ .*/$ ]]; then buildpath=${buildpath%/*}; fi +if [[ "$2" =~ .*/$ ]]; then installpath=${installpath%/*}; fi + +wget -t 0 -c -P $buildpath https://mafft.cbrc.jp/alignment/software/mafft-7.471-without-extensions-src.tgz +cd $buildpath +tar xf mafft-7.471-without-extensions-src.tgz +cd mafft-7.471-without-extensions/core +sed -i -e "s#^PREFIX =.*#PREFIX = $installpath/mafft#" \ + -e 's/gcc/clang/g' Makefile +make clean && make -j$(nproc) && make -j$(nproc) install diff --git a/LifeSciences/RepeatModeler-2.0.3/dependency/rmblast-2.10.0.sh b/LifeSciences/RepeatModeler-2.0.3/dependency/rmblast-2.10.0.sh new file mode 100644 index 0000000000000000000000000000000000000000..785b81633c79ce5d5aa7f3d6cc8e65841f9e0acf --- /dev/null +++ b/LifeSciences/RepeatModeler-2.0.3/dependency/rmblast-2.10.0.sh @@ -0,0 +1,33 @@ +#!/bin/bash + +if [[ $# -ne 2 ]]; then + echo "The format is as follows:" + echo "./rmblast-2.10.0.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 + +if [[ ! "$1" =~ ^/.* || ! -d "$1" || "$1" = "/" ]]; then echo "请输入正确的构建路径"; exit 1; fi +if [[ ! "$2" =~ ^/.* || ! -d "$2" || "$2" = "/" ]]; then echo "请输入正确的安装路径"; exit 1; fi +[[ "$1" = "$2" ]] && echo "构建路径与安装路径不能相同" && exit 1 +buildpath=$1 +installpath=$2 +if [[ "$1" =~ .*/$ ]]; then buildpath=${buildpath%/*}; fi +if [[ "$2" =~ .*/$ ]]; then installpath=${installpath%/*}; fi + +yum install lmdb* -y +echo "/usr/local/lib" >> /etc/ld.so.conf +/sbin/ldconfig +wget -t 0 -c -P $buildpath https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.10.0/ncbi-blast-2.10.0+-src.tar.gz +wget -t 0 -c -P $buildpath http://www.repeatmasker.org/isb-2.10.0+-rmblast.patch.gz +cd $buildpath +tar xf ncbi-blast-2.10.0+-src.tar.gz +gunzip isb-2.10.0+-rmblast.patch.gz +cd ncbi-blast-2.10.0+-src +patch -p1 < ../isb-2.10.0+-rmblast.patch +cd c++ +sed -i '/LIBS =/s/$/ -llmdb/' ./src/app/rmblastn/Makefile.rmblastn.app +./configure --with-mt --without-debug --without-krb5 --without-openssl --with-projects=scripts/projects/rmblastn/project.lst --prefix=$installpath/rmblast +make -j$(nproc) CC=clang CXX=clang++ +make -j$(nproc) install diff --git a/LifeSciences/RepeatModeler-2.0.3/dependency/trf-4.09.1.sh b/LifeSciences/RepeatModeler-2.0.3/dependency/trf-4.09.1.sh new file mode 100644 index 0000000000000000000000000000000000000000..b4f4c87444f859ceb92cdb28f94245da5a3d5e71 --- /dev/null +++ b/LifeSciences/RepeatModeler-2.0.3/dependency/trf-4.09.1.sh @@ -0,0 +1,24 @@ +#!/bin/bash + +if [[ $# -ne 2 ]]; then + echo "The format is as follows:" + echo "./trf-4.09.1.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 + +if [[ ! "$1" =~ ^/.* || ! -d "$1" || "$1" = "/" ]]; then echo "请输入正确的构建路径"; exit 1; fi +if [[ ! "$2" =~ ^/.* || ! -d "$2" || "$2" = "/" ]]; then echo "请输入正确的安装路径"; exit 1; fi +[[ "$1" = "$2" ]] && echo "构建路径与安装路径不能相同" && exit 1 +buildpath=$1 +installpath=$2 +if [[ "$1" =~ .*/$ ]]; then buildpath=${buildpath%/*}; fi +if [[ "$2" =~ .*/$ ]]; then installpath=${installpath%/*}; fi + +wget -t 0 -c -P $buildpath https://github.com/Benson-Genomics-Lab/TRF/archive/v4.09.1.tar.gz +tar xf $buildpath/v4.09.1.tar.gz -C $buildpath +cd $buildpath/TRF-4.09.1 +mkdir -p build && cd build +../configure && make -j$(nproc) CC=clang +cp -r ./src/trf $installpath/trf diff --git a/LifeSciences/RepeatModeler-2.0.3/dependency/ucsc_tools.sh b/LifeSciences/RepeatModeler-2.0.3/dependency/ucsc_tools.sh new file mode 100644 index 0000000000000000000000000000000000000000..fe21625094b799c8f95a1f3bb3d8062c31fa1f24 --- /dev/null +++ b/LifeSciences/RepeatModeler-2.0.3/dependency/ucsc_tools.sh @@ -0,0 +1,34 @@ +#!