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Port details
p5-Bio-DB-NCBIHelper Collection of routines useful for queries to NCBI databases
1.7.8 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 View this port on Repology. pkg-fallout 1.7.8Version of this port present on the latest quarterly branch.
Maintainer: sunpoet@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2019-12-08 16:52:43
Last Update: 2023-12-25 08:59:52
Commit Hash: 4107132
Also Listed In: perl5
License: ART10 GPLv1+
WWW:
https://metacpan.org/release/Bio-DB-NCBIHelper
Description:
Bio::DB::NCBIHelper provides a single place to setup some common methods for querying NCBI web databases. This module just centralizes the methods for constructing a URL for querying NCBI GenBank and NCBI GenPept and the common HTML stripping done in postprocess_data().
Homepage    cgit ¦ Codeberg ¦ GitHub ¦ GitLab ¦ SVNWeb

Manual pages:
FreshPorts has no man page information for this port.
pkg-plist: as obtained via: make generate-plist
Expand this list (25 items)
Collapse this list.
  1. /usr/local/share/licenses/p5-Bio-DB-NCBIHelper-1.7.8/catalog.mk
  2. /usr/local/share/licenses/p5-Bio-DB-NCBIHelper-1.7.8/LICENSE
  3. /usr/local/share/licenses/p5-Bio-DB-NCBIHelper-1.7.8/ART10
  4. /usr/local/share/licenses/p5-Bio-DB-NCBIHelper-1.7.8/GPLv1+
  5. bin/bp_biofetch_genbank_proxy
  6. bin/bp_download_query_genbank
  7. bin/bp_query_entrez_taxa
  8. lib/perl5/site_perl/Bio/DB/EntrezGene.pm
  9. lib/perl5/site_perl/Bio/DB/GenBank.pm
  10. lib/perl5/site_perl/Bio/DB/GenPept.pm
  11. lib/perl5/site_perl/Bio/DB/NCBIHelper.pm
  12. lib/perl5/site_perl/Bio/DB/Query/GenBank.pm
  13. lib/perl5/site_perl/Bio/DB/Taxonomy/entrez.pm
  14. lib/perl5/site_perl/man/man1/bp_biofetch_genbank_proxy.1.gz
  15. lib/perl5/site_perl/man/man1/bp_download_query_genbank.1.gz
  16. lib/perl5/site_perl/man/man1/bp_query_entrez_taxa.1.gz
  17. lib/perl5/site_perl/man/man3/Bio::DB::EntrezGene.3.gz
  18. lib/perl5/site_perl/man/man3/Bio::DB::GenBank.3.gz
  19. lib/perl5/site_perl/man/man3/Bio::DB::GenPept.3.gz
  20. lib/perl5/site_perl/man/man3/Bio::DB::NCBIHelper.3.gz
  21. lib/perl5/site_perl/man/man3/Bio::DB::Query::GenBank.3.gz
  22. lib/perl5/site_perl/man/man3/Bio::DB::Taxonomy::entrez.3.gz
  23. @owner
  24. @group
  25. @mode
Collapse this list.
Dependency lines:
  • p5-Bio-DB-NCBIHelper>0:biology/p5-Bio-DB-NCBIHelper
To install the port:
cd /usr/ports/biology/p5-Bio-DB-NCBIHelper/ && make install clean
To add the package, run one of these commands:
  • pkg install biology/p5-Bio-DB-NCBIHelper
  • pkg install p5-Bio-DB-NCBIHelper
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.
PKGNAME: p5-Bio-DB-NCBIHelper
Flavors: there is no flavor information for this port.
distinfo:
TIMESTAMP = 1703227832 SHA256 (Bio-DB-NCBIHelper-1.7.8.tar.gz) = f8e2a739c872608a24003a642a686b6e9c72af59a3bc0aceea6e5a5c2ea5ecbf SIZE (Bio-DB-NCBIHelper-1.7.8.tar.gz) = 45770

