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Port details
p5-bioperl 1.6.1_4 biology on this many watch lists=2 search for ports that depend on this port
A collection of Perl modules for bioinformatics
Maintained by: wen@FreeBSD.org search for ports maintained by this maintainer
Port Added: 28 Jul 2000 11:06:03
Also Listed In: perl5
License: not specified in port


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://bioperl.org/GetStarted/tpj_ls_bio.html)

WWW: http://bioperl.org/
SVNWeb : Main Web Site : Distfiles Availability : PortsMon

NOTE: FreshPorts displays only required dependencies information. 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. biology/p5-AcePerl
  26. devel/p5-Clone
  27. databases/p5-DBD-mysql
  28. graphics/p5-GD
  29. www/p5-HTML-Parser
  30. www/p5-HTML-Parser
  31. textproc/p5-XML-Parser
  32. textproc/p5-Spreadsheet-ParseExcel
  33. converters/p5-Convert-Binary-C
  34. math/p5-Algorithm-Munkres
  35. misc/p5-Array-Compare
  36. graphics/p5-GraphViz
  37. math/p5-Math-Random
  38. print/p5-PostScript
  39. devel/p5-Set-Scalar
  40. net/p5-URI
  41. devel/p5-Module-Build
  42. lang/perl5.14
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. biology/p5-AcePerl
  26. devel/p5-Clone
  27. databases/p5-DBD-mysql
  28. graphics/p5-GD
  29. www/p5-HTML-Parser
  30. www/p5-HTML-Parser
  31. textproc/p5-XML-Parser
  32. textproc/p5-Spreadsheet-ParseExcel
  33. converters/p5-Convert-Binary-C
  34. math/p5-Algorithm-Munkres
  35. misc/p5-Array-Compare
  36. graphics/p5-GraphViz
  37. math/p5-Math-Random
  38. print/p5-PostScript
  39. devel/p5-Set-Scalar
  40. net/p5-URI
  41. lang/perl5.14

This port is required by:

for Build for Run

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


Configuration Options
     No options to configure

Master Sites:
  1. ftp://ftp.FreeBSD.org/pub/FreeBSD/ports/distfiles/
  2. ftp://ftp.auckland.ac.nz/pub/perl/CPAN/modules/by-module/bioperl/
  3. ftp://ftp.cpan.org/pub/CPAN/modules/by-module/bioperl/
  4. ftp://ftp.cpan.org/pub/CPAN/modules/by-module/bioperl/
  5. ftp://ftp.dti.ad.jp/pub/lang/CPAN/modules/by-module/bioperl/
  6. ftp://ftp.funet.fi/pub/languages/perl/CPAN/modules/by-module/bioperl/
  7. ftp://ftp.kddlabs.co.jp/lang/perl/CPAN/modules/by-module/bioperl/
  8. ftp://ftp.mirrorservice.org/sites/cpan.perl.org/CPAN/modules/by-module/bioperl/
  9. ftp://ftp.sunet.se/pub/lang/perl/CPAN/modules/by-module/bioperl/
  10. ftp://mirror.hiwaay.net/CPAN/modules/by-module/bioperl/
  11. http://at.cpan.org/modules/by-module/bioperl/
  12. http://backpan.perl.org/modules/by-module/bioperl/
  13. http://bioperl.org/DIST/
  14. http://cpan.nctu.edu.tw/modules/by-module/bioperl/
  15. http://ftp.jaist.ac.jp/pub/CPAN/modules/by-module/bioperl/
  16. http://ftp.twaren.net/Unix/Lang/CPAN/modules/by-module/bioperl/
  17. http://www.cpan.dk/modules/by-module/bioperl/
  18. http://www.cpan.dk/modules/by-module/bioperl/

Number of commits found: 37

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
07 Jun 2013 06:51:42
Original commit files touched by this commit  1.6.1_4
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
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
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: 37

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