Sunday, 20 October 2013

Installing python dependencies for Decombinator

I've written previously about Decombinator, the TCR repertoire analysis program developed in our laboratory.

Having just formatted my computer and reinstalled all my packages, I've been reminded of what a faff this can be.

This time around I did things a lot more efficiently than I had before. Seeing as how my colleague responsible for updating the current readme is busy writing up his thesis, here's my quick guide to installing all the python modules required by Decombinator in Linux - at least in Ubuntu.

 sudo apt-get install python-numpy python-biopython python-matplotlib python-levenshtein   
 sudo apt-get install python-pip  
 sudo pip install acora  

Most of the modules are available in the repositories, which has the added bonus of filling in all their required dependencies. Acora (the module that enacts the Aho-Corasick finite-state machine) however is not, but is easily installed from the command line using pip.

Easy. Time to get decombining.

August 2016 update:
Decombinator has gone through a number of improvements since writing this post. The current version (and installation details) can be found on the Innate2Adaptive lab's Github repo.

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