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 ch(){ 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.