reaper软件安装_CurseForge整合包安装

RepeatModeler的安装（包含RepeatMasker安装）

nym 2021-8-15

一、RepeatMasker官网地址（http://www.repeatmasker.org/）

安装RepeatMasker需要TRF、rmblast

1、TRF的安装

#下载（https://github.com/Benson-Genomics-Lab/TRF） git clone https://github.com/Benson-Genomics-Lab/TRF.git #Check actual version #tar -xzvf trf-4.10.0.tar.gz cd TRF mkdir build cd build ../configure make #To install to system sudo make install 

2、rmblast的安装

#下载（http://www.repeatmasker.org/rmblast-2.11.0+-x64-linux.tar.gz） tar -xzvf rmblast-2.11.0+-x64-linux.tar.gz 

3、RepeatMasker的安装

#下载 tar xzvf RepeatMasker-4.1.2-p1.tar.gz cd RepeatMasker chmod -R 755 * #编译 ./configure # 添加到环境变量中 vi ~/.bashrc export PATH="$PATH:/home/nieyimeng/biosoft/RepeatMasker" source ~/.bashrc 

二、RepeatMoleder的安装

1、安装RepeatMasker、TRF、RMblast

2、安装RECON

wget -c http://www.repeatmasker.org/RepeatModeler/RECON-1.08.tar.gz tar -xzvf RECON-1.08.tar.gz cd RECON-1.08/src make 

3、安装RepeatScount

wget -c http://www.repeatmasker.org/RepeatScout-1.0.6.tar.gz tar -zxvf RepeatScout-1.0.6.tar.gz cd RepeatScout-1.0.6 make 

4、可选软件，运行LTR结构搜索必须软件，也可以不安装

4.1、LtrHarvest，LtrHarvest程序是GenomeTools套件的一部分，安装genometools即可

wget -c http://genometools.org/pub/genometools-1.5.9.tar.gz tar -zxvf genometools-1.5.9.tar.gz cd genometools-1.5.9 make threads=yes 

4.2、Ltr_retriever

#下载地址（https://github.com/oushujun/LTR_retriever/archive/master.zip)` unzip LTR_retriever-master.zip 

4.3、MAFFT

#下载地址（https://mafft.cbrc.jp/alignment/software/mafft-7.487-with-extensions-src.tgz) tar xfvz mafft-7.487-with-extensions-src.tgz cd mafft-7.487-with-extensions/core/ vi Makefile (any other text editor is ok.) #第一行 From: PREFIX = /usr/local To: PREFIX = /home/your_home/somewhere (must be absolute path) #第三行 From: BINDIR = $(PREFIX)/bin To: BINDIR = /home/your_home/bin (or elsewhere in your command-search path) #有sudo权限可以直接sudo安装 sudo apt install mafft 

4.4、CD-HIT

#下载地址（https://github.com/weizhongli/cdhit/archive/master.zip） unzip cdhit-master.zip cd cdhit-master make 

4.5、Ninja

#下载地址（https://github.com/TravisWheelerLab/NINJA/releases/tag/0.95-cluster_only） unzip NINJA-0.95-cluster_only.zip cd NINJA-0.95-cluster_only cd NINJA make all 

4.6、twoBitToFa, faToTwoBit, twoBitInfo

#twoBitToFa(http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/twoBitToFa) #faToTwoBit(http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/faToTwoBit) #twoBitInfo(http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/twoBitInfo) mkdir UCSCTOOLS chmod 755 * #将三个文件放在新建的UCSCTOOLS文件夹中 

5、RepeatModeler安装

#下载地址（http://www.repeatmasker.org/RepeatModeler/RepeatModeler-2.0.2a.tar.gz） tar -zxvf RepeatModeler-2.0.2a.tar.gz cd RepeatModeler-2.0.2a perl ./configure #设置各安装文件位置。注意一些地址是src下，一些地址是bin，一些是文件目录下 RECON_DIR:/public/home/huangyuan_nym/biosoft/RECON-1.08/src RSCOUT_DIR:/public/home/huangyuan_nym/biosoft/RepeatScout-1.0.6 TRF_PRGM: /public/home/huangyuan_nym/biosoft/TRF-master/build/src/trf CD-HIT_DIR:/public/home/huangyuan_nym/biosoft/cdhit-master UCSCTOOLS_DIR: /public/home/huangyuan_nym/biosoft/UCSCTOOLS/ RMBLAST_DIR: /public/home/huangyuan_nym/biosoft/rmblast-2.11.0/bin GENOMETOOLS_DIR: /public/home/huangyuan_nym/biosoft/genometools-1.5.9/bin LTR_RETRIEVER_DIR: /public/home/huangyuan_nym/biosoft/LTR_retriever-master MAFFT_DIR:/public/home/huangyuan_nym/biosoft/mafft-7.487-with-extensions/core NINJA_DIR: /public/home/huangyuan_nym/biosoft/NINJA-0.95-cluster_only/NINJA 

三、安装遇到问题补充

问题：报错，需要安装一个perl模块 Devel::Size

#Can’t locate Devel/Size.pm in @INC (@INC contains: /public/home/huangyuan_nym/biosoft/RepeatMasker /public/home/huangyuan_nym/biosoft/RepeatModeler-2.0.2a /usr/lib/perl5/site_perl /usr/local/lib64/perl5 /usr/local/share/perl5 /usr/lib64/perl5/vendor_perl /usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5 .) at ./RepeatModeler line 140

解决：在个人账户下安装perl模块

#下载该模块（https://cpan.metacpan.org/authors/id/N/NW/NWCLARK/Devel-Size-0.83.tar.gz） tar -zxvf Devel-Size-0.83.tar.gz perl Makefile.PL INSTALL_BASE=/public/home/huangyuan_nym/perl5 make make install #可以在CPAN.pm配置中进行设置，以便在使用CPAN.pm shell时模块自动安装在私有库目录中 % cpan cpan> o conf makepl_arg INSTALL_BASE=/public/home/huangyuan_nym/perl5 cpan> o conf commit #在环境变量中添加库的位置 vi ~/.bashrc #在最后一行添加 export PERL5LIB=/public/home/huangyuan_nym/perl5/lib/perl5 

注：如果一直报错，可以尝试使用RepeatModeler之前的版本进行编译安装。