[Bioperl-l] BioPerl 1.6 RC1

Alex Lancaster alexl at users.sourceforge.net
Sun Dec 28 18:20:20 EST 2008

>>>>>>> "SB" == Sendu Bala writes:


> SB> BioPerl has started to move toward a number of smaller packages
> SB> that will let people install only what they actually need. There
> SB> will be a core' package of essential modules, and a bunch of these
> SB> new smaller packages that rely on core.

> Alex Lancaster wrote:

> OK, so this will happen sometime post-1.6?  It seems that currently
> for 1.5.9 there is still just one tarball/CPAN module.  
> How many separate modules are we talking about?  If it's core + 4-5
> separate CPAN modules that doesn't seem too bad

SB> It'll be a small number. Note that currently it is a large core +
SB> Bio::Graphics + Bio::ASN1::EntrezGene + BioPerl-run + BioPerl-db +
SB> BioPerl-network + BioPerl-ext. So already it's at least 7
SB> different tarballs if you wanted 'everything' BioPerl related.

Right, and Fedora currently only packages two of them: bioperl (core)
and bioperl-run.  At the time I generated the original packages,
bioperl-{db,network,ext} seemed in flux with respect to the 1.5.2
release that I wasn't sure if it was appropriate to package them as
yet and core + -run seemed like it was the part of bioperl used by 90%
of users, so it was a good place to start.

Also can you clarify the expected name of the tarball, is it bioperl,
or BioPerl?  The 1.5.2 release used bioperl-1.5.2_102.tar.bz2 whereas
1.5.9._1 uses BioPerl-1.5.9._1.tar.bz2 and it would be good if there
was consistency as it really helps from maintaining the packages and
generating links etc.

> SB> From a certain point of view it could be that 'to install bioperl'
> SB> == to install bioperl core', in which case the answer to your
> SB> question is 1' .tar.gz to install.

> SB> As a convenience to the user who wants to install all BioPerl
> SB> packages, there will be a CPAN Bundle (at the least). Fedora
> SB> package-wise, I guess you'd do whatever you currently do to
> SB> emulate CPAN bundles.

> Would these CPAN bundles be updated to include the latest CPAN modules
> as they are individually updated?

SB> There would most likely be a single CPAN bundle specifying all the
SB> different BioPerl packages but without any version number
SB> specifications. When a user installs the bundle it would install
SB> the latest version of each package.

SB> Each individual sub-package, on the other hand, would specify the
SB> version of any other sub-packages or core that it depends on.

OK, right.  So if any of the sub-packages were incremented
independently, would a new bundle be generated, or would new bundles
only be updated for major releases?  Hmm, I'm not sure if subpackages
with different version numbers from the main package can be generated
from a single SRPM, so that might be a bit tricky.  But if core is
only a small number of CPAN pakcages, that might not be so bad,
although it would mean having to go through review for each of the
(new) CPAN modules and more maintainance, so it might be a while
before it would be in Fedora.  When is this scheduled to happen?
(post-1.6, I hope!)


> OK, thanks for the clarification, although I'm still puzzled as to why
> the package still generates:

> "Requires: perl(Bio::Graphics)"

> see bottom of:

> http://koji.fedoraproject.org/koji/getfile?taskID=1022559&name=build.log

SB> I don't understand that output. Can you state what caused that
SB> particular require? Nothing should: it's a bug that must be fixed.

RPM has a script with heuristics that search .pm and .pl files for
'use <module-name>' type constructs to automatically generate
'Requires", that sometimes guess wrong.  To check, I grepped an
exploded package for instances of 'Bio::Graphics' and what returned is
below, at the end of the e-mail.  I suspect that the 'use
Bio::Graphics' in some of the installed scripts in bin/ such as
bp_glyphs2-demo.pl are causing the issue.  Shouldn't these scripts
perhaps be moved to the Bio::Graphics CPAN module (along with the
scripts in examples/)?

If the Bio::Graphics is truly not needed, for the moment it is
possible to also override and filter out the bogus Requires until such
time as these scripts are moved to the appropriate place.


