maker安装

在该页面登记后会弹出下载链接：http://weatherby.genetics.utah.edu/cgi-bin/registration/maker_license.cgi

1. 安装perl包

source activate maker
conda install perl-inline-c perl-perl-unsafe-signals perl-want perl-forks perl-dbd-pg

2. 配置mpi

用conda安装mpich2，我这里安装的版本是mpich2-1.4.1p1。

conda install mpich2=1.4.1p1

我这里使用的是mpich2，用openmpi不是很好使。

3. 安装依赖软件

3.1 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

3.2 安装snap

wget -c http://korflab.ucdavis.edu/Software/snap-2013-11-29.tar.gz
tar -zxvf snap-2013-11-29.tar.gz
make
echo "export PATH=/home/chenhx/software/snap:"'$PATH' >> ~/.bashrc
echo "export Zoe=/home/chenhx/software/snap/Zoe:"'$PATH' >> ~/.bashrc

3.3 安装RepeatMasker

见“RepeatModeler + RepeatMasker安装”篇

3.4 安装Exonerate 2.2

wget -c http://ftp.ebi.ac.uk/pub/software/vertebrategenomics/exonerate/exonerate-2.2.0-x86_64.tar.gz
tar -zxvf exonerate-2.2.0-x86_64.tar.gz
echo "export PATH=/home/chenhx/software/exonerate-2.2.0-x86_64/bin:"'$PATH' >> ~/.bashrc

3.5 安装Augustus

conda install Augustus

3.6 安装genemark-ES

下载genemark-ES，软件安装包可以自行下载http://exon.gatech.edu/GeneMark/license_download.cgi。

tar -zxvf gmes_linux_64.tar.gz
cp gm_key_64 ~/.gm_key
echo "export PATH=/home/chenhx/software/gmes_linux_64:"'$PATH' >> ~/.bashrc

3.7 安装maker

下载地址http://weatherby.genetics.utah.edu/cgi-bin/registration/maker_license.cgi

conda install perl-dbd-sqlite perl-io-all perl-bit-vector perl-Bio-Procedural
tar -zxvf maker-2.31.11.tgz 
cd maker/src
perl Build.PL
#编译时选择不用mpi，默认是N，直接回车即可
./Build install
echo "export PATH=/home/chenhx/software/maker/src/bin:"'$PATH' >> ~/.bashrc