1.Setup

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1.Setup

How to do our jobs efficiently and reproducibly
0) Get a Laptop or Desktop
​mac 使用技巧​
1) Get a Linux OS
1a) docker or VM
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##install and run a centos docker for the first time
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docker pull centos
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docker run -it --name=centos -h centos -v /Users/john/Documents/centos/:/mac centos
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# docker run -it --name=container_name -h hostname -v /HOST_ABSOLUTE_DIR:/CONTAINER_ABSOLUTE_DIR image_name:tag
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# simple version docker run -it centos
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​
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##add user
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useradd john
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passwd john
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su john
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​
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###detach (pause) and attach
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ctrl+p+q     # detach退出: 容器不关闭，容器内部正在运行的任务不会停止. ctrl+p+q表示按住ctrl不动，先按下p，后按下q
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docker attach container_name # attach进入
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​
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​
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###exit and delete a container
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exit #inside docker as root, then exit
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docker rm container_name
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install basic software for centos
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yum -y install vim
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yum -y install man
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yum -y install less
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yum -y install wget
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​
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yum -y install make
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yum -y install gcc gcc-c++
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yum -y install gcc-gfortran
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​
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yum -y install bzip2-devel
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yum -y install zlib-devel
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yum -y install zip unzip
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​
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yum -y install xz-devel.x86_64
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yum -y install libg2c.so.0
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yum -y install readline-devel
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yum -y install libXt-devel
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​
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mkdir /download
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cd /download
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wget -c http://www.cpan.org/src/5.0/perl-5.26.1.tar.gz
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tar -xvzf perl-5.26.1.tar.gz
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cd /download/perl-5.26.1
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sh Configure -de
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make
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make install
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You can also pull and run a ubuntu docker, then install basic software for ubuntu
docker run -it --name=ubuntu -h ubuntu -v /Users/john/Documents/unbuntu/:/mac ubuntu
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apt-get -qq update
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apt-get -y install vim
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...
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More: https://ygxing.gitbooks.io/docker/content/​
1b) ssh & login 
ssh/sftp -p XXX (default: 22)
You can also using the following SFTP/FTP clients to mount the remote server to the local desktop, so you can edit the scripts with a GUI editor like Atom:
Transmit
Fetch (education version)
2) Learn an Editor
A. Vim -- Learn Vim Progressively​
Learn vim and it will be your last text editor. There isn’t any better text editor that I know of. It is hard to learn, but incredible to use.I suggest you teach yourself Vim in 4 steps:
1.
Survive
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Feel comfortable
3.
Feel Better, Stronger, Faster
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Use superpowers of vim
B. Atom -- Tutorial and Tips ​
A hackable text editor for the 21st century
3) README and MD
Document your project using markdown language (available in wiki, gitbook, github, etc)
​https://github.com/adam-p/markdown-here/wiki/Markdown-Cheatsheet​
4)  Always Backup Data Files Regularly
​Tips on 备份数据、保存中间数据 | 数据安全​
It's necessary to backup data regularly.
5) More Readings and Practices
​Teaching Videos：
Week I.0.Setup Part I，
Week I.1.Setup Part II
for Beginners  
《Bioinformatics Data Skills》
1) How to Learn Bioinformatics
for Advanced Readers 
《鸟哥的Linux私房菜-基础学习篇》
第25章 LINUX备份策略
25.2.2完整备份的差异备份
25.3鸟哥的备份策略
25.4灾难恢复的考虑
25.5重点回顾
《Bioinformatics Data Skills》
1) How to Learn Bioinformatics
2) Setting up and Managing a Bioinformatics Projects
4）Working with Remote Machines
Video
5a) Setup 1
​@Youtube​
​@Bilibili​
5b) Setup 2
​@Youtube​
​@Bilibili​