[BioPython] versions and doc's

[Peter Cock]

On Wed, Aug 27, 2008 at 9:41 AM, Pavel SRB <srbanator at heckler-koch.cz> wrote:
> hi all, i am very new to biopython. I am working with debian etch stable
> version. During reading tutorial i have found out, that the current
> documentation works with version 1.47-1 (in debian it is in unstable
> repository).

Hi Pavel,

Yes - the documentation on our website, in particular the tutorial:
http://biopython.org/DIST/docs/tutorial/Tutorial.html
http://biopython.org/DIST/docs/tutorial/Tutorial.pdf
is for the current latest release of Biopython (i.e. Biopython 1.47 at
this time)

> Are there old tutorials related to 1.42-2 version (debian stable), or
> you believe i should rather start studying biopython in it's newest version?

Debian may have installed the Biopython 1.42 version of the tutorial
for you (but if it did, I don't know where to look).  If you want the
old tutorial you can either get the LaTeX source from from CVS and
recompile it, or more simply download the Biopython 1.42 source code
release, which contain both the HTML and PDF versions of the tutorial
under the Doc folder:
http://biopython.org/DIST/biopython-1.42.tar.gz
http://biopython.org/DIST/biopython-1.42.zip

However, I would strongly encourage you to install the current version
of Biopython instead - there have been a lot of bug fixes plus the
addition modules like Bio.SeqIO, Bio.AlignIO and Bio.Entrez.  In
addition, several of the modules present in Biopython 1.42 have since
been moved or deprecated and some have even been removed.

For debian (or ubuntu), I would suggest you install Biopython from
source.  First uninstall the debian package for Biopython 1.42, then
you should be able to install the build dependencies automatically
using:

sudo apt-get build-dep python-biopython

Then you should be ready to install Biopython 1.47 from source. See
http://biopython.org/wiki/Download for more details.

Peter