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* merge changes from main trunk

* bump alpha to 5 (final one, mainly for Strawberry Perl tests)

svn path=/bioperl-live/branches/branch-1-6/; revision=16186
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1 parent daceb0b commit 2834e5b630cebb2120c000db75459ad4a6d53321 cjfields committed Sep 28, 2009
Showing with 116 additions and 53 deletions.
  1. +4 −3 Bio/Root/Build.pm
  2. +1 −1 Bio/Root/Version.pm
  3. +1 −5 Bio/SeqIO/tinyseq.pm
  4. +103 −43 BioPerl.pod → BioPerl.pm
  5. +6 −0 Changes
  6. +1 −1 README
View
7 Bio/Root/Build.pm
@@ -1,5 +1,3 @@
-#!/usr/bin/perl -w
-
# $Id$
#
# BioPerl module for Bio::Root::Build
@@ -87,7 +85,7 @@ BEGIN {
use strict;
use warnings;
-our $VERSION = '1.006000_004';
+our $VERSION = '1.006000_005';
our @extra_types = qw(options excludes_os feature_requires test); # test must always be last in the list!
our $checking_types = "requires|conflicts|".join("|", @extra_types);
@@ -209,6 +207,9 @@ sub process_script_files {
$final =~ s/^/bp_/ unless $final =~ /^bp/; # add the "bp" prefix
$final = File::Spec->catfile($script_dir, $final);
$self->log_info("$result -> $final\n");
+ if (-e $final) {
+ unlink $final || warn "[WARNING] Deleting '$final' failed!\n";
+ }
File::Copy::move($result, $final) or die "Can't rename '$result' to '$final': $!";
}
}
View
2 Bio/Root/Version.pm
@@ -98,7 +98,7 @@ methods. Internal methods are usually preceded with a _
package Bio::Root::Version;
use strict;
-our $VERSION = '1.006000_004';
+our $VERSION = '1.006000_005';
$VERSION = eval $VERSION;
sub import {
View
6 Bio/SeqIO/tinyseq.pm
@@ -84,15 +84,11 @@ Internal methods are usually preceded with a _
package Bio::SeqIO::tinyseq;
use strict;
-use Bio::Root::Root;
use Bio::Seq::SeqFastaSpeedFactory;
use Bio::Species;
use Bio::SeqIO::tinyseq::tinyseqHandler;
use XML::Parser::PerlSAX;
use XML::Writer;
-use Bio::Root::Version;
-
-our $VERSION = ${Bio::Root::Version::VERSION};
use base qw(Bio::SeqIO);
@@ -361,7 +357,7 @@ sub _get_writer {
);
$writer->doctype('TSeqSet', '-//NCBI//NCBI TSeq/EN', 'http://www.ncbi.nlm.nih.gov/dtd/NCBI_TSeq.dtd');
- $writer->comment("Generated by Bio::SeqIO::tinyseq VERSION $VERSION");
+ $writer->comment("Generated by Bio::SeqIO::tinyseq VERSION ".$Bio::SeqIO::tinyseq::VERSION);
$writer->startTag('TSeqSet');
View
146 BioPerl.pod → BioPerl.pm
@@ -1,43 +1,73 @@
+package BioPerl;
+
+use strict;
+
+# At some future point, when we break the current core into more maintainable
+# bits, this will have a direct VERSION number, but for now we will be using
+# the root version for everything
+use Bio::Root::Version;
+
+our $VERSION = $Bio::Root::Version::VERSION;
+eval $VERSION;
+
+1;
+
+__END__
+
=head1 NAME
BioPerl - Perl Modules for Biology
=head1 SYNOPSIS
-If you're new to BioPerl, you should start reading L<<a href="http://www.bioperl.org/wiki/Bptutorial">bptutorial</a>>, an
-overview of the BioPerl toolkit.
