| Port details |
- p5-BioPerl Collection of Perl modules for bioinformatics
- 1.007008 biology
 =0      1.007008Version of this port present on the latest quarterly branch. - Maintainer: sunpoet@FreeBSD.org
- Port Added: 2016-12-18 15:27:08
- Last Update: 2023-10-11 12:57:41
- Commit Hash: 0567b2d
- Also Listed In: perl5
- License: ART10 GPLv1+
- WWW:
- https://metacpan.org/dist/BioPerl
- https://bioperl.org/
- Description:
- 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)
  ¦  ¦  ¦  ¦ 
- Manual pages:
- FreshPorts has no man page information for this port.
- pkg-plist: as obtained via:
make generate-plist - Dependency lines:
-
- p5-BioPerl>0:biology/p5-BioPerl
- To install the port:
- cd /usr/ports/biology/p5-BioPerl/ && make install clean
- To add the package, run one of these commands:
- pkg install biology/p5-BioPerl
- pkg install p5-BioPerl
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.- PKGNAME: p5-BioPerl
- Flavors: there is no flavor information for this port.
- distinfo:
- TIMESTAMP = 1696904108
SHA256 (BioPerl-1.7.8.tar.gz) = c490a3be7715ea6e4305efd9710e5edab82dabc55fd786b6505b550a30d71738
SIZE (BioPerl-1.7.8.tar.gz) = 7527658
Packages (timestamps in pop-ups are UTC):
- Dependencies
- NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
- Build dependencies:
-
- p5-Data-Stag>=0 : devel/p5-Data-Stag
- p5-Error>=0 : lang/p5-Error
- p5-Graph>=0 : math/p5-Graph
- p5-HTTP-Message>=0 : www/p5-HTTP-Message
- p5-IO-String>=0 : devel/p5-IO-String
- p5-IO-Stringy>=0 : devel/p5-IO-Stringy
- p5-IPC-Run>=0 : devel/p5-IPC-Run
- p5-List-MoreUtils>=0 : lang/p5-List-MoreUtils
- p5-Module-Build>=0 : devel/p5-Module-Build
- p5-Set-Scalar>=0 : devel/p5-Set-Scalar
- p5-Test-Most>=0 : devel/p5-Test-Most
- p5-Test-RequiresInternet>=0 : devel/p5-Test-RequiresInternet
- p5-URI>=0 : net/p5-URI
- p5-XML-DOM>=0 : textproc/p5-XML-DOM
- p5-XML-LibXML>=0 : textproc/p5-XML-LibXML
- p5-XML-SAX>=0 : textproc/p5-XML-SAX
- p5-XML-SAX-Base>=0 : textproc/p5-XML-SAX-Base
- p5-XML-SAX-Writer>=0 : textproc/p5-XML-SAX-Writer
- p5-XML-Twig>=0 : textproc/p5-XML-Twig
- p5-XML-Writer>=0 : textproc/p5-XML-Writer
- p5-YAML>=0 : textproc/p5-YAML
- p5-libwww>=0 : www/p5-libwww
- p5-libxml>=0 : textproc/p5-libxml
- perl5>=5.34<5.35 : lang/perl5.34
- perl5>=5.34<5.35 : lang/perl5.34
- Test dependencies:
-
- p5-Test-Memory-Cycle>=0 : devel/p5-Test-Memory-Cycle
- p5-Test-Weaken>=0 : devel/p5-Test-Weaken
- Runtime dependencies:
-
- p5-Data-Stag>=0 : devel/p5-Data-Stag
- p5-Error>=0 : lang/p5-Error
- p5-Graph>=0 : math/p5-Graph
- p5-HTTP-Message>=0 : www/p5-HTTP-Message
- p5-IO-String>=0 : devel/p5-IO-String
- p5-IO-Stringy>=0 : devel/p5-IO-Stringy
- p5-IPC-Run>=0 : devel/p5-IPC-Run
- p5-List-MoreUtils>=0 : lang/p5-List-MoreUtils
- p5-Module-Build>=0 : devel/p5-Module-Build
