Showing posts from July, 2017

Shell aliases for bioinformatics

Using shell allows us to take advantage of some nice features to make our bioinformatics lives a little easier for things we do very frequently. In Ubuntu, the ~/.bashrc file is run as a new terminal window is opened to customise the shell. Here are a few of my favourite general shortcuts. Let me know your favourites in the comments section below!

#shorten ls forms
alias ll='ls -alF'
alias la='ls -A'
alias l='ls -CF'

#shorten file viewing
alias h='head'
alias t='tail'
alias n='nano -S'
#the -S option to nano makes scrolling smoother
alias nano='nano -S'

#easy update
alias update='sudo apt-get update && sudo apt-get upgrade -y'

#search through history
alias hgrep='history | grep'

#Get col headers of tab delim file
cat $1 | tr '\t' '\n' | nl -n ln
export -f ch

#login with ssh where IP is constant (X is the IP address)
alias login1='ssh -Y username@X.X.X.X' #scp can be done as above

#login with …