+If you're new to BioPerl, you should start reading the BioPerl tutorial, an
+overview of the BioPerl toolkit:
-In the style of the perl documentation, core Bioperl documentation has been
-split up into the following sections:
+L<http://www.bioperl.org/wiki/BioPerl_Tutorial>
-=head2 Overview
+=head2 Current Overview
-=over 3
+Core Bioperl documentation has been split up into the following sections:
-=item *
+=over 3
-bioperl
+=item * bioperl
BioPerl overview (this document)
-=item *
+=back
-biodatabases
+We may add more documents in the future, including:
-How to use databases with BioPerl
+=over 3
+
+=item * biodatabases
-=item *
+How to use databases with BioPerl
-biodesign
+=item * biodesign
A guide for authoring a BioPerl module
+=item * bioscripts
+
+Description and overview of BioPerl scripts (in the I</scripts> directory)
+
=back
=head2 Tutorials
- bptutorial.pl Bioperl tutorial for beginners
- http://www.pasteur.fr/recherche/unites/sis/formation/bioperl
+=over 3
+
+=item * BioPerl tutorial for beginners
+
+L<http://www.bioperl.org/wiki/BioPerl_Tutorial>
+
+=item * Institut Pasteur BioPerl tutorial (note: for older versions of BioPerl)
+
+L<http://www.pasteur.fr/recherche/unites/sis/formation/bioperl>
+
+=back
=head2 References for Individual Modules
@@ -70,20 +100,23 @@ useful scripts.
The intent of the BioPerl development effort is to make reusable tools that aid
people in creating their own sites or job-specific applications.
-The BioPerl website at http://bioperl.org also attempts to maintain links
+The BioPerl website at L<http://bioperl.org> also attempts to maintain links
and archives of standalone bio-related Perl tools that are not affiliated or
related to the core BioPerl effort. Check the site for useful code ideas and
contribute your own if possible.
=head1 DOCUMENTATION
-The Bio::Perl module is designed to flatten the learning curve for newcomers to
-Perl/Bioperl. This is a good place to start if you want some simple
-functionality. We have a cookbook tutorial in bptutorial.pl which has embedded
-documentation. Start there if learning-by-example suits you most, or examine the
-BioPerl online course at
+The Bio::Perl module (not this document) is designed to flatten the learning
+curve for newcomers to Perl/Bioperl. This is a good place to start if you want
+some simple functionality. We have a cookbook tutorial on-line:
+
+L<http://bioperl.org/wiki/BioPerl_Tutorial>
+
+which has embedded documentation. Start there if learning-by-example suits you
+most, or examine the BioPerl online course at:
-http://www.pasteur.fr/recherche/unites/sis/formation/bioperl
+L<http://www.pasteur.fr/recherche/unites/sis/formation/bioperl>
Make sure to check the documentation in the modules as well - there are over 900
modules in BioPerl, and counting, and there's detail in the modules'
@@ -95,27 +128,46 @@ The BioPerl modules are distributed as a tar file that expands into a standard
perl CPAN distribution. Detailed installation directions can be found in the
distribution INSTALL file. Installing on windows using ActiveState Perl is
covered in the INSTALL.WIN file. We highly suggest reading the installation
-instructions on the BioPerl website.
+instructions on the BioPerl website:
+L<http://www.bioperl.org/wiki/Installing_BioPerl>
+
+=for TODO: Do we want to add biodesign and biodatabases back in?
The BioPerl modules can interact with local flat file and relational databases.
To learn how to set this up, look at the biodatabases.pod documentation
('perldoc biodatabases.pod' should work once BioPerl has been installed).
-The BioPerl-db, BioPerl-run, BioPerl-gui, corba-server, BioPerl-ext,
-BioPerl-pipeline, BioPerl-microarray and corba-client packages are installed
-separately from BioPerl. Please refer to their respective documentation for more
-information.
+Some BioPerl-related distributions such as Bio::Graphics, BioPerl-db,
+BioPerl-run, BioPerl-gui, corba-server, BioPerl-ext, BioPerl-pipeline,
+BioPerl-microarray and corba-client packages are installed separately from
+BioPerl. Please refer to their respective documentation for more information.
+Note that only the following are supported at this time with the current API:
+
+=over 3
+
+=item BioPerl-db
+
+=item BioPerl-network
+
+=item BioPerl-run
+
+=item BioPerl-pedigree
+
+=item Bio::Graphics
+
+=back
=head1 GETTING STARTED
-A good place to start is by reading and running the cookbook script,
-bptutorial.pl.
+A good place to start is by reading the tutorial : L<http://bioperl.org/wiki/BioPerl_Tutorial>
The distribution I<scripts/> directory has working scripts for use with BioPerl,
-check the self-described examples/ directory as well. A list and brief
-description of all these scripts is found in bioscripts.pod. You are more than
+check the self-described I<examples/> directory as well. You are more than
welcome to contribute your script!
+=for TODO Should we add bioscripts back to the distributions?
+A list and brief description of all these scripts is found in bioscripts.pod.
