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Port details
p5-bioperl Collection of Perl modules for bioinformatics
1.6.924 biology on this many watch lists=2 search for ports that depend on this port
Maintained by: perl@FreeBSD.org search for ports maintained by this maintainer
Port Added: 28 Jul 2000 11:06:03
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 : Main Web Site : Distfiles Availability : PortsMon

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

Required To Build:
  1. textproc/p5-Text-Tabs+Wrap
  2. biology/p5-Bio-ASN1-EntrezGene
  3. devel/p5-Class-AutoClass
  4. devel/p5-Data-Stag
  5. devel/p5-Data-Stag
  6. devel/p5-Data-Stag
  7. graphics/p5-GD-SVG
  8. math/p5-Graph
  9. www/p5-libwww
  10. devel/p5-IO-stringy
  11. devel/p5-IO-String
  12. www/p5-libwww
  13. net/p5-SOAP-Lite
  14. textproc/p5-SVG
  15. graphics/p5-SVG-Graph
  16. textproc/p5-Text-Shellwords
  17. textproc/p5-XML-DOM
  18. textproc/p5-XML-DOM-XPath
  19. textproc/p5-libxml
  20. textproc/p5-XML-SAX
  21. textproc/p5-XML-SAX
  22. textproc/p5-XML-SAX-Writer
  23. textproc/p5-XML-Twig
  24. textproc/p5-XML-Writer
  25. devel/p5-Clone
  26. databases/p5-DBD-mysql
  27. graphics/p5-GD
  28. www/p5-HTML-Parser
  29. www/p5-HTML-Parser
  30. textproc/p5-XML-Parser
  31. textproc/p5-Spreadsheet-ParseExcel
  32. converters/p5-Convert-Binary-C
  33. math/p5-Algorithm-Munkres
  34. misc/p5-Array-Compare
  35. graphics/p5-GraphViz
  36. math/p5-Math-Random
  37. print/p5-PostScript
  38. devel/p5-Set-Scalar
  39. net/p5-URI
  40. devel/p5-Test-Most
  41. www/p5-HTML-TableExtract
  42. textproc/p5-Sort-Naturally
  43. textproc/p5-XML-Simple
  44. textproc/p5-YAML
  45. lang/p5-Error
  46. devel/p5-Module-Build
  47. lang/perl5.16
Required To Run:
  1. textproc/p5-Text-Tabs+Wrap
  2. biology/p5-Bio-ASN1-EntrezGene
  3. devel/p5-Class-AutoClass
  4. devel/p5-Data-Stag
  5. devel/p5-Data-Stag
  6. devel/p5-Data-Stag
  7. graphics/p5-GD-SVG
  8. math/p5-Graph
  9. www/p5-libwww
  10. devel/p5-IO-stringy
  11. devel/p5-IO-String
  12. www/p5-libwww
  13. net/p5-SOAP-Lite
  14. textproc/p5-SVG
  15. graphics/p5-SVG-Graph
  16. textproc/p5-Text-Shellwords
  17. textproc/p5-XML-DOM
  18. textproc/p5-XML-DOM-XPath
  19. textproc/p5-libxml
  20. textproc/p5-XML-SAX
  21. textproc/p5-XML-SAX
  22. textproc/p5-XML-SAX-Writer
  23. textproc/p5-XML-Twig
  24. textproc/p5-XML-Writer
  25. devel/p5-Clone
  26. databases/p5-DBD-mysql
  27. graphics/p5-GD
  28. www/p5-HTML-Parser
  29. www/p5-HTML-Parser
  30. textproc/p5-XML-Parser
  31. textproc/p5-Spreadsheet-ParseExcel
  32. converters/p5-Convert-Binary-C
  33. math/p5-Algorithm-Munkres
  34. misc/p5-Array-Compare
  35. graphics/p5-GraphViz
  36. math/p5-Math-Random
  37. print/p5-PostScript
  38. devel/p5-Set-Scalar
  39. net/p5-URI
  40. devel/p5-Test-Most
  41. www/p5-HTML-TableExtract
  42. textproc/p5-Sort-Naturally
  43. textproc/p5-XML-Simple
  44. textproc/p5-YAML
  45. lang/p5-Error
  46. lang/perl5.16

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...

