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

##install and run a centos docker for the first time
docker pull centos
docker run -it --name=centos -h centos -v /Users/john/Documents/centos/:/mac centos
# docker run -it --name=container_name -h hostname -v /HOST_ABSOLUTE_DIR:/CONTAINER_ABSOLUTE_DIR image_name:tag
# simple version docker run -it centos

##add user
useradd john
passwd john
su john

###detach (pause) and attach
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
docker attach container_name # attach进入


###exit and delete a container
exit #inside docker as root, then exit
docker rm container_name

install basic software for centos

yum -y install vim

yum -y install man
yum -y install less
yum -y install wget

yum -y install make
yum -y install gcc gcc-c++
yum -y install gcc-gfortran

yum -y install bzip2-devel
yum -y install zlib-devel
yum -y install zip unzip

yum -y install xz-devel.x86_64
yum -y install libg2c.so.0
yum -y install readline-devel
yum -y install libXt-devel

mkdir /download
cd /download
wget -c http://www.cpan.org/src/5.0/perl-5.26.1.tar.gz
tar -xvzf perl-5.26.1.tar.gz
cd /download/perl-5.26.1
sh Configure -de
make
make install

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

apt-get -qq update
apt-get -y install vim
...

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

2. Feel comfortable

3. Feel Better, Stronger, Faster

4. 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