基因组

第三天：软件安装

2020-05-20  本文已影响0人  焱黎

1. RepeatMasker安装

功能：重复序列屏蔽（已知什么序列是重复序列了）

(1) 准备工作

~$ conda install rmblast trf 
# 下载RepeatMasker
~$ cd software 
~/software$ wget http://www.repeatmasker.org/RepeatMasker-4.1.0.tar.gz
~/software$ tar -zxvf  RepeatMasker-4.1.0.tar.gz
~/software$ cd RepeatMasker
# 进入RepeatMasker文件夹，配置repbase数据库
~/software/RepeatMasker$ wget  https://www.girinst.org/server/RepBase/protected/repeatmaskerlibraries/RepBaseRepeatMaskerEdition-20181026.tar.gz
~/software/RepeatMasker$ tar -zxvf RepBaseRepeatMaskerEdition-20181026.tar.gz
# 准备工作完事了

(2) 安装RepeatMasker

~/software/RepeatMasker$ cat INSTALL
Installation
------------

  1. Unpack the files to the directory you wish to install
     them in.

  2. Configure the distribution by invoking Perl on the
     the "configure" script, i.e.:

            perl ./configure

     The configure script will prompt you for all the
     information needed to setup the RepeatMasker suite of
     programs.


Library Cache Directories
-------------------------
~/software/RepeatMasker$ perl ./configure

然后就会出现下图片的提示：

~/software/RepeatMasker$ ./RepeatMasker
Can't locate Text/Soundex.pm in @INC (you may need to install the Text::Soundex module) (@INC contains: /home/u2145/software/RepeatMasker /home/u2145/miniconda3/lib/site_perl/5.26.2/x86_64-linux-thread-multi /home/u2145/miniconda3/lib/site_perl/5.26.2 /home/u2145/miniconda3/lib/5.26.2/x86_64-linux-thread-multi /home/u2145/miniconda3/lib/5.26.2 .) at /home/u2145/software/RepeatMasker/Taxonomy.pm line 80.
BEGIN failed--compilation aborted at /home/u2145/software/RepeatMasker/Taxonomy.pm line 80.
Compilation failed in require at ./RepeatMasker line 332.
BEGIN failed--compilation aborted at ./RepeatMasker line 332.
# 返回的是这种错误不能加载Text/Soundex.pm ，这是一个perl模块，安装一下
~/software/RepeatMasker$ conda install perl-text-soundex
# 这样就可以了

2. RepeatModeler安装

功能：重复序列鉴定(不知道某序列为重复序列)

(1) 安装依赖软件

~$ conda install recon RepeatScout Ltr_retriever MAFFT CD-HIT
# 这几个软件可以用conda安装
# 但是LtrHarvest软件不可以用conda，属于[GenomeTools]软件的
# 下载GenomeTools
~/software$ wget https://github.com/genometools/genometools/archive/v1.6.1.tar.gz
~/software$ tar -zxvf genometools-1.6.1.tar.gz
~/software$ cd genometools-1.6.1
~/software/genometools-1.6.1$ cat INSTALL 
Building GenomeTools
--------------------

Invoke GNU make, e.g.:

$ make [argument ...]

to build GenomeTools. You need at least version 3.80 of GNU make, you can check
which version you have by invoking

$ make --version

On *BSD GNU make is often called ``gmake''.

Possible arguments:

- 64bit=no         to compile a 32-bit version
- 32bit=yes        to compile a 32-bit version
- opt=no           to disable optimization
- assert=no        to disable assertions
- amalgamation=yes to compile as an amalgamation
- cairo=no         to disable AnnotationSketch, dropping Cairo/Pango deps
- errorcheck=no    to disable the handling of compiler warnings as errors
- universal=yes    to build a universal binary
- useshared=yes    to use the system's shared libraries
- verbose=yes      to make the build more verbose
# 出现以上提示，只用一个make命令就可以了
~/software/genometools-1.6.1$ make 64bit=yes threads=yes cairo=no -j4 # 这样就安装完事了
# 安装Ninja
~/software$ wget https://github.com/TravisWheelerLab/NINJA/releases/tag/0.95-cluster_only
~/software$ tar -zxvf NINJA-0.95-cluster_only.tar.gz
~/software$ cd NINJA-0.95-cluster_only
~/software/NINJA-0.95-cluster_only$ cd NINJA/
~/software/NINJA-0.95-cluster_only/NINJA$ make all # 这样Ninja就安装完事了

(2)安装RepeatModeler

~/software$ wget http://www.repeatmasker.org/RepeatModeler/RepeatModeler-2.0.1.tar.gz
~/software$ tar -zxvf RepeatModeler-2.0.1.tar.gz
~/software$ cd RepeatModeler-2.0.1
~/software/RepeatModeler-2.0.1$ perl ./configure

出现以下提示信息，需要填写：

3. Braker安装

功能：基因参数模型训练

（1）安装依赖: 依赖spaln、exonerate、File::Spec::Functions、Hash::Merge、 List::Util、Logger::Simple、Module::Load::Conditional、Parallel::ForkManager、POSIX、Scalar::Util::Numeric、YAML、bamtools、augustus、GeneMark-ET、GenomeThreader这些软件。

~$ conda install -y spaln exonerate 
~$ cpanm File::Spec::Functions Hash::Merge List::Util Logger::Simple Module::Load::Conditional Parallel::ForkManager POSIX Scalar::Util::Numeric YAML # 安装这些依赖的perl模块