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


Configuration Options
===> The following configuration options are available for p5-bioperl-1.6.924:
     DOCS=on: Build and/or install documentation
     PGTEST=off: Test PostGreSQL
     SQLITETEST=off: Test SQLite
===> Use 'make config' to modify these settings

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/
  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://distcache.FreeBSD.org/ports-distfiles/
  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.dk/modules/by-module/
  15. http://www.cpan.org/authors/id/C/CJ/CJFIELDS/

Number of commits found: 47

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
20 Oct 2014 07:10:48
Original commit files touched by this commit  1.6.924
Revision:371237
bapt search for other commits by this committer
Cleanup plist
04 Aug 2014 04:32:38
Original commit files touched by this commit  1.6.924
Revision:363961
pi search for other commits by this committer
biology/p5-bioperl: fix pkg-descr sidenote link
27 Jul 2014 07:27:18
Original commit files touched by this commit  1.6.924
Revision:363015
wen search for other commits by this committer
- Update to 1.6.924 [1]
- Reset maintainer to perl@

PR:		192088 [1]
Submitted by:	Kurt Jaeger<pi@FreeBSD.org> [1]
30 May 2014 15:46:05
Original commit files touched by this commit  1.6.923
Revision:355863
wen search for other commits by this committer
- Update to 1.6.923
- Add STAGE support

PR:		190342
Submitted by:	Muhammad Moinur Rahman <5u623l20@gmail.com>
09 Apr 2014 09:49:03
Original commit files touched by this commit  1.6.1_4
Revision:350675
bapt search for other commits by this committer
Mark as broken unstaged perl ports

With hat:	portmgr
21 Feb 2014 13:35:26
Original commit files touched by this commit  1.6.1_4
Revision:345397
ehaupt search for other commits by this committer
Remove trailing whitespaces from category biology
10 Feb 2014 13:54:28
Original commit files touched by this commit  1.6.1_4
Revision:343634
ehaupt search for other commits by this committer
According to the Porter's Handbook (5.12.2.3.) default options must be added to
OPTIONS_DEFINE. This policy has been implemented only recently that's why we
have many ports violating this policy.

This patch adds the default options specified in the Porter's Handbook to
OPTIONS_DEFINE where they are being used. Ports maintained by
gnome@FreeBSD.org, kde@FreeBSD.org and x11@FreeBSD.org have been excluded.

Approved by:    portmgr (bapt)
03 Jan 2014 15:46:52
Original commit files touched by this commit  1.6.1_4
Revision:338550
adamw search for other commits by this committer
Convert biology to MDOCS and MEXAMPLES
20 Sep 2013 15:55:44
Original commit files touched by this commit  1.6.1_4
Revision:327709
bapt search for other commits by this committer
Add NO_STAGE all over the place in preparation for the staging support (cat:
biology)
06 Aug 2013 08:50:49
Original commit files touched by this commit  1.6.1_4
Revision:324306
az search for other commits by this committer
- Convert to new perl framework
- Trim Makefile header

Approved by:	wen@ (maintainer)
07 Jun 2013 06:51:42
Original commit files touched by this commit  1.6.1_4
Revision:320153
az search for other commits by this committer
- Avoid of using SITE_PERL
- Remove depend on DB_File.pm since it part of perl distribution

PR:		ports/178877
Submitted by:	az
Approved by:	matainer (timeout)
01 Oct 2012 14:55:55
Original commit files touched by this commit  1.6.1_4
Revision:305131
wen search for other commits by this committer
- Take maintainership
01 Oct 2012 14:45:17
Original commit files touched by this commit  1.6.1_4
Revision:305130
tabthorpe search for other commits by this committer
- Reassign to the heap at maintainer's request
30 Jun 2012 05:21:38
Original commit files touched by this commit  1.6.1_4
az search for other commits by this committer
- Remove SITE_PERL from *_DEPENDS

Approved by: portmgr@ (bapt@)
01 Jun 2012 05:26:28
Original commit files touched by this commit  1.6.1_4
dinoex search for other commits by this committer
- update png to 1.5.10
21 Jan 2012 17:40:15
Original commit files touched by this commit  1.6.1_3
eadler search for other commits by this committer
At the moment 1385 ports use BUILD_DEPENDS= ${RUN_DEPENDS} and 450
ports use BUILD_DEPENDS:= ${RUN_DEPENDS}. This patch fixes ports that are
currently broken. This is a temporary measure until we organically stop using
:= or someone(s) spend a lot of time changing all the ports over.

