基因预测软件：【BRAKER2】软件的安装

基因预测软件：【BRAKER2】 软件的安装

nym 2023-02-27

软件链接 https://github.com/Gaius-Augustus/BRAKER

一、软件介绍

BRAKER是GeneMark-ET和AUGUSTU的组合，使用基因组和RNA-Seq数据自动生成新基因组的全基因结构注释,将来自RNA-Seq的外部证据和蛋白质同源信息整合到预测中。
与其他依赖蛋白质同源性信息的方法不同，BRAKER2即使在没有非常近缘物种注释和没有RNA-Seq数据的情况下也能达到较高的基因预测准确性。

二、软件安装

使用conda配置perl环境

#创建名为BRAKER的环境
conda create -n BRAKER
conda activate BRAKER
#安装所需要的perl包
conda install -c anaconda perl
conda install -c bioconda perl-app-cpanminus
conda install -c bioconda perl-hash-merge
conda install -c bioconda perl-parallel-forkmanager
conda install -c bioconda perl-scalar-util-numeric
conda install -c bioconda perl-yaml
conda install -c bioconda perl-class-data-inheritable
conda install -c bioconda perl-exception-class
conda install -c bioconda perl-test-pod
conda install -c anaconda biopython
conda install -c bioconda perl-file-which # skip if you are not comparing to reference annotation
conda install -c bioconda perl-mce
conda install -c bioconda perl-threaded
conda install -c bioconda perl-list-util
conda install -c bioconda perl-math-utils
conda install -c bioconda cdbtools

BRAKER

cd ~/biosoft/BRAKER/scripts
chmod a+x *.pl *.py
添加到环境变量中
vim ~/.bashrc
文件末尾添加：
export PATH="$PATH:/home/nieyimeng/biosoft/BRAKER/scripts"

GeneMark-EX

2.1.下载GeneMark-ES/ET/EP ver 4.71_lic
 http://topaz.gatech.edu/GeneMark/license_download.cgi
2.安装
gunzip gm_key_64.gz
cp gm_key_64 ~/.gm_key

Augustus安装

git clone https://github.com/Gaius-Augustus/Augustus.git
cd Augustus
make augustus
#报错：fatal error: mysql++/mysql++.h: 没有那个文件或目录
#解决方案：
mysql_config --libs --cflags
$-L/usr/lib/x86_64-linux-gnu -lmysqlclient -lpthread -lm -lrt -latomic -lssl -lcrypto -ldl
$-I/usr/include/mysql
cd Augustus/src
vim Makefile
INCLS += -I/usr/include/mysql -I/nfs/research1/mysql++_install

auxprogs/bam2wig无法安装，有对应的py脚本

安装mysql++ library
#wget https://tangentsoft.com/mysqlpp/releases/mysql++-3.3.0.tar.gz
#tar -zxvf mysql++-3.3.0.tar.gz
#cd mysql++-3.2.5
mkdir /nfs/research1/mysql++_install
./configure --prefix=/nfs/research1/mysql++_install
make
make install
cd Augustus/src
nano Makefile
#change make file in src

添加环境变量
vim ~/.bashrc
文件末尾添加：
export PATH="$PATH:/home/nieyimeng/biosoft/Augustus/bin"
export AUGUSTUS_CONFIG_PATH=/home/nieyimeng/biosoft/Augustus/config

python3安装（略）

Bamtools安装

git clone https://github.com/pezmaster31/bamtools.git). 
cd bamtools
mkdir build 
cd build 
cmake .. 
#cmake报错
#CMake Error at CMakeLists.txt:1 (cmake_minimum_required):
#  CMake 3.11 or higher is required.  You are running version 3.10.2

#-- Configuring incomplete, errors occurred!
#解决方案：
#sudo apt remove --purge cmake
#hash -r
#sudo snap install cmake --classic
make
make install

Diamond安装

wget http://github.com/bbuchfink/diamond/releases/download/v0.9.24/diamond-linux64.tar.gz
tar xzf diamond-linux64.tar.gz
vim ~/.bashrc
文件末尾添加：
export PATH="$PATH:/home/nieyimeng/biosoft/"

ProtHint安装

git clone https://github.com/gatech-genemark/ProtHint.git
#配置perl环境
cpan>
install MCE::Mutex
install YAML
#将prohint/bin添加到环境路径中
vim ~/.bashrc
文件末尾添加：
export PATH="$PATH:/home/nieyimeng/biosoft/ProtHint/bin"

Optional tools

Samtools(略)

Biopython（略）

cdbfasta（略）

GenomeThreader

wget https://genomethreader.org/distributions/gth-1.7.3-Linux_x86_64-64bit.tar.gz```
tar -zxvf gth-1.7.3-Linux_x86_64-64bit.tar.gz
将bin文件夹添加到环境变量中
vim ~/.bashrc
文件末尾添加：
export PATH="$PATH:/home/nieyimeng/data/gth-1.7.3-Linux_x86_64-64bit/bin"

Spaln

git clone https://github.com/ogotoh/spaln.git
cd src
./configure
make
make install
make clearall
添加到环境变量
vim ~/.bashrc
文件末尾添加：
export PATH="$PATH:/home/nieyimeng/biosoft/spaln/bin"

Exonerate安装

git clone https://github.com/nathanweeks/exonerate.git
cd exonerate
git checkout v2.4.0
./configure [YOUR_CONFIGURE_OPTIONS]
make
make install

GUSHR安装

git clone https://github.com/Gaius-Augustus/GUSHR.git
vim ~/.bashrc
文件末尾添加：
export PATH="$PATH:/home/nieyimeng/biosoft/GUSHR"

蛋白质数据库下载

wget https://v100.orthodb.org/download/odb10_arthropoda_fasta.tar.gz
tar xvf odb10_arthropoda_fasta.tar.gz
cat arthropoda/Rawdata/* > proteins.fasta

三、软件运行

举例：

conda activate BRAKER
nohup braker.pl --genome=X.fasta --prot_seq=proteins_Lomigra.fasta --workingdir=~/data/X-SEX/BRAKER &