[Biopython-dev] Installation documentation

[Peter]

Giovanni Marco Dall'Olio wrote:
>
>Peter wrote:
>> Well, easy_install isn't (yet) an official python standard so I hadn't
>> previously worried about it - our wiki Downloads page does mention it.
>> Frankly the less "official" ways the are to install, the less ways it
>> can go wrong, and then the less questions need to be asked when it
>> goes wrong.
>
> If I can say mine, pypi and easy_install are very cool! :-)
>
> The biopython package on pypi works very well and it is the quickest
> way to get the latest version of biopython.
> It is more reliable than the packages in the repositories of many linux
> distro (some of them are outdated), and with respect to the manual
> installation, it makes it a lot easier to update biopython and to install
> all the dependencies.

Using the packages from your Linux distribution is probably the
easiest and most reliable way to get Biopython on Linux - but
these are inevitably a little out of date most of the time.

If it works, then yes, easy_install / pypi is nice and easy to use. As
long as Brad (or someone) is happy to support this, that's fine with
me.

However, easy_install isn't perfect. If you browse the NumPy/SciPy
mailing lists you'll see plenty of issues with easy_install - they have
problems with CPU specific optimised builds and so on which are
rather complicated to deal with. This is relevant because we would
need easy_install to handle NumPy for us.

I can certainly see the appeal of easy_install where a tool has lots
of dependencies you would otherwise have to manually install.
[If you've never tried, install BioPerl from CPAN and try and count
how many other perl libraries it depends on - quite an eye opener!]

This isn't really the case for Biopython, all we really need are Python
and NumPy (and even that can be skipped if you don't want to use
Bio.PDB, Bio.Cluster and a few other bits).

> I saw that some packages, when installed with easy_install, are
> downloaded from their own project home pages. For example,
> when you do easy_install numpy, it downloads the egg code from
> sourceforge. ...

Using easy_install for Biopython should download from biopython.org

Peter