[Biopython-dev] Releasing biopython - lessons

Brad Chapman chapmanb at 50mail.com
Fri Dec 6 15:19:52 UTC 2013


> With much help from Peter, 1.63 was released. I have a few comments/ideas I
> would like to share:
> 1. I think that there is a need to maintain an exhaustive list of
> dependencies that a full biopython distribution will need (python packages
> and external applications). I am offering to do that here:
> http://biopython.org/wiki/List_of_applications_executed_via_Biopython (over
> the next few days).
> 2. I was planning on creating a Linux virtual box image (and make it
> available) with everything that is needed to fully test and run a Biopython
> distribution. This would allow to have an extremely stable environment for
> testing (testing PCs normally have other uses and things can be broken by
> other stuff).

Great idea. One of the things we've been doing a lot of work on in
CloudBioLinux is making it easy to automate these type of local
installs. The advantage is that you have full documentation (lists of
packages), and automated way to install it, and a script you can use for
generating images for testing/distribution purposes.

I put together a starter package for a Biopython 'flavor' here:


You can run with:

git clone https://github.com/chapmanb/cloudbiolinux.git
fab -H localhost install_biolinux:flavor=biopython

By default it will install an Anaconda Python, Biopython dependencies
and associated tools into ~/biopython.

If you like this approach, happy to help with pointers on adding more
tools. Thanks again for taking this on,

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