Explicit duplication > := > = and this just moves ports one step to the left

Approved by:    portmgr
22 Oct 2011 23:50:23
Original commit files touched by this commit  1.6.1_3
eadler search for other commits by this committer
- remove maintainer tags from pkg-descr

Approved by:    portmgr
Approved by:    bapt (mentor)
19 Mar 2011 12:38:54
Original commit files touched by this commit  1.6.1_3
miwi search for other commits by this committer
- Get Rid MD5 support
28 Mar 2010 06:47:48
Original commit files touched by this commit  1.6.1_3
dinoex search for other commits by this committer
- update to 1.4.1
Reviewed by:    exp8 run on pointyhat
Supported by:   miwi
05 Feb 2010 11:46:55
Original commit files touched by this commit  1.6.1_2
dinoex search for other commits by this committer
- update to jpeg-8
29 Jan 2010 14:52:21
Original commit files touched by this commit  1.6.1_1
kuriyama search for other commits by this committer
- Remove unneeded dependencies which is in perl-5.8.9 dist
  (part 19; last!).

Approved by:    portmgr (itetcu)
04 Dec 2009 11:50:10
Original commit files touched by this commit  1.6.1
wen search for other commits by this committer
- Update to 1.6.1

Approved by:    maintainer (via Email)
31 Jul 2009 13:57:52
Original commit files touched by this commit  1.6.0_1
dinoex search for other commits by this committer
- bump all port that indirectly depends on libjpeg and have not yet been bumped
or updated
Requested by:   edwin
22 Jul 2009 16:27:08
Original commit files touched by this commit  1.6.0
pgollucci search for other commits by this committer
- lang/perl5.6 is dead, remove PERL_LEVEL/PERL_VERSION < 500801 checks

PR:             ports/135398
Tested by:      2 -exp runs by pav
Approved by:    portmgr (pav)
05 Mar 2009 17:56:24
Original commit files touched by this commit  1.6.0
skv search for other commits by this committer
Remove variable PERL_VER from the ports tree at all - because
it is obsolete since Perl 5.6.0.
23 Feb 2009 19:31:43
Original commit files touched by this commit  1.6.0
garga search for other commits by this committer
- Update to 1.6.0

PR:             ports/131989
Submitted by:   maintainer
14 Jan 2009 14:51:38
Original commit files touched by this commit  1.4_2
tobez search for other commits by this committer
Fix plist with perl 5.8.9.

Approved by:    portmgr (pav, implicit)
17 Apr 2008 14:30:31
Original commit files touched by this commit  1.4_1
araujo search for other commits by this committer
- Take advantage of CPAN macro from bsd.sites.mk, change
${MASTER_SITE_PERL_CPAN} to CPAN.

PR:             ports/122674
Submitted by:   Philip M. Gollucci <pgollucci@p6m7g8.com>
Reworked by:    araujo (myself)
Approved by:    portmgr (pav)
08 Sep 2007 00:53:15
Original commit files touched by this commit  1.4_1
linimon search for other commits by this committer
Welcome bsd.perl.mk.  Add support for constructs such as USE_PERL5=5.8.0+.
Drop support for antique perl.

Work done by:   gabor
Sponsored by:   Google Summer of Code 2007
Hat:            portmgr
19 May 2007 20:32:57
Original commit files touched by this commit  1.4_1
flz search for other commits by this committer
- Welcome X.org 7.2 \o/.
- Set X11BASE to ${LOCALBASE} for recent ${OSVERSION}.
- Bump PORTREVISION for ports intalling files in ${X11BASE}.
22 Jan 2006 08:20:34
Original commit files touched by this commit  1.4
edwin search for other commits by this committer
SHA256ify

Approved by:    krion@
04 Dec 2005 22:11:44
Original commit files touched by this commit  1.4
edwin search for other commits by this committer
Add conflicst:
CONFLICTS=     p5-bioperl-1.[13579]*

