| Port details |
- p5-Bio-FeatureIO Handler for FeatureIO
- 1.6.905 biology
 =2      1.6.905Version of this port present on the latest quarterly branch. - Maintainer: sunpoet@FreeBSD.org
- Port Added: 2017-09-15 19:17:29
- Last Update: 2022-09-07 21:58:51
- Commit Hash: fb16dfe
- People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py39-PyOpenGL, p5-Sane
- Also Listed In: perl5
- License: ART10 GPLv1+
- WWW:
- https://metacpan.org/release/Bio-FeatureIO
- Description:
- Bio::FeatureIO is an iterator subsystem for genomic sequence features.
Bio::FeatureIO is a handler module for the formats in the FeatureIO set (eg,
Bio::FeatureIO::GFF). It is the officially sanctioned way of getting at the
format objects, which most people should use.
The Bio::FeatureIO system can be thought of like biological file handles. They
are attached to filehandles with smart formatting rules (eg, GFF format, or BED
format) and can either read or write feature objects (Bio::SeqFeature objects,
or more correctly, Bio::FeatureHolderI implementing objects, of which
Bio::SeqFeature is one such object). If you want to know what to do with a
Bio::SeqFeatureI object, read Bio::SeqFeatureI.
The idea is that you request a stream object for a particular format. All the
stream objects have a notion of an internal file that is read from or written
to. A particular FeatureIO object instance is configured for either input or
output. A specific example of a stream object is the Bio::FeatureIO::gff object.
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- Manual pages:
- FreshPorts has no man page information for this port.
- pkg-plist: as obtained via:
make generate-plist - Dependency lines:
-
- p5-Bio-FeatureIO>0:biology/p5-Bio-FeatureIO
- To install the port:
- cd /usr/ports/biology/p5-Bio-FeatureIO/ && make install clean
- To add the package, run one of these commands:
- pkg install biology/p5-Bio-FeatureIO
- pkg install p5-Bio-FeatureIO
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.- PKGNAME: p5-Bio-FeatureIO
- Flavors: there is no flavor information for this port.
- distinfo:
- TIMESTAMP = 1505488503
SHA256 (Bio-FeatureIO-1.6.905.tar.gz) = 322e5757b374f2fb90b8f20bdbdc75631f5cb4d122f81a4d35c3a177cf950c7a
SIZE (Bio-FeatureIO-1.6.905.tar.gz) = 54906
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-BioPerl>=0 : biology/p5-BioPerl
- p5-Tree-DAG_Node>=0 : devel/p5-Tree-DAG_Node
- p5-URI>=0 : net/p5-URI
- p5-XML-DOM>=0 : textproc/p5-XML-DOM
- p5-XML-DOM-XPath>=0 : textproc/p5-XML-DOM-XPath
- perl5>=5.32.r0<5.33 : lang/perl5.32
- perl5>=5.32.r0<5.33 : lang/perl5.32
- Runtime dependencies:
-
- p5-BioPerl>=0 : biology/p5-BioPerl
- p5-Tree-DAG_Node>=0 : devel/p5-Tree-DAG_Node
- p5-URI>=0 : net/p5-URI
- p5-XML-DOM>=0 : textproc/p5-XML-DOM
- p5-XML-DOM-XPath>=0 : textproc/p5-XML-DOM-XPath
- perl5>=5.32.r0<5.33 : lang/perl5.32
- This port is required by:
- for Build
-
- biology/p5-BioPerl-Run
- for Run
-
- biology/p5-BioPerl-Run
Configuration Options:- No options to configure
- Options name:
- biology_p5-Bio-FeatureIO
- USES:
- perl5
- FreshPorts was unable to extract/find any pkg message
- Master Sites:
|
Number of commits found: 8
| Commit History - (may be incomplete: for full details, see links to repositories near top of page) |
| Commit | Credits | Log message |
|---|
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) |
1.6.905
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  ) |
1.6.905
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 ) |
1.6.905
06 Apr 2021 14:31:07
|
Mathieu Arnold (mat) |
Remove # $FreeBSD$ from Makefiles. |
1.6.905
02 Apr 2020 12:01:35
 |
sunpoet |
Cosmetic change |
1.6.905
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) |
1.6.905
27 May 2018 20:15:20
|
sunpoet |
Update WWW
search.cpan.org is shutting down.
It will redirect to metacpan.org after June 25, 2018.
With hat: perl |
1.6.905
15 Sep 2017 19:17:18
|
sunpoet |
Add p5-Bio-FeatureIO 1.6.905
Bio::FeatureIO is an iterator subsystem for genomic sequence features.
Bio::FeatureIO is a handler module for the formats in the FeatureIO set (eg,
Bio::FeatureIO::GFF). It is the officially sanctioned way of getting at the
format objects, which most people should use.
The Bio::FeatureIO system can be thought of like biological file handles. They
are attached to filehandles with smart formatting rules (eg, GFF format, or BED
format) and can either read or write feature objects (Bio::SeqFeature objects,
or more correctly, Bio::FeatureHolderI implementing objects, of which
Bio::SeqFeature is one such object). If you want to know what to do with a
Bio::SeqFeatureI object, read Bio::SeqFeatureI.
The idea is that you request a stream object for a particular format. All the
stream objects have a notion of an internal file that is read from or written
to. A particular FeatureIO object instance is configured for either input or
output. A specific example of a stream object is the Bio::FeatureIO::gff object.
WWW: http://search.cpan.org/dist/Bio-FeatureIO/ |
Number of commits found: 8
|
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