$ grep -r 'Bio::Graphics' *
bin/bp_glyphs2-demo.pl:use Bio::Graphics::Panel;
bin/bp_glyphs2-demo.pl:bp_glyphs2-demo.pl - Second demo of Bio::Graphics glyphs
bin/bp_glyphs2-demo.pl:Generates a PNG image of some of the more esoteric Bio::Graphics glyphs.
bin/bp_glyphs2-demo.pl:L<Bio::Graphics>, the BioGraphics HOWTO.
bin/bp_glyphs2-demo.pl:my $ftr = 'Bio::Graphics::Feature';
bin/bp_glyphs2-demo.pl:my $panel = Bio::Graphics::Panel->new(
bin/bp_embl2picture.pl:use Bio::Graphics;
bin/bp_embl2picture.pl:L<Bio::Graphics>, the BioGraphics HOWTO.
bin/bp_embl2picture.pl:my $panel = Bio::Graphics::Panel->new(
bin/bp_glyphs1-demo.pl:use Bio::Graphics::Panel;
bin/bp_glyphs1-demo.pl:bp_glyphs1-demo.pl - First demo of Bio::Graphics glyphs
bin/bp_glyphs1-demo.pl:Generates a PNG image of some of the more esoteric Bio::Graphics glyphs.
bin/bp_glyphs1-demo.pl:L<Bio::Graphics>, the BioGraphics HOWTO.
bin/bp_glyphs1-demo.pl:my $ftr = 'Bio::Graphics::Feature';
bin/bp_glyphs1-demo.pl:my $panel = Bio::Graphics::Panel->new(
lib/perl5/vendor_perl/5.10.0/Bio/Das/SegmentI.pm:the Bio::Graphics engine to render segments just like a feature in order
lib/perl5/vendor_perl/5.10.0/Bio/Das/SegmentI.pm:that identifies it as being strandless.  This allows the Bio::Graphics
lib/perl5/vendor_perl/5.10.0/Bio/SeqFeature/Lite.pm:with Bio::Graphics::Panel.  With it you can create lightweight feature
lib/perl5/vendor_perl/5.10.0/Bio/SeqFeature/Lite.pm:  -url         a URL to link to when rendered with Bio::Graphics
lib/perl5/vendor_perl/5.10.0/Bio/DB/GFF.pm:SeqFeatureI interface, allowing their use by the Bio::Graphics and
lib/perl5/vendor_perl/5.10.0/Bio/DB/SeqFeature.pm:Bio::Graphics::Feature-E<gt>new(). The most important difference is the
lib/perl5/vendor_perl/5.10.0/Bio/DB/SeqFeature.pm:  -segments     a list of subfeatures (see Bio::Graphics::Feature)
lib/perl5/vendor_perl/5.10.0/Bio/DB/SeqFeature.pm:  -url          a URL to link to when rendered with Bio::Graphics
lib/perl5/vendor_perl/5.10.0/Bio/DB/SeqFeature/NormalizedFeature.pm:Bio::Graphics::Feature-E<gt>new(). The most important difference is the
lib/perl5/vendor_perl/5.10.0/Bio/DB/SeqFeature/NormalizedFeature.pm:  -segments     a list of subfeatures (see Bio::Graphics::Feature)
lib/perl5/vendor_perl/5.10.0/Bio/DB/SeqFeature/NormalizedFeature.pm:  -url          a URL to link to when rendered with Bio::Graphics
lib/perl5/vendor_perl/5.10.0/Bio/DB/SeqFeature/NormalizedFeature.pm:convenience for Bio::Graphics, which looks for notes() when it
lib/perl5/vendor_perl/5.10.0/Bio/DB/SeqFeature/Store/FeatureFileLoader.pm: URL     A URL to link to (via the Bio::Graphics library).
lib/perl5/vendor_perl/5.10.0/Bio/DB/SeqFeature/Store/FeatureFileLoader.pm: Note    A note to attach to the feature for display by the Bio::Graphics library.
lib/perl5/vendor_perl/5.10.0/Bio/DB/SeqFeature/Store/FeatureFileLoader.pm:Return the default SeqFeatureI class (Bio::Graphics::Feature).
lib/perl5/vendor_perl/5.10.0/Bio/DB/SeqFeature/Store/FeatureFileLoader.pm:  return 'Bio::Graphics::Feature';
lib/perl5/vendor_perl/5.10.0/Bio/DB/SeqFeature/Store.pm:Bio::Graphics::Feature-E<gt>new(). The most important difference is the
