[Bioperl-l] Initial draft of bioperl tutorial committed

Heikki Lehvaslaiho heikki@ebi.ac.uk
Tue, 09 Jan 2001 10:45:56 +0000


Running of any part of the script is dependent on bioperl-ext package.
Since I do not have it, I can not run any demos. A workaround is


odo ~/src/bioperl-live> perl -w  bptutorial.pl 0
The C-compiled engine for Smith Waterman alignments (Bio::Ext::Align)
has not been installed.
 Please install the bioperl-ext package
odo ~/src/bioperl-live> perl -w  bptutorial.pl 4
The C-compiled engine for Smith Waterman alignments (Bio::Ext::Align)
has not been installed.
 Please install the bioperl-ext package

odo ~/src/bioperl-live>

Peter Schattner wrote:
> Hello all
> I have committed an initial draft of an introductory bioperl tutorial
> (called "bptutorial.pl") to the bioperl-live (main) repository.  The
> draft tutorial pretty much follows the outline from my proposal:
> http://bioperl.org/pipermail/bioperl-l/2000-December/001972.html
> One addition to the original proposal is that I have included an
> "appendix" which is a working script that demonstrates most of the
> bioperl features described in the tutorial. (The script is largely
> cut-and-pasted from various test and example files with print statements
> added to make it clearer as to what is going on).
> I believe that having a clear and accurate tutorial could make bioperl
> more accessible and widely used.  On the other hand, if the tutorial is
> confusing or contains mistakes, it will turn people away from trying
> bioperl (and probably be worse than not having one at all).   So I have
> a request.  I would appreciate it if some of you would read the tutorial
> and give me feedback in terms of clarity and accuracy.  I am interested
> in both general comments (eg "this section is too long - cut out
> such-and-such" or "this module description fits better in this section"
> or "this module will not be included in the 0.7 release so don't include
> it" ) and specific places where there are errors or misleading or
> confusing statements.  (If you think that the tutorial is clear and/or
> that specific parts are particularly helpful I'd of course be happy to
> get that feedback too :--).  Suggestions on improving the formatting
> would also be appreciated.
> I would definitely like feedback from people who have written modules
> which are in the 0.7 release to make sure that I have captured your
> intent and the proper usage of your module(s). I would also like
> comments from folks who are simply bioperl users and, ideally, from a
> few people who haven't used bioperl much before to see in what ways the
> tutorial makes it easier to use or get started using bioperl (or
> doesn't).  Feel free to write to me directly at schattner@alum.mit.edu
> or via this list.  Thanks.
> If you just want to look at the tutorial, you can view it through the
> web browsable CVS at :
> http://cvs.bioperl.org/cgi-bin/viewcvs/viewcvs.cgi/bioperl-live/bptutorial.pl?rev=1.1&content-type=text/vnd.viewcvs-markup&cvsroot=bioperl.
> (Note: you may need to view the tutorial through a word processor to get
> the lines to wrap properly and to get rid of extra '^M's.  If someone
> can tell me how I need to reformat the file so this is not necessary I'd
> be grateful.)
> If you want to also run the tutorial script, you will need to have a
> copy  of CVS "bioperl-live". The tutorial script will *not* work with
> release 0.6. (Note that the contents of bioperl-live are being updated
> often so some of the demo scripts may fail - they're working for me now
> and if they start failing I'd appreciate finding out).
> Cheers
> Peter
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@bioperl.org
> http://bioperl.org/mailman/listinfo/bioperl-l

______ _/      _/_____________________________________________________
      _/      _/                      http://www.ebi.ac.uk/mutations/
     _/  _/  _/  Heikki Lehvaslaiho          heikki@ebi.ac.uk
    _/_/_/_/_/  EMBL Outstation, European Bioinformatics Institute
   _/  _/  _/  Wellcome Trust Genome Campus, Hinxton
  _/  _/  _/  Cambs. CB10 1SD, United Kingdom
     _/      Phone: +44 (0)1223 494 644   FAX: +44 (0)1223 494 468
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