The command line is the usual working environment in bioinformatics. This repository gathers scripts and tweaks to improve the handling of biological data and programs when using the zsh. This includes extensions to the famous z shell autocompletion system which outshines bash.

biozsh should be able to be installed using one of the ZSH package managers, e.g. zgen. Just add the following to your zshrc, before zgen save:

zgen load kloetzl/biozsh

I still have to figure out, how to do a proper installation. But this should work for now:

git clone https://github.com/kloetzl/biozsh
cd biozsh
make install-dev

Restarting the shell will give you access to the new features.

Depending on your ZSH style using the auto completion is as simple as pressing TAB. Here is what it looks like for me if I press TAB, just after typing blastn -db.

Blastn supports a variety of different output format. Now you don't have to remember their weird codes anymore, just press TAB!

Checkout the completions directory for all supported tools.

Copyright (c) 2017 Fabian Klötzl
MIT License, See License for details.

Some files may be licensed differently.