lib/perl5/vendor_perl/5.10.0/Bio/DB/SeqFeature/Store.pm:  -segments     a list of subfeatures (see Bio::Graphics::Feature)
lib/perl5/vendor_perl/5.10.0/Bio/DB/SeqFeature/Store.pm:  -url          a URL to link to when rendered with Bio::Graphics
lib/perl5/vendor_perl/5.10.0/Bio/DB/GFF/Aggregator/orf.pm:L<Bio::DB::GFF::Aggregator>, L<Bio::Graphics::Glyph::cds>
share/doc/perl-bioperl-1.5.9/examples/biographics/all_glyphs.pl:use Bio::Graphics::Panel;
share/doc/perl-bioperl-1.5.9/examples/biographics/all_glyphs.pl:use Bio::Graphics::Feature;
share/doc/perl-bioperl-1.5.9/examples/biographics/all_glyphs.pl:my $ftr = 'Bio::Graphics::Feature';
share/doc/perl-bioperl-1.5.9/examples/biographics/all_glyphs.pl:my $panel = Bio::Graphics::Panel->new(
share/doc/perl-bioperl-1.5.9/examples/biographics/lots_of_glyphs.pl:use Bio::Graphics::Panel;
share/doc/perl-bioperl-1.5.9/examples/biographics/lots_of_glyphs.pl:use Bio::Graphics::Feature;
share/doc/perl-bioperl-1.5.9/examples/biographics/lots_of_glyphs.pl:my $ftr = 'Bio::Graphics::Feature';
share/doc/perl-bioperl-1.5.9/examples/biographics/lots_of_glyphs.pl:my $pan* Shengqiang Shu <sshu at bdgp.lbl.gov> - Bio::Graphics::Glyph
share/doc/perl-bioperl-1.5.9/ChangeLog:* [r15129] remove Bio::Graphics (separate package now)
share/doc/perl-bioperl-1.5.9/ChangeLog:* [r15127] Remove dependencies for Bio::Graphics and deprecated
share/doc/perl-bioperl-1.5.9/ChangeLog:* [r15125] removed Bio::Graphics itself
share/doc/perl-bioperl-1.5.9/ChangeLog:* [r15119] Bio::Graphics has become its own module; latest version
share/doc/perl-bioperl-1.5.9/ChangeLog:* [r14794] added feature grouping to SVG output from Bio::Graphics
share/doc/perl-bioperl-1.5.9/ChangeLog:* [r14734] Bio::Graphics::Glyph::minmax is the base class that
share/doc/perl-bioperl-1.5.9/ChangeLog:  rendering correctly on Bio::Graphics::Panels (label missing)
share/doc/perl-bioperl-1.5.9/ChangeLog:  Bio::Graphics::Panel to fail under some versions of perl
share/doc/perl-bioperl-1.5.9/ChangeLog:  # Bio::Graphics::FeatureBase->new (or to Bio::DB::SeqFeature,
share/doc/perl-bioperl-1.5.9/ChangeLog:  # Bio::Graphics::Feature). Such homogenous subfeatures created in
share/doc/perl-bioperl-1.5.9/ChangeLog:  Bio::Graphics::FeatureBase; (1) was dumping empty Alias
share/doc/perl-bioperl-1.5.9/ChangeLog:* [r11164] made Bio::Graphics::FeatureBase more consistent with
share/doc/perl-bioperl-1.5.9/ChangeLog:  Bio::Graphics::FeatureBase->to_FTString() behaves a little more
share/doc/perl-bioperl-1.5.9/Changes:    o Bio::Graphics
share/doc/perl-bioperl-1.5.9/Changes:    o Bio::Graphics has many bug fixes and shiny new glyphs.
share/doc/perl-bioperl-1.5.9/Changes:  o Bio::Graphics will work with gd1 or gd2
share/doc/perl-bioperl-1.5.9/Changes:   o Bio::Graphics
share/doc/perl-bioperl-1.5.9/Changes:     o Bio::Graphics
share/doc/perl-bioperl-1.5.9/Changes:    o Bio::Graphics glyph set improved and extended for GBrowse release
share/doc/perl-bioperl-1.5.9/Changes:    o Bio::Graphics for rendering sequences as PNG,JPG, or GIFs has

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