- p5-Set-Scalar>=0 : devel/p5-Set-Scalar
- p5-Test-Most>=0 : devel/p5-Test-Most
- p5-Test-RequiresInternet>=0 : devel/p5-Test-RequiresInternet
- p5-URI>=0 : net/p5-URI
- p5-XML-DOM>=0 : textproc/p5-XML-DOM
- p5-XML-LibXML>=0 : textproc/p5-XML-LibXML
- p5-XML-SAX>=0 : textproc/p5-XML-SAX
- p5-XML-SAX-Base>=0 : textproc/p5-XML-SAX-Base
- p5-XML-SAX-Writer>=0 : textproc/p5-XML-SAX-Writer
- p5-XML-Twig>=0 : textproc/p5-XML-Twig
- p5-XML-Writer>=0 : textproc/p5-XML-Writer
- p5-YAML>=0 : textproc/p5-YAML
- p5-libwww>=0 : www/p5-libwww
- p5-libxml>=0 : textproc/p5-libxml
- perl5>=5.34<5.35 : lang/perl5.34
- This port is required by:
- for Build
-
- biology/p5-Bio-ASN1-EntrezGene
- biology/p5-Bio-Cluster
- biology/p5-Bio-Coordinate
- biology/p5-Bio-DB-EMBL
- biology/p5-Bio-DB-NCBIHelper
- biology/p5-Bio-Das
- biology/p5-Bio-FeatureIO
- for Run
-
- biology/p5-Bio-ASN1-EntrezGene
- biology/p5-Bio-Cluster
- biology/p5-Bio-Coordinate
- biology/p5-Bio-DB-EMBL
- biology/p5-Bio-DB-NCBIHelper
- biology/p5-Bio-Das
- biology/p5-Bio-FeatureIO
Configuration Options:- ===> The following configuration options are available for p5-BioPerl-1.007008:
DOCS=on: Build and/or install documentation
EXAMPLES=on: Build and/or install examples
===> Use 'make config' to modify these settings
- Options name:
- biology_p5-BioPerl
- USES:
- perl5 shebangfix
- FreshPorts was unable to extract/find any pkg message
- Master Sites:
|
| Commit History - (may be incomplete: for full details, see links to repositories near top of page) |
| Commit | Credits | Log message |
|---|
1.007008
11 Oct 2023 12:57:41
 |
Po-Chuan Hsieh (sunpoet) |
biology/p5-BioPerl: Update to 1.007008
- Update WWW
- Sort *_DEPENDS
Changes: https://metacpan.org/dist/BioPerl/changes |
07 Sep 2022 21:58:51
|
Stefan Eßer (se) |
Remove WWW entries moved into port Makefiles
Commit b7f05445c00f has added WWW entries to port Makefiles based on
WWW: lines in pkg-descr files.
This commit removes the WWW: lines of moved-over URLs from these
pkg-descr files.
Approved by: portmgr (tcberner) |
1.007007_1
07 Sep 2022 21:10:59
|
Stefan Eßer (se) |
Add WWW entries to port Makefiles
It has been common practice to have one or more URLs at the end of the
ports' pkg-descr files, one per line and prefixed with "WWW:". These
URLs should point at a project website or other relevant resources.
Access to these URLs required processing of the pkg-descr files, and
they have often become stale over time. If more than one such URL was
present in a pkg-descr file, only the first one was tarnsfered into
the port INDEX, but for many ports only the last line did contain the
port specific URL to further information.
There have been several proposals to make a project URL available as
a macro in the ports' Makefiles, over time.
