[Bioperl-l] Installing Bioperl on Ubuntu and Mac OS X Snow Leopard (perl 5.10.0)

Kai Blin kai.blin at biotech.uni-tuebingen.de
Sat Jul 3 03:05:26 EDT 2010

On Fri, 2010-07-02 at 10:46 -0500, Chris Fields wrote:

Hi Chris,

> > As for the ubuntu platform a simple command like: "sudo apt-get
> > install bioperl" simply does the trick!
> > However I couldn't find this simple command in your installation
> > guidelines, and I don't really understand why I should set up a
> > server, before installing bioperl and then follow this complicated
> > series of instructions, to achieve something that is so simple!
> That's b/c the bioperl that is installed with apt is not up to date.
> CPAN has v.1.6.1; apt for karmic had 1.6.0 last I looked, v1.5.2 for
> bioperl-run (where CPAN is at v.1.6.1).  

As Steffen already said, the current Ubuntu version is 1.6.1, for both
bioperl and bioperl-run. I don't think providing backports for
Debian/Ubuntu versions wouldn't be too hard.

> I would like to get the releases to a point where they are easily
> packaged for apt/yum/ppm/fink/macports/whatever, so any help along
> those lines is greatly appreciated.

There currently is only an "automated port" of Bioperl on the openSuse
Build Service (OBS). I'll probably end up looking into packaging BioPerl
for SLES11, and would do that on OBS. Supporting other suse distros is
trivial, other RPM-based distros are doable once you figure out the
package names.

I'd say if Debian, Fedora, Suse and Ubuntu are covered, you're doing
pretty fine for Linux. People using more exotic distros will be used to
build their own stuff anyway. :) I've got no idea about packaging for

> > I understand that you try to give complete instructions for people who
> > may be pleased with more advanced stuff, but please don't forget
> > biology students who don't have a deep computational background. These
> > guys like me would appreciate some simple stuff to get their job and
> > their projects done, without needing to waste days to figure out
> > complicated-guru stuff.

I think some of the instructions on installing BioPerl are pretty
concise and allow you to just copy&paste the commands (see the
ubuntu-server install instructions). They might be a bit outdated, I
didn't check that. And of course I agree that it would be nicer if you
could just point your package manager at the appropriate repository and
be done.

However, there's only a few people working on BioPerl, and packaging can
eat a lot of time, as does keeping install instructions up-to-date.
Especially on install instructions, every user can help. Once you wasted
days on figuring out the complicated guru-stuff, write a wiki page to
explain it in a less complicated way. :)


Dipl.-Inform. Kai Blin         kai.blin at biotech.uni-tuebingen.de
Interfakultäres Institut für Mikrobiologie und Infektionsmedizin
Abteilung Mikrobiologie/Biotechnologie
Eberhard-Karls-Universität Tübingen
Auf der Morgenstelle 28                 Phone : ++49 7071 29-78841
D-72076 Tübingen                        Fax :   ++49 7071 29-5979
Homepage: http://www.mikrobio.uni-tuebingen.de/ag_wohlleben

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