Submitted by:   Mauricio Herrera Cuadra <arareko@yahoo.com>,Fernan Aguero
<fernan@iib.unsam.edu.ar>
03 Sep 2004 17:04:38
Original commit files touched by this commit  1.4
leeym search for other commits by this committer
- add missing MAN1 and MAN3
- apply DATADIR, EXAMPLESDIR, and DOCSDIR in PLIST
- update the usage of NOPORTDOCS

PR:             71322
Submitted by:   leeym
Approved by:    Fernan Aguero <fernan@iib.unsam.edu.ar>
12 Aug 2004 12:48:01
Original commit files touched by this commit  1.4
mat search for other commits by this committer
After devel/p5-File-Temp has gained an IGNORE for PERL_LEVEL > 500800, all
these ports were broken because they always depended on it. I've rearranged all
the dependencies to fit the new scheme.
18 Mar 2004 18:01:13
Original commit files touched by this commit  1.4
trevor search for other commits by this committer
Add size data, approved by maintainers.
08 Mar 2004 03:29:16
Original commit files touched by this commit  1.4
linimon search for other commits by this committer
Unmark as broken for 4.x; instead, mark as ignore for perl < 5.6.
22 Feb 2004 00:06:35
Original commit files touched by this commit  1.4
kris search for other commits by this committer
BROKEN on 4.x: Configure fails
21 Jan 2004 08:34:33
Original commit files touched by this commit  1.4
linimon search for other commits by this committer
Major update from 0.7.2 to 1.4 by new maintainer.  This is almost a complete
rework of the port.

See the page http://news.open-bio.org/archives/cat_bioperl.html for the
changes between 1.2 and 1.4.  The older changes are in the CVS tree.

From the new maintainer:

        Note that this new port just handles the installation of bioperl and
        not of additional extra stuff (bioperl-gui, bioperl-corba-server,
        bioperl-corba-client). This is unlike the behaviour of the current
        port.

        The extra stuff, though still functional, had very little adoption
        among users, and does not appear to be currently supported/maintained.

PR:             ports/47303 (and subsequent)
Submitted by:   Fernan Aguero <fernan@iib.unsam.edu.ar> (new maintainer)
24 Oct 2003 12:05:09
Original commit files touched by this commit  0.7.2
ijliao search for other commits by this committer
utilize SITE_PERL

PR:             58166
Submitted by:   Cheng-Lung Sung <clsung@dragon2.net>
07 Mar 2003 05:56:43
Original commit files touched by this commit  0.7.2
ade search for other commits by this committer
Clear moonlight beckons.
Requiem mors pacem pkg-comment,
And be calm ports tree.

E Nomini Patri, E Fili, E Spiritu Sancti.
25 Jan 2002 11:46:09
files touched by this commit
wjv search for other commits by this committer
- Update to version 0.7.2, somewhat overdue.  :-)    
13 Aug 2001 11:26:44
files touched by this commit
wjv search for other commits by this committer
- Properly list run-time dependencies in RUN_DEPENDS in Makefile.   - Deploy
%%PERL_VER%% and %%PERL_ARCH%% pragmas consistently throughout     pkg-plist. 
(Ouch, that was embarrassing.)   - Bump PORTREVISION due to the above.   -
Update my email address and the project's URL in pkg-descr.    
04 Jul 2001 14:22:15
files touched by this commit
wjv search for other commits by this committer
- Update to version 0.7.1   - Add a build-time message to inform the user of
available options.    
26 Jun 2001 16:09:40
files touched by this commit
wjv search for other commits by this committer
Embarrassingly long overdue update to 0.7.0, including optional support for  
GUI (Tk) and CORBA extensions.    
13 Oct 2000 13:43:24
files touched by this commit
jeh search for other commits by this committer
Update to version 0.6.2    
08 Oct 2000 00:23:30
files touched by this commit
asami search for other commits by this committer
Convert category biology to new layout.  
28 Jul 2000 15:06:03
files touched by this commit
nbm search for other commits by this committer
Add BioPerl, a collection of Perl5 mods for bioinformatics/genomics    

Number of commits found: 47

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