(Only the first 15 lines of the commit message are shown above  ) |
1.007007_1
20 Jul 2022 14:20:57
|
Tobias C. Berner (tcberner) |
biology: remove 'Created by' lines
A big Thank You to the original contributors of these ports:
* Aaron Dalton <aaron@FreeBSD.org>
* Akinori MUSHA aka knu <knu@idaemons.org>
* Andrey Zakhvatov
* Bob Zimmermann <rpz@cse.wustl.edu>
* Camson Huynh <chuynh@biolateral.com.au>
* Dan Siercks <dsiercks@uwm.edu>
* Fernan Aguero <fernan@iib.unsam.edu.ar>
* Hannes Hauswedell <h2+fbsdports@fsfe.org>
* J. Bacon <jwb@FreeBSD.org>
* Jason Bacon <jwb@FreeBSD.org>
* Jeremy <karlj000@unbc.ca> (Only the first 15 lines of the commit message are shown above ) |
1.007007_1
06 Apr 2021 14:31:07
|
Mathieu Arnold (mat) |
Remove # $FreeBSD$ from Makefiles. |
1.007007_1
26 Jun 2020 11:55:23
 |
sunpoet |
Move devel/p5-IO-stringy to devel/p5-IO-Stringy and update to 2.113
- Fix LICENSE_FILE
- Update pkg-descr
- Update WWW
- Bump PORTREVISION of dependent ports for dependency change
Changes: https://metacpan.org/changes/distribution/IO-Stringy |
1.007007
08 Dec 2019 16:57:24
|
sunpoet |
Update to 1.007007 (1.7.7)
Changes: https://metacpan.org/changes/distribution/BioPerl |
1.007006
07 Sep 2019 22:44:02
|
sunpoet |
Update to 1.007006 (1.7.6)
- Remove PGTEST and SQLITETEST options: DBD::Pg and DBD::SQLite have been
removed from BioPerl by upstream for the move of modules and programs into
separate distributions
Changes: https://metacpan.org/changes/distribution/BioPerl |
1.007005_1
11 Aug 2019 16:49:24
|
sunpoet |
Update to 1.007005 (1.7.5)
- Fix DISTNAME
- Bump PORTREVISION for package change
Changes: https://metacpan.org/changes/distribution/BioPerl |
1.007005
11 Aug 2019 11:28:17
|
sunpoet |
Update WWW |
1.007005
22 Feb 2019 19:54:12
|
sunpoet |
Update to 1.007005 (1.7.5)
Changes: https://metacpan.org/changes/distribution/BioPerl |
1.007004
20 Feb 2019 20:46:53
|
sunpoet |
Update to 1.007004 (1.7.4)
- Add LICENSE_FILE
- Use USES=shebangfix
- Use COPYTREE_SHARE instead of CP -R
- Take maintainership
Changes: https://metacpan.org/changes/distribution/BioPerl |
1.007002
06 Oct 2018 13:06:45
|
des |
Fix every instance of RUN_DEPENDS:=${BUILD_DEPENDS} in p5 ports, except
for where it resulted in a change in output from build-depends-list or
run-depends-list.
Approved by: portmgr (adamw) |
1.007002
15 Sep 2017 08:58:50
|
mat |
Fix license information for portgs that use "the same license as Perl".
Sponsored by: Absolight |
1.007002
13 Sep 2017 01:45:35
|
wen |
- Update to 1.007002
Changes: http://search.cpan.org/src/CJFIELDS/BioPerl-1.007002/Changes |
1.007001_2
01 Jun 2017 23:50:33
|
sunpoet |
Remove outdated PERL_LEVEL check |
1.007001_2
22 Apr 2017 12:45:43
|
miwi |
- Fix shebangs |
1.007001_1
31 Jan 2017 16:21:46
|
mat |
Bump PORTREVISION for ports affected by the fix the last commit.
Done with: Tools/scripts/bump-revision.sh
Sponsored by: Absolight |
1.007001
19 Dec 2016 15:54:29
|
sunpoet |
- 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 |
1.6.924_5
18 Dec 2016 15:25:04
|
sunpoet |
- Move biology/p5-bioperl to biology/p5-BioPerl
- Sort *_DEPENDS
- Bump PORTREVISION for dependent ports |
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