Windows love ubuntu

安装编译环境GCC和G++

sudo apt-get install gcc

sudo apt-get install g++

安装编译工具make

sudo apt install make

sudo apt install make-guile

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安装alien，赋予ubuntu安装rpm软件包的功能

sudo apt-get install alien

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创建tools目录存放软件包

mkdir tools

进入tools目录

cd tools

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安装谷歌sparsehash

git clone https://github.com/sparsehash/sparsehash.git

cd sparsehash

./configure

make

sudo make install

cd ..

安装openMPI

wget https://download.open-mpi.org/release/open-mpi/v4.0/openmpi-4.0.0.tar.gz

tar zxvf openmpi-4.0.0.tar.gz

cd openmpi-4.0.0

./configure --prefix=/usr/local/bin

sudo make all install

cd ..

#测试是否安装成功

ompi_info

若不成功，直接运行以下命令安装：

sudo apt-get install openmpi

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安装ABySS原核生物基因组组装软件

wget http://www.bcgsc.ca/platform/bioinfo/software/abyss/releases/2.1.5/abyss-2.1.5.tar.gz

tar zxvf abyss-2.1.5.tar.gz

cd abyss-2.1.5

#安装boost依赖

wget http://downloads.sourceforge.net/project/boost/boost/1.56.0/boost_1_56_0.tar.bz2

tar jxf boost_1_56_0.tar.bz2

./configure --enable-maxk=160 --with-mpi=/usr/local/lib/openmpi

#（注：openmpi的路径用“whereis openmpi”寻找）  

make

sudo make install 

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安装blast+

sudo apt-get install ncbi-blast+

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安装bioperl

sudo apt-get install bioperl

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安装biopython

（1）安装python-dev，不然会出现Setup script exited with error: command ‘gcc’ failed with exit status 1错误

sudo apt-get install python-dev

（2）安装pip工具

sudo apt-get install python-pip

（3）安装biopython

sudo pip install -f http://biopython.org/DIST/ biopython

#(DIST/和biopython之间有个空格)

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安装prokka原核注释软件

依赖：

sudo apt-get install parallel

sudo apt-get install prodigal

sudo apt install hmmer

sudo apt-get install barrnap

sudo apt-get install aragorn

JAVA:

wget http://download.oracle.com/otn-pub/java/jdk/8u181-b13/96a7b8442fe848ef90c96a2fad6ed6d1/jdk-8u181-linux-x64.tar.gz

#下载失败就手动下吧

tar zxvf jdk-8u181-linux-x64.tar.gz

sudo ln -s /home/lhl/tools/jdk1.8.0_201/bin/java /usr/local/bin/java

vim ~/.bashrc

export JAVA_HOME=/home/lhl/tools/jdk1.8.0_201

export JRE_HOME=${JAVA_HOME}/jre

export CLASSPATH=.:${JAVA_HOME}/lib:${JRE_HOME}/lib

export PATH=${JAVA_HOME}/bin:$PATH

minced：

git clone https://github.com/ctSkennerton/minced.git

cd minced

make

sudo ln -s /home/lhl/tools/minced/minced /usr/local/bin/minced

tbl2asn：下载最新版，更名为tbl2asn，拷贝到包含在环境变量的目录下

sudo apt-get install libdatetime-perl libxml-simple-perl libdigest-md5-perl git default-jre bioperl

sudo cpan Bio::Perl

git clone https://github.com/tseemann/prokka.git

#将$HOME/prokka/bin/加入环境变量

prokka --setupdb