/bin/bash + +if [[ $# -ne 2 ]]; then + echo "The format is as follows:" + echo "./ucsc_tools.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 + +if [[ ! "$1" =~ ^/.* || ! -d "$1" || "$1" = "/" ]]; then echo "请输入正确的构建路径"; exit 1; fi +if [[ ! "$2" =~ ^/.* || ! -d "$2" || "$2" = "/" ]]; then echo "请输入正确的安装路径"; exit 1; fi +[[ "$1" = "$2" ]] && echo "构建路径与安装路径不能相同" && exit 1 +buildpath=$1 +installpath=$2 +if [[ "$1" =~ .*/$ ]]; then buildpath=${buildpath%/*}; fi +if [[ "$2" =~ .*/$ ]]; then installpath=${installpath%/*}; fi + +yum install libpng libpng-devel libuuid-devel -y +wget -t 0 -c -P $buildpath/ucsc_tools https://hgdownload.soe.ucsc.edu/admin/jksrc.zip +cd $buildpath/ucsc_tools +unzip jksrc.zip +MACHTYPE=aarch64 && mkdir -p ~/bin/$MACHTYPE +cd kent/src/lib +sed -i -e '714c if (format != NULL)' htmshell.c +sed -i -e '1c CC=clang' ../inc/localEnvironment.mk +make -j$(nproc) +cd ../jkOwnLib && make -j$(nproc) CC=clang +cd ../htslib && make -j$(nproc) CC=clang +cd ../utils/faToTwoBit && make -j$(nproc) CC=clang +cd ../twoBitInfo && make -j$(nproc) CC=clang +cd ../twoBitToFa && make -j$(nproc) CC=clang +cp -r ~/bin/$MACHTYPE $installpath/ucsc_tools + diff --git "a/LifeSciences/RepeatModeler-2.0.3/doc/RepeatModeler-2.0.3\345\272\224\347\224\250\346\265\213\350\257\225\346\212\245\345\221\212.docx" "b/LifeSciences/RepeatModeler-2.0.3/doc/RepeatModeler-2.0.3\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..a8da81d84674cbaf06e2519de0d6162b051d8256 Binary files /dev/null and "b/LifeSciences/RepeatModeler-2.0.3/doc/RepeatModeler-2.0.3\345\272\224\347\224\250\346\265\213\350\257\225\346\212\245\345\221\212.docx" differ diff --git "a/LifeSciences/RepeatModeler-2.0.3/doc/RepeatModeler-2.0.3\345\272\224\347\224\250\347\247\273\346\244\215\346\214\207\345\215\227.docx" "b/LifeSciences/RepeatModeler-2.0.3/doc/RepeatModeler-2.0.3\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..2046b24d41203ae9498517a3a0a332554ba287e8 Binary files /dev/null and "b/LifeSciences/RepeatModeler-2.0.3/doc/RepeatModeler-2.0.3\345\272\224\347\224\250\347\247\273\346\244\215\346\214\207\345\215\227.docx" differ diff --git "a/LifeSciences/RepeatModeler-2.0.3/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/RepeatModeler-2.0.3/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..133fde730ed5a6490631f5148cdc68eed282f3b8 Binary files /dev/null and "b/LifeSciences/RepeatModeler-2.0.3/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/README.md b/README.md index f76b5597fa1983b4b6fac5c03c296f27be507f33..38683497dfbc63aa797c61ed1b288c5cf785bd68 100644 --- a/README.md +++ b/README.md @@ -6,4 +6,5 @@ HPC Software List: - repositories: LifeSciences/RepeatMasker-4.1.2 - repositories: LifeSciences/eigensoft-7.2.1 - repositories: LifeSciences/redundans-v0.13c -- repositories: LifeSciences/bamtools-2.5.2 \ No newline at end of file +- repositories: LifeSciences/bamtools-2.5.2 +- repositories: LifeSciences/RepeatModeler-2.0.3