+
If you have installed BioPerl in the standard way, as detailed in the INSTALL in
the distribution, these scripts should work by just running them. If you have
not installed it in a standard way you will have to change the 'use lib' to
@@ -127,7 +179,7 @@ BioPerl is a completely open community of developers. We are not funded and we
don't have a mission statement. We encourage collaborative code, in particular
in Perl. You can help us in many different ways, from just a simple statement
about how you have used BioPerl to doing something interesting to contributing a
-whole new object hierarchy. See http://bioperl.org for more information. Here
+whole new object hierarchy. See L<http://bioperl.org> for more information. Here
are some ways of helping us:
=head2 Asking questions and telling us you used it
@@ -145,15 +197,21 @@ useful.
By writing a good script that uses BioPerl you both show that BioPerl is useful
and probably save someone elsewhere writing it. If you contribute it to the
-'script central' at http://bioperl.org then other people can view and use it.
+'script central' at L<http://bioperl.org> then other people can view and use it.
Don't be nervous if you've never done this sort of work, advice is freely given
and all are welcome!
=head2 Find bugs!
-We know that there are bugs in there. If you find something which you are pretty
-sure is a problem, post a note to bioperl-bugs@bioperl.org and we will get on it
-as soon as possible. You can also access the bug system through the web pages.
+We know that there are bugs in this code. If you find something which you are pretty
+sure is a problem, post a bug report using our Bugzilla tracking system:
+
+L<http://bugzilla.open-bio.org/>
+
+Please read the main bug tracking (L<http://www.bioperl.org/wiki/Bugs>) for an
+overview of what we expect in a bug report. Specifically, having a code and
+data example where appropriate helps tremendously. We gladly accept all patches
+after a quick code review.
=head2 Suggest new functionality
@@ -165,9 +223,11 @@ her and suggest changes.
=head2 Make your own objects
If you can make a useful object we will happily include it into the core.
-Probably you will want to read a lot of the documentation in L<Bio::Root>, talk
-to people on the BioPerl mailing list, B<bioperl-l@bioperl.org>, and read
-biodesign.pod. biodesign.pod provides documentation on the conventions and ideas
+Probably you will want to read a lot of the documentation in L<Bio::Root::Root>
+and talk to people on the BioPerl mailing list, B<bioperl-l@bioperl.org>.
+
+=for TODO Add biodesign.pod back?
+biodesign.pod provides documentation on the conventions and ideas
used in BioPerl, it's definitely worth a read if you would like to be a BioPerl
developer.
@@ -179,14 +239,14 @@ workings of the package. Feel free to contribute.
=head1 ACKNOWLEDGEMENTS
-For a more detailed history of the BioPerl project, we recommend the
-History of BioPerl:
+For a more detailed history of the BioPerl project, we recommend the History of
+BioPerl:
-http://www.bioperl.org/wiki/History_of_BioPerl
+L<http://www.bioperl.org/wiki/History_of_BioPerl>
=head1 COPYRIGHT
-Copyright (c) 1996-2003 Georg Fuellen, Richard Resnick, Steven E. Brenner, Chris
+Copyright (c) 1996-2009 Georg Fuellen, Richard Resnick, Steven E. Brenner, Chris
Dagdigian, Steve Chervitz, Ewan Birney, James Gilbert, Elia Stupka, and others.
All Rights Reserved. This module is free software; you can redistribute it
and/or modify it under the same terms as Perl itself.
View
6 Changes
@@ -17,6 +17,12 @@ http://www.bioperl.org/wiki/Change_log. Bugs remaining to be addressed
are online at http://bugzilla.open-bio.org, with specific bugs intended
for this release series highlighted in BUGS.
+1.6.0_5 Sept. 27, 2009 (fifth 1.6.1 alpha)
+ * Possible fix for RT 49950 (Strawberry Perl installation) [cjfields]
+ * [RT 50048] - removed redundant VERSION, which was borking CPANPLUS
+ [cjfields]
+ * BioPerl.pod -> BioPerl.pm (Perl Best Practices) [cjfields]
+
1.6.0_4 Sept. 25, 2009 (fourth 1.6.1 alpha)
* WinXP test fixes [cjfields, maj]
* BioPerl.pod added for descriptive information, fixes CPAN indexing
View
2 README
@@ -4,7 +4,7 @@ This is the README file for the Bioperl central distribution.
o Version
- This is Bioperl version 1.6.0, from the BioPerl Subversion release branch
+ This is Bioperl version 1.6.1, from the BioPerl Subversion release branch
branch-1-6
o Getting Started

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