[Bioperl-l] Installation (was Notification: i...)

[Jason Stajich]

On Tue, 15 May 2001, Todd Richmond wrote:

> On 5/15/01 2:51 PM, "Peter Schattner" <schattner@alum.mit.edu> wrote:
> 
> > For what it's worth, the bioperl tutorial (bptutorial.pl) has the following
> > installation instructions:
> > 
> 
> <snip>
> 
> > If someone suggests wording to make these instructions clearer, I will
> > gladly edit the install instructions in the tutorial.
> > 
> 
> I think the problem is that people are not going to look at the tutorial
> before they install bioperl. They'll do the install, watch the tests fail,
> and wonder why. Personally, I wouldn't/didn't think to go to the tutorial to
> figure out why the tests were failing - I went straight to the .t files, and
> then to the .pm files. Setting the directory variables should be mentioned
> in the README at the root - or maybe spit out during the 'perl Makefile.PL'
> phase.
> 
good idea, let's see if we can implement that.

> The README file appears to be a bit out-of-date anyway. Part of it says:
> 

Exactly.  All are should feel free to update it to meet what you think is
helpful to new users.  We encourage anyone to make changes to the README
to make it easier for new people to use.  Typically it is left to the last
minute so changes now definitely are a good idea.  I'll make sure that
re-reading the README is in the todo list for the next release in case no
one makes the changes before then.

> ---
> BUILDING THE COMPILED EXTENSIONS
> Move to the directory Compile/SW. This is where the C code and XS
> extension for the bp_sw module is held and execute these commands:
> ---
> 
> There's no longer a Compile/SW directory is there? In fact, the compiled
> extension stuff isn't even being distributed with bioperl-0.7 is it? In any
> case, I don't think the directions for the compiles extensions in any way
> resembles the actual steps you have to take.
> 
It is in bioperl-ext.  We don't distribute it with bioperl core code, but
offer it as an extension that people may optionally install since it
probably won't work on anything but un*x.  README should definitely be
updated to reflect this.

> -- 
> Todd Richmond                    http://cellwall.stanford.edu/todd
> Carnegie Institution             email: todd@andrew2.stanford.edu
> Department of Plant Biology      fax: 1-650-325-6857
> 260 Panama Street                phone: 1-650-325-1521 x431
> Stanford, CA 94305
> 
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Jason Stajich
jason@chg.mc.duke.edu
Center for Human Genetics
Duke University Medical Center 
http://www.chg.duke.edu/