usefull tools for linux command line
Make terminal cool, install OhMyZsh
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| # install zsh
sudo apt-get install zsh # ubuntu
# change default shell to zsh
chsh -s /usr/bin/zsh
# install ohmyzsh
sh -c "$(wget https://raw.github.com/robbyrussell/oh-my-zsh/master/tools/install.sh -O -)"
source ~/.zshrc
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ssh login withoutpassword
- on your local machine, run
press Enter 3 time until finished. a "~/.ssh/id_rsa.pub" and "~/.ssh.id_rsa" will be generated.
- copy the public key file to the remote machine
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| ssh-copy-id remote_username@remote_server_ip_address
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- then you can login without password
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| ssh remote_username@remote_server_ip_address
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Terminal keyboard shortcuts
- Jump to head:
Ctrl + a - Jump to end:
Ctrl + e - Delete strings ahead:
Ctrl + u - Delete strings follow:
Ctrl + k
Program keeps running in the background
Run cmd using nohup
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| nohup command [options] &
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Run cmd using zellij.
zellij is drop-in replacement of tmux
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# create a new session
zellij
# specify a new session, named bio
zellij -s bio
# subcommds
zellij ls # list all session
zellij a bio # attach session
zellij ka # kill all sessions
zellij k bio # kill a specfic session, bio
zellij da # delete all session
zellji d bio # detelete a specifc session, bio
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Run cmd using Tmux
Outside Tmux:
Typically these are run outside, but you can also run them inside an existing session
a. Start New Session
b. Attach To Existing Session
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| tmux attach -t myname #by name
tmux attach 4 #by number (in this case 4)
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c. List Sessions
d. Kill Session
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| tmux kill-session -t myname
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Inside Tmux Session:
Start each command with CTRL + b, release, then press one of the following:
| Panes | |
|---|
| % | vertical split |
| " | horizontal split |
| d | detach from session (it keeps running in the background) |
| x | kill pane |
| Up/Down/Left/Right | move between panes |
| PageUP/PageDown | CTRL+c to exit the PageUp/Down mode |
Fn+Up/Down | PageUp/Down: Mac keyboard |
| : + resize-pane -D | Resizes the current pane down |
| : + resize-pane -U | Resizes the current pane upward |
| : + resize-pane -L | Resizes the current pane left |
| : + resize-pane -R | Resizes the current pane right |
| : + resize-pane -D 20 | Resizes the current pane down by 20 cells |
File compression and decompression
Decompression
| File type | Cmd | e.g. |
|---|
| *.tar | tar -xvf | |
| *.tar.gz or *.tgz | tar -xvzf | |
| *bz2 | bzip2 -d or bunzip2 | |
| *.tar.bz2 | tar -xjf | |
| *.Z | uncompress | |
| *.tar.Z | tar -xZf | |
| *.rar | unrar e or rar x | unrar e file.rar |
| *.zip | unzip | |
| *.gz | gunzip | |
Compression
| File type | Cmd | e.g. |
|---|
| *.tar | tar -cvf | |
| *.tar.gz or *.tgz | tar -cvzf | |
| *bz2 | bzip2 -z | |
| *.tar.bz2 | tar -cjf | |
| *.Z | compress | |
| *.tar.Z | tar -cZf | |
| *.rar | rar a | rar a -ep1 newname /home/user/cpp |
| *.zip | zip | |
| *.gz | gzip | |
For rar installation
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| sudo apt-get install rar
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Handy tricks for handling filepath
very useful to strip file sufix, path et.al.
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| # e.g.
var=./home/fastq/filename_R1.fq.gz
# extract filename
${var#*/} # -> home/fastq/filename_R1.fq.gz
var1=${var##*/} # -> filename_R1.fq.gz
# remove file suffix
${var1%.*} # -> filename_R1.fq
${var1%%.*} # -> filename_R1
# get basebame
var2=$(basename "${var}" .fq.gz) #-> filename_R1
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vim shortcuts
In view mode, curso movement
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| ^ (shift + 6): jump to the start of current line
$ (shift + 4): jump to the end of current line
gg: go to the first line of the document
G: go to the last line of the document
H: move to the top of screen
M: move to the middle of screen
L: move to the bottom of screen
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