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

Chris Fields cjfields at illinois.edu
Fri Jul 2 11:46:46 EDT 2010


On Jul 1, 2010, at 11:21 PM, George Iatropoulos wrote:

> Hi guys!
> 
> I'd like to thank you for this important project. I currently develop
> a script that uses the SeqIO module to read fasta  or files with other
> bio-formats. However your installation instructions are too difficult
> to be followed, or even outdated, especially for the mac platform.
> 
> After trying a week I really can't install bioperl on a Snow Leopard
> machine (perl 5.10.0) and I tried the CPAN and the fink method. None
> of them works! Especially cpan seems to mess up with itself and now
> doesn't install anything!

That's odd.  Can you send me what you are seeing?  

> 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).  

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.  Now, re: Ubuntu I haven't had any problems with 9.04 or 9.10 (haven't jumped into 10.04 yet), but I'm a core bioperl dev.  There are a few recommended modules that require outside libraries (GD first among them).  These modules are not required for most core functionality.

> 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.

We're actually working on segmenting BioPerl into separate packages, something I intend on bringing up next week at BOSC.  

> Best wishes and many thanks to all of you because bioperl is really
> important for us!
> 
> Georgios Iatropoulos

Sorry for the troubles, and thanks for letting us know.  Any additional details about installation problems are very welcome.  Also, the installation page on the bioperl website is editable (it is a wiki :).  So, feel free to add more detail where needed, or use the discussion page to point out problems.

chris


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