[Biopython-dev] Installing all biopython dependencies

[Peter Cock]

On Mon, Mar 10, 2014 at 5:02 PM, Tiago Antao <tra at popgen.net> wrote:
> Hi,
>
> I am trying to create a easy-to-install, easy-to-replicate Virtual
> Machine(*) with all the requirements for Biopython. The idea is mainly
> to make it easy to have reliable testing, but it can also be used as a
> very fast installation of Biopython.

Sounds good :)

> The VM is currently based on Ubuntu saucy, and I am trying to
> make sure all the dependencies are met.

Some of this would apply to the TravisCI VM, which is also
Debian/Ubuntu based. There we have to balance total run
time (install everything & run tests) against full coverage).
https://travis-ci.org/biopython/biopython/builds

It would be neat to have an instance of your docker based
VM running as a buildslave too...
http://testing.open-bio.org/biopython/tgrid

> I would like some advice on the following please:
>
> EmbossPhylipNew - the ubuntu package (embassy-phylip) has dependency
> problems, so I guess this requires a manual download/install?
> reportlab - What is the best way to get the fonts?
> XXmotif - What is this???
> PAML - There seemed to be a ubuntu package, but no more?
>
>
> The following packages require manual installation (no ubuntu
> package), please correct me if I am wrong (makes my life easier)...
>
> DSSP
> Dialign
> msaprobs
> NACCESS
> Prank
> Probcons
> TCoffee

For TravisCI we install a Debian/Ubuntu package for t-coffee,
so at least that ought to be easy. e.g.
https://packages.debian.org/sid/t-coffee

Others (where the licence permits) we can request DebianMed/
BioLinux look at for packaging...

Peter