# 安装bamtools
~$ cd software
~/software$ wget https://github.com/pezmaster31/bamtools/archive/v2.5.1.tar.gz
~/software$ tar -zxvf bamtools-2.5.1.tar.gz
~/software$ mkdir bamtools # bamtools需要用cmake命令编译，所以不要在解压文件中直接安装软件
~/software$ cd bamtools-2.5.1
~/software/bamtools-2.5.1$ mkdir build # 在build文件中cmake
~/software/bamtools-2.5.1$ cd build
~/software/bamtools-2.5.1/build$ cmake -DCMAKE_INSTALL_PREFIX=/home/ug0063/software/bamtools ..
~/software/bamtools-2.5.1/build$ make
~/software/bamtools-2.5.1/build$ make install # 这样bamtools就安装到了bamtools文件夹中了

# 安装augustus软件（真核生物结构注释软件）
~/software$ wget http://bioinf.uni-greifswald.de/augustus/binaries/augustus-3.3.3.tar.gz
~/software$ tar -zxvf augustus-3.3.3.tar.gz
~/software$ cd augustus-3.3.3
# 由于直接进行make会报错，所以需要修改三个文件: auxprogs/bam2hints/Makefile、auxprogs/filterBam/src/Makefile、auxprogs/bam2wig/Makefile

# samtools、htslib、bcftools三者是同一个作者开发的，一定要在安装到同一个文件夹下，而且必须将每个软件的文件夹名称就叫软件的名称，必须按照htslib、bcftools、samtools这个顺序安装，不然容易报错。
~/software$ git clone https://github.com/samtools/htslib.git
~/software$ cd htslib
~/software/htslib$ make
~/software/htslib$ cd ..
~/software$ git clone https://github.com/samtools/bcftools.git
~/software$ cd bcftools
~/software/bcftools$ make 
~/software/bcftools$ cd ..
~/software$ git clone https://github.com/samtools/samtools.git
~/software$ cd samtools
~/software/samtools$ make
~/software/samtools$ cd ..
~/software$ git clone https://github.com/samtools/tabix.git
~/software$ cd tabix
~/software/tabix$ make
# 这样bam2wig依赖的四个软件就安装完事了，然后在修改auxprogs/bam2wig/Makefile的第9、10行
~/software/tabix$ cd ../augustus-3.3.3/
~/software/augustus-3.3.3$ vi auxprogs/bam2wig/Makefile

~/software/augustus-3.3.3$ make
# 添加环境变量
~/software/augustus-3.3.3$ vi ~/.bashrc 
# 然后在.bashrc最末尾加上以下内容：
export PATH="/home/ug0063/software/augustus-3.3.3/bin:$PATH"
export PATH="/home/ug0063/software/augustus-3.3.3/scripts:$PATH"
export AUGUSTUS_CONFIG_PATH=/home/ug0063/software/augustus-3.3.3/config
# 这样augustus软件就安装完了

#安装[GeneMark-ET](http://topaz.gatech.edu/GeneMark/license_download.cgi)
# 从上面网址上下载软件，需要注册信息才能下载, 下载两个文件一个是gm_et_linux_64.tar.gz, 另一个是证书文件需要下载到家目录下：gm_key_64.gz。
~$ gunzip gm_key_64.gz 
~$ mv gm_key_64 .gm_key # 因为GeneMark-ET就在家目录下找.gm_key文件
~/software$ tar -zxvf gm_et_linux_64.tar.gz
~/software$ cd gm_et_linux_64/gmes_petap
~/software/gm_et_linux_64/gmes_petap$ ll 
# 可以看到所有程序都是用perl编写的，但是每个程序的开头注释的都是#!/usr/bin/perl，
# 是直接调用的/usr/bin里面的perl命令，但是我们安装的模块都是在/home/ug0063/miniconda3/这里，
# 所有我们需要将每个以pl结尾的文件第一行修改为#!/home/ug0063/miniconda3/bin/perl，也可以让其在环境变量里找，
# 即：#!/usr/bin/env perl
~/software/gm_et_linux_64/gmes_petap$ ls *.pl | xargs -i sed -i 's/#!\/usr\/bin\/perl/#!\/usr\/bin\/env perl/' {}
# 这样就安装完事了

# 安装GenomeThreader
~/software$ wget http://genomethreader.org/distributions/gth-1.7.3-Linux_x86_64-64bit.tar.gz
# 这样就可以了

# 以上依赖软件全部安装完成了，就可以安装Braker了
~/software$ wget https://github.com/Gaius-Augustus/BRAKER/archive/v2.1.5.zip
~/software$ unzip v2.1.5.zip
~/software$ mv v2.1.5 BRAKER-2.1.5
# 然后将以下语句加到环境变量.bashrc中末尾处
# export PATH=/home/ug0063/software/BRAKER-2.1.2/scripts:$PATH
~$ sounrce .bashrc
# 这样就大功告成了！

4.Masker安装

功能：基因结构注释

~/software$ wget http://www.yandell-lab.org/software/maker.html
~/software$ tar -zxvf maker-2.31.10.tgz
~/software$ cd maker
# 查看INSTALL文件得知，进入maker/src/，然后执行perl Build.PL
~software/maker$ cd src
~/software/maker/src$ perl Build.PL

5. MCScanX安装

功能：共线性分析

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