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Port details
p5-BioPerl Collection of Perl modules for bioinformatics
1.007002 biology on this many watch lists=0 search for ports that depend on this port Find issues related to this port Report an issue related to this port
Maintainer: perl@FreeBSD.org search for ports maintained by this maintainer
Port Added: 18 Dec 2016 15:27:08
Also Listed In: perl5
License: ART10 GPLv1+
The BioPerl Project is an international association of developers of open
source Perl tools for bioinformatics, genomics and life science research.

BioPerl is a collection of object-oriented Perl modules created by the
BioPerl Project. It forms the basis of a large number of bioinformatics and
genomics applications.

(For an interesting aside on "How Perl saved the Human Genome Project", see
http://www.bioperl.org/wiki/How_Perl_saved_human_genome)

WWW: http://bioperl.org/
SVNWeb : Homepage : PortsMon : pkg-plist

To install the port: cd /usr/ports/biology/p5-BioPerl/ && make install clean
To add the package: pkg install p5-BioPerl

PKGNAME: p5-BioPerl

distinfo:

TIMESTAMP = 1505232617
SHA256 (BioPerl-1.007002.tar.gz) = 17aa3aaab2f381bbcaffdc370002eaf28f2c341b538068d6586b2276a76464a1
SIZE (BioPerl-1.007002.tar.gz) = 12362741


NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.

Build dependencies:
  1. p5-Algorithm-Munkres>=0 : math/p5-Algorithm-Munkres
  2. p5-Array-Compare>=0 : misc/p5-Array-Compare
  3. p5-CGI>=0 : www/p5-CGI
  4. p5-Clone>=0 : devel/p5-Clone
  5. p5-Convert-Binary-C>=0 : converters/p5-Convert-Binary-C
  6. p5-DBD-mysql>=0 : databases/p5-DBD-mysql
  7. p5-DBI>=0 : databases/p5-DBI
  8. p5-Data-Stag>=0.11 : devel/p5-Data-Stag
  9. p5-Error>=0 : lang/p5-Error
  10. p5-GD>=0 : graphics/p5-GD
  11. p5-Graph>=0.50 : math/p5-Graph
  12. p5-GraphViz>=0 : graphics/p5-GraphViz
  13. p5-HTML-Parser>=3 : www/p5-HTML-Parser
  14. p5-HTML-TableExtract>=0 : www/p5-HTML-TableExtract
  15. p5-HTTP-Message>=0 : www/p5-HTTP-Message
  16. p5-IO-String>=0 : devel/p5-IO-String
  17. p5-IO-stringy>=0 : devel/p5-IO-stringy
  18. p5-Inline-C>=0.67 : devel/p5-Inline-C
  19. p5-List-MoreUtils>=0 : lang/p5-List-MoreUtils
  20. p5-PostScript>=0 : print/p5-PostScript
  21. p5-SVG>=2.26 : textproc/p5-SVG
  22. p5-SVG-Graph>=0.01 : graphics/p5-SVG-Graph
  23. p5-Set-Scalar>=0 : devel/p5-Set-Scalar
  24. p5-Sort-Naturally>=0 : textproc/p5-Sort-Naturally
  25. p5-Spreadsheet-ParseExcel>=0 : textproc/p5-Spreadsheet-ParseExcel
  26. p5-XML-DOM>=0 : textproc/p5-XML-DOM
  27. p5-XML-DOM-XPath>=0 : textproc/p5-XML-DOM-XPath
  28. p5-XML-LibXML>=0 : textproc/p5-XML-LibXML
  29. p5-XML-Parser>=0 : textproc/p5-XML-Parser
  30. p5-XML-SAX>=0.15 : textproc/p5-XML-SAX
  31. p5-XML-SAX-Writer>=0 : textproc/p5-XML-SAX-Writer
  32. p5-XML-Simple>=0 : textproc/p5-XML-Simple
  33. p5-XML-Twig>=0 : textproc/p5-XML-Twig
  34. p5-XML-Writer>=0.400 : textproc/p5-XML-Writer
  35. p5-YAML>=0 : textproc/p5-YAML
  36. p5-libwww>=0 : www/p5-libwww
  37. p5-libxml>=0 : textproc/p5-libxml
  38. p5-Module-Build>=0.4206 : devel/p5-Module-Build
  39. perl5>=5.24<5.25 : lang/perl5.24
Runtime dependencies:
  1. p5-Algorithm-Munkres>=0 : math/p5-Algorithm-Munkres
  2. p5-Array-Compare>=0 : misc/p5-Array-Compare
  3. p5-CGI>=0 : www/p5-CGI
  4. p5-Clone>=0 : devel/p5-Clone
  5. p5-Convert-Binary-C>=0 : converters/p5-Convert-Binary-C
  6. p5-DBD-mysql>=0 : databases/p5-DBD-mysql
  7. p5-DBI>=0 : databases/p5-DBI
  8. p5-Data-Stag>=0.11 : devel/p5-Data-Stag
  9. p5-Error>=0 : lang/p5-Error
  10. p5-GD>=0 : graphics/p5-GD
  11. p5-Graph>=0.50 : math/p5-Graph
  12. p5-GraphViz>=0 : graphics/p5-GraphViz
  13. p5-HTML-Parser>=3 : www/p5-HTML-Parser
  14. p5-HTML-TableExtract>=0 : www/p5-HTML-TableExtract
  15. p5-HTTP-Message>=0 : www/p5-HTTP-Message
  16. p5-IO-String>=0 : devel/p5-IO-String
  17. p5-IO-stringy>=0 : devel/p5-IO-stringy
  18. p5-Inline-C>=0.67 : devel/p5-Inline-C
  19. p5-List-MoreUtils>=0 : lang/p5-List-MoreUtils
  20. p5-PostScript>=0 : print/p5-PostScript
  21. p5-SVG>=2.26 : textproc/p5-SVG
  22. p5-SVG-Graph>=0.01 : graphics/p5-SVG-Graph
  23. p5-Set-Scalar>=0 : devel/p5-Set-Scalar
  24. p5-Sort-Naturally>=0 : textproc/p5-Sort-Naturally
  25. p5-Spreadsheet-ParseExcel>=0 : textproc/p5-Spreadsheet-ParseExcel
  26. p5-XML-DOM>=0 : textproc/p5-XML-DOM
  27. p5-XML-DOM-XPath>=0 : textproc/p5-XML-DOM-XPath
  28. p5-XML-LibXML>=0 : textproc/p5-XML-LibXML
  29. p5-XML-Parser>=0 : textproc/p5-XML-Parser
  30. p5-XML-SAX>=0.15 : textproc/p5-XML-SAX
  31. p5-XML-SAX-Writer>=0 : textproc/p5-XML-SAX-Writer
  32. p5-XML-Simple>=0 : textproc/p5-XML-Simple
  33. p5-XML-Twig>=0 : textproc/p5-XML-Twig
  34. p5-XML-Writer>=0.400 : textproc/p5-XML-Writer
  35. p5-YAML>=0 : textproc/p5-YAML
  36. p5-libwww>=0 : www/p5-libwww
  37. p5-libxml>=0 : textproc/p5-libxml
  38. perl5>=5.24<5.25 : lang/perl5.24

