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Readme.md

biozsh — the z in bioinformatics

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.

Installation

biozsh should be able to be installed using one of the ZSH package managers of your choice. See these links for detailed installation instructions.

Manual installation

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. If you want to manually source the biozsh.zsh script, note that you have to do so with the absolute path.

Usage

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 -db completion

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

blastn -outfmt completion

Checkout the completions directory for all supported tools.

biozsh in action

Follow this link to have a glimpse of the power of biozsh in action.

asciicast

License

Copyright (c) 2017 – 2018 Fabian Klötzl
MIT License, See License for details.

Some files may be licensed differently.

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