一、安装RepeatModeler
1. 下载RepeatModeler,地址为http://www.repeatmasker.org/RepeatModeler/
2. 安装依赖软件
- perl
- RECON
- RepeatScout
- TRF
- RMBlast
- RepeatMasker及其一些库
- MAFFT
- CD-HIT
- GenomeTools
- LTR_retriever
- NINJA
软件及版本下载地址http://www.repeatmasker.org/RepeatModeler/
安装RECON
wget -c http://www.repeatmasker.org/RepeatModeler/RECON-1.08.tar.gz
tar -zxvf RECON-1.08.tar.gz
cd RECON-1.08/src
make && make install
#给RECON-1.08/scripts/recon.pl脚本中添加路径,将第三行改为
$path = "/home/chenhx/software/RECON-1.08/bin"
#将bin目录添加到环境变量
echo "export PATH=/home/chenhx/software/RECON-1.08/bin:"'$PATH' >> ~/.bashrc
安装RepeatScout
tar -zxvf RepeatScout-1.0.4.tar.gz
cd RepeatScout-1
#生成build_lmer_table、RepeatScout两个程序
#添加环境变量
echo "export PATH=/home/chenhx/software/RepeatScout-1:"'$PATH' >> ~/.bashrc
安装TRF
#下载地址为https://tandem.bu.edu/trf/trf409.linux64.download.html,下载之后通过文件传输上传至linux系统中,我这里的目录为/home/chenhx/software。
ln -s trf409.linux64 TRF
chmod 755 trf409.linux64
#添加环境变量
echo "export PATH=/home/chenhx/software:"'$PATH' >> ~/.bashrc
安装RMBlast
wget -c http://www.repeatmasker.org/rmblast-2.11.0+-x64-linux.tar.gz
#添加环境变量
echo "export PATH=/home/chenhx/software/rmblast-2.11.0/bin:"'$PATH' >> ~/.bashrc
安装RepeatMasker
wget -c http://www.repeatmasker.org/RepeatMasker/RepeatMasker-4.1.0.tar.gz
tar -zxvf RepeatMasker-4.1.0.tar.gz
cd RepeatMasker
chmod -R 755 *
#将RepBaseRepeatMaskerEdition-20181026.tar.gz放至RepeatMasker文件夹中
tar -zxvf RepBaseRepeatMaskerEdition-20181026.tar.gz
./configure
#执行后输入各个软件的路径
#输入包含TRF的路径
#序列搜索引擎,刚才安装了RMblast,先选择RMblast,然后回车,然后选择5 done
#安装完成,添加环境变量
echo "export PATH=/home/chenhx/software/RepeatMasker:"'$PATH' >> ~/.bashrc
安装MAFFT、CD-HIT、GenomeTools
conda create -n maker
source activate maker
conda install perl
conda install MAFFT CD-HIT genometools-genometools
安装Ltr_retriever
source activate maker
git clone https://github.com/oushujun/LTR_retriever.git
./LTR_retriever/LTR_retriever -h
#修改paths文件中的路径使之与各个软件对应起来
#添加环境变量
echo "export PATH=/home/chenhx/software/LTR_retriever-2.9.0:"'$PATH' >> ~/.bashrc
安装NINJA
#下载安装包https://github.com/TravisWheelerLab/NINJA/releases,我这里是用的版本是NINJA-0.98-cluster_only.tar.gz
tar -zxvf NINJA-0.98-cluster_only.tar.gz
cd NINJA-0.98-cluster_only/NINJA
make all
#添加环境变量
echo "export PATH=/home/chenhx/software/NINJA-0.98-cluster_only/NINJA:"'$PATH' >> ~/.bashrc
安装RepeatModeler
wget -c http://www.repeatmasker.org/RepeatModeler/RepeatModeler-2.0.1.tar.gz
tar -zxvf RepeatModeler-2.0.1.tar.gz
cd RepeatModeler-2.0.1
conda install perl-json perl-uri perl-file-which=1.23 perl-libwww-perl -y
perl ./configure
#接下来就是配置各种软件的路径
最后就可以安装成功并使用了!