[Bioperl-l] questions

[simon andrews (BI)]

> -----Original Message-----
> From: Wijk, Rik van [mailto:Rik.vanWijk@wur.nl]
> Sent: 03 September 2002 21:38
> To: bioperl-l@bioperl.org
> Subject: [Bioperl-l] questions
> 
> - I installed BioPerl, but whenever I run a test program it says:
> Can't locate Bio/SeqIO.pm in @INC (@INC contains: C:/Perl/lib 
> C:/Perl/site/lib .) at C:\...\...\testsript.pl line 26. 
> 
> BEGIN failed--compilation aborted at C:\...\...\testscript.pl line 26.
> What is wrong? SeqIO.pm is in both directories mentioned 
> above. How can I install it properly 

It looks like you're running under Windows - if so you're probably running Activestate Perl (if not you should take a look, it makes this sort of thing really easy).  

In that case the easiest way to install Bioperl is to use the Perl Package Manager (PPM) utility which comes with Activeperl for installing new modules.

At a command prompt type:

#####################################################
ppm
install --location=ftp://bioperl.org/pub/DIST bioperl
[snip lots of stuff which scrolls past]
quit
#####################################################

...and it will magically install itself for you.

**If this doesn't work see the bottom of the message for an extra step which you need on some systems.

[Just out of interest - shouldn't this information be included on the download page of the BioPerl website??]

Although you can now use much of the functionality of BioPerl, you will find that some things still won't work because they rely on other Perl modules which are not part of the core distribution.  A full list of dependancies can be found here:

	http://bioperl.org/Core/external.shtml

Don't feel you have to install all of these, but bear in mind that certain things won't work because you don't have them.  If a bioperl module needs one of these dependencies to work it will tell you about it when the time comes.  To install any extra Perl modules you need you can again use the PPM utility.  Eg:

##################
ppm
install IO::Scalar
quit
##################

It really is that easy!

 
> - Were can I find a description of the functionalities of all 
> different modules? I have the feeling that there are numerous 
> modules with much more functionalities that are usefull but 
> how do I know what there is exactly and what you can do with it?

The online documentation can be found here:

	http://bioperl.org/Core/Latest/modules.html

Also, there is documentation for each module included with the distribution.  For any module you can look at its documentation using the 'perldoc' program.

Eg:

#####################################
>perldoc Bio::SeqIO
NAME
    Bio::SeqIO - Handler for SeqIO Formats

SYNOPSIS
        use Bio::SeqIO;

        $in  = Bio::SeqIO->new(-file => "inputfilename" , '-format' => 'Fasta');
        $out = Bio::SeqIO->new(-file => ">outputfilename" , '-format' => 'EMBL');
        # note: we quote -format to keep older perl's from complaining.

        while ( my $seq = $in->next_seq() ) {
            $out->write_seq($seq);
        }

etc. etc.
#####################################

Hope this helps you to get started.

	TTFN

	Simon.

** If PPM fails to work, it's usually because your network setup requires you to access the internet via a proxy server.  If this is the case you need to tell PPM where your proxy server is.  To do this simply set the environment variable HTTP_proxy.

eg: At a command prompt
###############################################
set HTTP_proxy=http://your.proxy.address:port
ppm 
etc. etc.
###############################################

If you don't know your proxy address or port number then ask your network admins or ISP.

This will set the variable for one command prompt session. If you want to permanently add this to your environment you can do so, but the exact method will  depend on which version of windows you are using.