This port is required by:

for Build for Run * - deleted ports are only shown under the This port is required by section. It was harder to do for the Required section. Perhaps later...
Configuration Options
===> The following configuration options are available for p5-BioPerl-1.007002:
     DOCS=on: Build and/or install documentation
     EXAMPLES=on: Build and/or install examples
     PGTEST=off: Test PostGreSQL
     SQLITETEST=off: Test SQLite
===> Use 'make config' to modify these settings

USES:
perl5 shebangfix

Master Sites:
  1. ftp://ftp.auckland.ac.nz/pub/perl/CPAN/authors/id/C/CJ/CJFIELDS/
  2. ftp://ftp.cpan.org/pub/CPAN/authors/id/C/CJ/CJFIELDS/
  3. ftp://ftp.cpan.org/pub/CPAN/modules/by-module/BioPerl/
  4. ftp://ftp.funet.fi/pub/languages/perl/CPAN/authors/id/C/CJ/CJFIELDS/
  5. ftp://ftp.kddlabs.co.jp/lang/perl/CPAN/authors/id/C/CJ/CJFIELDS/
  6. ftp://ftp.mirrorservice.org/sites/cpan.perl.org/CPAN/authors/id/C/CJ/CJFIELDS/
  7. ftp://ftp.sunet.se/pub/lang/perl/CPAN/authors/id/C/CJ/CJFIELDS/
  8. http://backpan.perl.org/authors/id/C/CJ/CJFIELDS/
  9. http://cpan.metacpan.org/authors/id/C/CJ/CJFIELDS/
  10. http://cpan.metacpan.org/modules/by-module/BioPerl/
  11. http://ftp.jaist.ac.jp/pub/CPAN/authors/id/C/CJ/CJFIELDS/
  12. http://ftp.twaren.net/Unix/Lang/CPAN/authors/id/C/CJ/CJFIELDS/
  13. http://www.cpan.dk/authors/id/C/CJ/CJFIELDS/
  14. http://www.cpan.org/authors/id/C/CJ/CJFIELDS/
Port Moves
  • port moved here from biology/p5-bioperl on 2016-12-18
    REASON: Rename to match upstream naming

Number of commits found: 7

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
15 Sep 2017 08:58:50
Original commit files touched by this commit  1.007002
Revision:449893
mat search for other commits by this committer
Fix license information for portgs that use "the same license as Perl".

Sponsored by:	Absolight
13 Sep 2017 01:45:35
Original commit files touched by this commit  1.007002
Revision:449746
wen search for other commits by this committer
- Update to 1.007002
Changes: http://search.cpan.org/src/CJFIELDS/BioPerl-1.007002/Changes
01 Jun 2017 23:50:33
Original commit files touched by this commit  1.007001_2
Revision:442335
sunpoet search for other commits by this committer
Remove outdated PERL_LEVEL check
22 Apr 2017 12:45:43
Original commit files touched by this commit  1.007001_2
Revision:439170
miwi search for other commits by this committer
- Fix shebangs
31 Jan 2017 16:21:46
Original commit files touched by this commit  1.007001_1
Revision:432932
mat search for other commits by this committer
Bump PORTREVISION for ports affected by the fix the last commit.

Done with:	Tools/scripts/bump-revision.sh
Sponsored by:	Absolight
19 Dec 2016 15:54:29
Original commit files touched by this commit  1.007001
Revision:428940
sunpoet search for other commits by this committer
- Update to 1.007001
- Update *_DEPENDS
- Use TEST_DEPENDS: Test::Most and URI::Escape are test-only dependencies
- Use PORTDATA, PORTDOCS and PORTEXAMPLES

Changes:	http://search.cpan.org/dist/BioPerl/Changes
18 Dec 2016 15:25:04
Original commit files touched by this commit  1.6.924_5
Revision:428868
sunpoet search for other commits by this committer
- Move biology/p5-bioperl to biology/p5-BioPerl
- Sort *_DEPENDS
- Bump PORTREVISION for dependent ports

Number of commits found: 7

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