[Bioperl-l] Size of BioPerl distribution

[Mark A. Jensen]

t/data compresses from 21M to 9M. We could ship with 

$ tar -czf data.tar.gz data
$ rm -rf data

and do the following in Bio::Root::Test, if we're willing to expect 
Archive::Tar and IO::Zlib :

use vars qw( $ARCHIVE );
$ARCHIVE = "data.tar.gz";
...

sub test_input_file {
    # if it's there, fine
    my $fn =  File::Spec->catfile('t', 'data', @_);
    return $fn if -e $fn;
    # if it's not, expand the archive
    my $arch = File::Spec->catfile('t', $ARCHIVE);
    Bio::Root::Root->throw("Test data archive not present") unless (-e $arch);
    my $tar = Archive::Tar->new($arch);
    Bio::Root::Root->throw ("Can't extract test data archive") unless $tar;
    $tar->extract;
    return $fn if -e $fn;
    return;
}


----- Original Message ----- 
From: "Chris Fields" <cjfields at illinois.edu>
To: "BioPerl List" <bioperl-l at lists.open-bio.org>
Sent: Thursday, September 17, 2009 5:38 PM
Subject: [Bioperl-l] Size of BioPerl distribution


> After uploading the latest bioperl alpha to CPAN I noticed the size of  
> the distribution archive has jumped up from ~7 MB to just over 10 MB.   
> It looks like a majority of this is attributable to three data files  
> for testing in t/data added after the 1.6.0 release:
> 
> gmap_f9-multiple_results.txt  (3 MB)
> withrefm.906                  (2.5 MB)
> 1ZZ19XR301R-Alignment.tblastn (2 MB)
> 
> I'm not sure there is an easy way around the problem.  We could  
> attempt to reduce the file size down, but I'm not convinced that's a  
> long-term solution (the test data will only get larger as more test  
> cases come up).
> 
> Any ideas?  Should we try to have a common biodata repo again?
> 
> chris
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