本分析流程需要安装QIIME、VSEARCH等软件,测试Linux系统为Ubuntu 16.04LTS。 ## 更改Ubuntu更新源 #1.修改前先备份 sudo cp /etc/apt/sources.list /etc/apt/sources.list.bak #2.复制sources.list到windows文件目录 sudo cp /etc/apt/sources.list /mnt/c/ #3.然后在windows下用记事本打开sources.list文件,先删除所有内容, 并复制以下源,粘贴到sources.list # deb cdrom:[Ubuntu 16.04 LTS _Xenial Xerus_ - Release amd64 (20160420.1)]/ xenial main restricted deb http://mirrors.aliyun.com/ubuntu/ xenial main restricted deb-src http://mirrors.aliyun.com/ubuntu/ xenial main restricted multiverse universe #Added by software-properties deb http://mirrors.aliyun.com/ubuntu/ xenial-updates main restricted deb-src http://mirrors.aliyun.com/ubuntu/ xenial-updates main restricted multiverse universe #Added by software-properties deb http://mirrors.aliyun.com/ubuntu/ xenial universe deb http://mirrors.aliyun.com/ubuntu/ xenial-updates universe deb http://mirrors.aliyun.com/ubuntu/ xenial multiverse deb http://mirrors.aliyun.com/ubuntu/ xenial-updates multiverse deb http://mirrors.aliyun.com/ubuntu/ xenial-backports main restricted universe multiverse deb-src http://mirrors.aliyun.com/ubuntu/ xenial-backports main restricted universe multiverse #Added by software-properties deb http://mirrors.aliyun.com/ubuntu/ xenial-security main restricted deb-src http://mirrors.aliyun.com/ubuntu/ xenial-security main restricted multiverse universe #Added by software-properties deb http://mirrors.aliyun.com/ubuntu/ xenial-security universe deb http://mirrors.aliyun.com/ubuntu/ xenial-security multiverse deb http://archive.canonical.com/ubuntu xenial partner deb-src http://archive.canonical.com/ubuntu xenial partner #4. 复制sources.list到linux文件目录 sudo cp /mnt/c/sources.list /etc/apt/ #4. 最后执行源更新 sudo apt-get update ============================================================== ## 安装Linux常用工具 sudo apt-get install build-essential #Linux基础开发工具 sudo apt-get install python-minimal python-dev python-tk #安装python2.7 #如果python不是python2.7,请设置python2为默认版本:alias python=’/usr/bin/python2’(可把此命令写入~/.bashrc文件中)。 sudo apt-get install python-pip #可用pip安装python包 sudo apt-get install r-base -y #Install R sudo apt-get install default-jre -y #Install Java Run Environment (JRE) ============================================================== ## 安装QIIME sudo pip install --upgrade pip -i http://mirrors.aliyun.com/pypi/simple --trusted-host mirrors.aliyun.com sudo pip install numpy==1.10.0 -i http://mirrors.aliyun.com/pypi/simple --trusted-host mirrors.aliyun.com sudo pip install matplotlib==1.5.3 -i http://mirrors.aliyun.com/pypi/simple --trusted-host mirrors.aliyun.com $sudo pip install scipy==1.0.0 -i http://mirrors.aliyun.com/pypi/simple --trusted-host mirrors.aliyun.com $sudo pip install ipython==5.5.0 -i http://mirrors.aliyun.com/pypi/simple --trusted-host mirrors.aliyun.com sudo pip install pandas==0.21.1 -i http://mirrors.aliyun.com/pypi/simple --trusted-host mirrors.aliyun.com sudo pip install biom-format==2.1.4 -i http://mirrors.aliyun.com/pypi/simple --trusted-host mirrors.aliyun.com sudo pip install qiime -i http://mirrors.aliyun.com/pypi/simple --trusted-host mirrors.aliyun.com #测序QIIME安装是否成功 print_qiime_config.py -t ================================================================== ## 安装VSEARCH git clone https://github.com/torognes/vsearch.git cd vsearch ./autogen.sh ./configure make sudo make install #默认安装在/usr/local/bin/目录 sudo cp /usr/local/bin/vsearch /usr/local/bin/usearch61 #让qiime的参数usearch61使用vsearch程序 ======================================================= ## 安装ClustalW或Muscle sudo apt-get install clustalw sudo apt-get install muscle ## 安装RDP classifier #下载RDP Classifier v2.2(只有此版本能用),下载网址:https://sourceforge.net/projects/rdp-classifier/files/rdp-classifier/ #解压到windows系统的D盘根目录,并复制到Ubuntu系统的用户home目录: mv /mnt/d/rdp_classifier_2.2/ ~/ echo "export RDP_JAR_PATH=~/rdp_classifier_2.2/rdp_classifier-2.2.jar" >> ~/.bashrc source ~/.bashrc ## 安装Xming可运行X-windows图形程序 #下载安装包Xming-setup.exe(最新版本6.9.0.31),Xming官网:http://sourceforge.net/projects/xming/ echo "export DISPLAY=:0.0" >> ~/.bashrc #设置X图形显示端口 source ~/.bashrc #======== 安 装 问 题 =========== #安装qiime时停止不动,可试一下或反复运行几次这条命令: sudo pip install qiime -i http://mirrors.aliyun.com/pypi/simple --trusted-host mirrors.aliyun.com --extra-index-url http://mirrors.aliyun.com/pypi/simple #安装VSEARCH遇到问题:./autogen.sh:autoreconf: Not found sudo apt-get install autoconf