基因注释：MAKER3安装（非root）

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1.安装perl包

 requires:
    !  Bit::Vector is not installed
    !  IO::All is not installed
    !  Inline::C is not installed
    !  Perl::Unsafe::Signals is not installed
    !  Want is not installed
    !  forks is not installed
    !  forks::shared is not installed
  recommends:
    *  DBD::Pg is not installed

使用conda批量安装，将上述Perl包名全部写入requirements.txt文件中

$ vi requirements.txt
perl-inline-c
perl-perl-unsafe-signals
perl-want
perl-forks
perl-dbd-pg

conda install -c bioconda --file=requirements.txt

2.配置MPI

在OpenMPI官网（https://www.open-mpi.org/）下载合适的opemMPI版本

tar zvxf openmpi-4.1.2.tar.gz
mkdir MPI
cd openmpi-4.1.2
./configure --prefix=/path/MPI/ #写绝对路径

3.安装依赖软件

3.1 安装WuBlast或NCBI-BLAST

安装NCBI-BLAST 2.2.X或更高的版本
下载地址：Index of /blast/executables/blast+/LATEST (nih.gov)
解压并安装

vi ~/.bashrc
export PATH=/usr/local/ncbi-blast:$PATH

3.2 安装SNAP

下载地址：http://korflab.ucdavis.edu/software.html
解压并安装

vi ~/.bashrc
export ZOE=/usr/local/snap/Zoe:$PATH
export PATH=/usr/local/snap:$PATH

3.3 安装RepeatMasker

下载地址：Download Page (repeatmasker.org)

基因组重复序列检测：RepeatMasker的安装及使用 - 简书 (jianshu.com)

Tips：

需要安装TRF、如果没有安装WuBlast则还需安装RMBlast

在http://www.girinst.org下载Repeat Masker版本的Repbase repeat database, 解压在RepeatMasker/Libraries目录下,再执行编译，因为configure第一步就是检查数据库

tar zvxf RepeatMasker-4.1.2-p1.tar.gz
cd RepeatMasker
#准备数据库
wget https://www.dfam.org/releases/Dfam_3.2/families/Dfam.h5.gz
gunzip Dfam.h5.gz
mv Dfam.h5 /path/RepeatMasker/Libraries

cp RepBaseRepeatMaskerEdition-20181026.tar.gz /path/RepeatMasker/
cd /path/RepeatMasker
tar xzvf RepBaseRepeatMaskerEdition-20181026.tar
rm RepBaseRepeatMaskerEdition-20181026.tar

perl ./configure

vi ~/.bashrc
export PATH=/path/RepeatMasker:$PATH
export LIBDIR=/path/RepeatMasker/Libraries:$LIBDIR

3.4 安装Exonerate 2.2

下载地址： http://www.ebi.ac.uk/~guy/exonerate

解压安装包
./configure -prefix=/usr/local/exonerate
make && make install
vi ~/.bashrc
export PATH=/usr/local/exonerate/bin:$PATH

3.5 安装AUGUSTUS

下载地址：http://bioinf.uni-greifswald.de/augustus/
Augustus安装教程 - 简书 (jianshu.com)

3.5 安装MAKER

tar zvxf maker-3.01.04.tgz
cd ./maker/src
perl Build.PL
./Build install

~/.bashrc中必须包含:
        export ZOE=where_snap_is/Zoe:$PATH
        export AUGUSTUS_CONFIG_PATH=where_augustus_is/config:$PATH

vi ~/.bashrc
export PATH=/usr/local/maker/bin:$PATH

运行：
maker [options] <maker_opts> <maker_bopts> <maker_exe>

参考文章：使用Anconda批量安装Pythony库（依赖包）的方法_闫小亘的博客-CSDN博客_conda 批量安装
无sudo/root的情况下怎么安装OpenMPI_热爱可抵漫长岁月-CSDN博客