Repeatmasker4.1.7 RepeatModeler2.07

miniconda安装

conda create -n test
conda activate test

安装perl 及 perl 模块

conda install bioconda::perl-devel-size
conda install bioconda::perl-libwww-perl
conda install bioconda::perl-json
conda install bioconda::perl-file-which
conda install -c bioconda h5py
conda install -c bioconda TRF
conda install -c bioconda RECON
conda install -c bioconda CD-Hit

#### 安装RMBlast

```bash
#下载链接：https://www.repeatmasker.org/  二进制包
$ tar -xf rmblast-2.11.0+-x64-linux.tar.gz -C software
$ vim .bashrc #配置环境变量

安装Repeatmasker

#安装Libraries 下载链接：https://www.repeatmasker.org/
$ tar -xf RepeatMasker-4.1.7-p1.tar.gz
#  tar -xf RepeatMaskerMetaData-20181026.tar.gz  #### 新版本的有这个文件 提示覆盖，选择不覆盖
# cp -r  Libraries/* RepeatMasker/Libraries/  
$ cd RepeatMasker
$ ./configrue
$ vim .bashrc

安装RepeatScout

#下载链接：https://www.repeatmasker.org/
$ tar -xf RepeatScout
$ vim .bashrc

安装UCSC

mkdir UCSC
 cd UCSC/
wget https://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/twoBitInfo
wget https://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/faToTwoBit
wget https://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/twoBitToFa
#不用编译，可添加环境变量

LTR_retriever

# https://github.com/oushujun/LTR_retriever/releases 版本2.9.0

mafft

https://mafft.cbrc.jp/alignment/software/mafft-7.526-linux.tgz

Ninjia

https://codeload.github.com/TravisWheelerLab/NINJA/tar.gz/refs/tags/0.95-cluster_only
tar -zxvf NINJA-0.95-cluster_only.tar.gz
cd NINJA-0.95-cluster_only
cd NINJA
make all 
#添加环境变量

LtrHarvest

https://github.com/genometools/genometools/releases/download/v1.6.5/gt-1.6.5-Linux_x86_64-64bit-complete.tar.gz
##选择二进制包就行

安装RepeatModeler

$ tar -xf RepeatModeler-2.0.7.tar.gz
$ cd RepeatModeler-2.0.7 ; perl ./configure
## 报错：缺失perl模块，进行安装 conda 
#设置各安装文件位置，如果前面添加了环境变量会显示默认的地址，如果没有，复制添加即可。
将RepeatModeler添加至环境变量