RepeatModeler的安装（包含RepeatMasker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。