New Port: p5-bioperl

[tonym@…]

BioPerl is a collection of Perl Modules for Bioinformatics.

HomePage::

​http://www.bioperl.org/wiki/Main_Page

CPAN Page::

​http://search.cpan.org/~cjfields/BioPerl-1.6.1/BioPerl.pm

Requested in ticket #24022.

[ryandesign (Ryan Carsten Schmidt)]

revised portfile

[ryandesign (Ryan Carsten Schmidt)]

Attached is a revised portfile with these changes:

• reformatted
• added "universal_variant no" because dependency p5-libwww-perl does not have a universal variant
• added dependency on p5-io-string because I noticed it was downloading IO::String
• added dependency on p5-data-stag because I noticed it was downloading Data::Stag

Unfortunately we have no port p5-data-stag yet so please create and submit a port p5-data-stag. Please add any other required dependencies also.

[tonym@…]

Replying to ryandesign@…:

Unfortunately we have no port p5-data-stag yet so please create and submit a port p5-data-stag. Please add any other required dependencies also.

Will do.

[tonym@…]

Replying to ryandesign@…:

Unfortunately we have no port p5-data-stag yet so please create and submit a port p5-data-stag. Please add any other required dependencies also.

p5-data-stag has been submitted in ticket #26529

[larry+macports@…]

It looks to me like the only showstopper for this issue has been resolved.

[andreas.wilm@…]

Works fine for me

MacPorts 1.9.2
perl5                          @5.8.9          lang/perl5
expat                          @2.0.1          textproc/expat
p5-data-stag                   @0.11           perl/p5-data-stag
p5-io-string                   @1.08           perl/p5-io-string
p5-module-build                @0.3607         perl/p5-module-build
p5-libwww-perl                 @5.837          perl/p5-libwww-perl
OS X 10.6.6

Andreas

[andreas.wilm@…]

Cc Me!

[ryandesign (Ryan Carsten Schmidt)]

Sorry for forgetting about this submission.

I remember now what the next problem was. When installing, it tries to download DB::File. It says "DB_File is absolutely required prior to installation: shall I install it now using a CPAN shell?" We don't have a p5-db-file port yet.

[ryandesign (Ryan Carsten Schmidt)]

Replying to ryandesign@…:

We don't have a p5-db-file port yet.

I filed #28174 for this and will write some notes there about what I know about this.

[jason@…]

1.6.9 was released, here is a portfile that includes more dependencies

[mojca (Mojca Miklavec)]

Cc Me!

[dbevans (David B. Evans)]

Revised Portfile version 1.6.924

[dbevans (David B. Evans)]

Seeing that this submission has been struck for some time now, I've attached a revised version of the Portfile that works with the current perl5 PortGroup. Version is updated to 1.6.924 and dependencies have been updated as well to match META.json.

This builds and test runs without errors (for me), although a few tests are skipped due to absence of some optional modules.

Any further changes needed?

[dbevans (David B. Evans)]

FYI, related module p5-bio-phylo (recommended by p5-bioperl) has been committed in r135149, r135150 as nomaintainer.
Additionally, module p5-bio-asn1-entrezgene which depends on p5-bioperl has been submitted for review in #47480, also nomaintainer.

Perhaps someone from the bioperl community would like to take up maintainership of one or both of these ports.

[dbevans (David B. Evans)]

Cc Me!

[dbevans (David B. Evans)]

Hearing no objections, committed in r135244.