Packages (timestamps in pop-ups are UTC):
p5-Bio-DB-NCBIHelper
ABIaarch64amd64armv6armv7i386powerpcpowerpc64powerpc64le
FreeBSD:13:latest1.7.81.7.81.7.61.7.81.7.8-1.7.6-
FreeBSD:13:quarterly1.7.81.7.81.7.71.7.81.7.81.7.81.7.81.7.8
FreeBSD:14:latest1.7.81.7.81.7.71.7.81.7.81.7.7-1.7.7
FreeBSD:14:quarterly1.7.81.7.8-1.7.81.7.81.7.81.7.81.7.8
FreeBSD:15:latest1.7.81.7.8n/a1.7.8n/a1.7.81.7.81.7.8
FreeBSD:15:quarterly--n/a-n/a---
Dependencies
NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
Build dependencies:
  1. p5-Bio-ASN1-EntrezGene>=0 : biology/p5-Bio-ASN1-EntrezGene
  2. p5-BioPerl>=1.007007 : biology/p5-BioPerl
  3. p5-CGI>=0 : www/p5-CGI
  4. p5-Cache-Cache>=0 : devel/p5-Cache-Cache
  5. p5-HTTP-Message>=0 : www/p5-HTTP-Message
  6. p5-LWP-Protocol-https>=0 : www/p5-LWP-Protocol-https
  7. p5-URI>=0 : net/p5-URI
  8. p5-XML-Twig>=0 : textproc/p5-XML-Twig
  9. p5-libwww>=0 : www/p5-libwww
  10. perl5>=5.36<5.37 : lang/perl5.36
  11. perl5>=5.36<5.37 : lang/perl5.36
Test dependencies:
  1. p5-Test-Exception>=0 : devel/p5-Test-Exception
  2. p5-Test-Most>=0 : devel/p5-Test-Most
  3. p5-Test-RequiresInternet>=0 : devel/p5-Test-RequiresInternet
Runtime dependencies:
  1. p5-Bio-ASN1-EntrezGene>=0 : biology/p5-Bio-ASN1-EntrezGene
  2. p5-BioPerl>=1.007007 : biology/p5-BioPerl
  3. p5-CGI>=0 : www/p5-CGI
  4. p5-Cache-Cache>=0 : devel/p5-Cache-Cache
  5. p5-HTTP-Message>=0 : www/p5-HTTP-Message
  6. p5-LWP-Protocol-https>=0 : www/p5-LWP-Protocol-https
  7. p5-URI>=0 : net/p5-URI
  8. p5-XML-Twig>=0 : textproc/p5-XML-Twig
  9. p5-libwww>=0 : www/p5-libwww
  10. perl5>=5.36<5.37 : lang/perl5.36
There are no ports dependent upon this port

Configuration Options:
No options to configure
Options name:
biology_p5-Bio-DB-NCBIHelper
USES:
perl5
FreshPorts was unable to extract/find any pkg message
Master Sites:
Expand this list (12 items)
Collapse this list.
  1. ftp://ftp.auckland.ac.nz/pub/perl/CPAN/modules/by-module/Bio/
  2. ftp://ftp.cpan.org/pub/CPAN/modules/by-module/
  3. ftp://ftp.cpan.org/pub/CPAN/modules/by-module/Bio/
  4. ftp://ftp.funet.fi/pub/languages/perl/CPAN/modules/by-module/Bio/
  5. ftp://ftp.kddlabs.co.jp/lang/perl/CPAN/modules/by-module/Bio/
  6. ftp://ftp.mirrorservice.org/sites/cpan.perl.org/CPAN/modules/by-module/Bio/
  7. http://backpan.perl.org/modules/by-module/Bio/
  8. http://ftp.jaist.ac.jp/pub/CPAN/modules/by-module/Bio/
  9. http://ftp.twaren.net/Unix/Lang/CPAN/modules/by-module/Bio/
  10. https://cpan.metacpan.org/modules/by-module/
  11. https://cpan.metacpan.org/modules/by-module/Bio/
  12. https://www.cpan.org/modules/by-module/Bio/
Collapse this list.

Number of commits found: 7

Commit History - (may be incomplete: for full details, see links to repositories near top of page)
CommitCreditsLog message
1.7.8
25 Dec 2023 08:59:52
commit hash: 4107132118f49ac23520fe3e9f4400ddc26b7e0ecommit hash: 4107132118f49ac23520fe3e9f4400ddc26b7e0ecommit hash: 4107132118f49ac23520fe3e9f4400ddc26b7e0ecommit hash: 4107132118f49ac23520fe3e9f4400ddc26b7e0e files touched by this commit
Po-Chuan Hsieh (sunpoet) search for other commits by this committer
biology/p5-Bio-DB-NCBIHelper: Update to 1.7.8

- Update LICENSE_FILE

Changes:	https://metacpan.org/dist/Bio-DB-NCBIHelper/changes
07 Sep 2022 21:58:51
commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4 files touched by this commit
Stefan Eßer (se) search for other commits by this committer
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)
1.7.7
07 Sep 2022 21:10:59
commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52 files touched by this commit
Stefan Eßer (se) search for other commits by this committer
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 View all of this commit message)
1.7.7
20 Jul 2022 14:20:57
commit hash: 37526bbd4e50616d87f70e1c788ae4895d88d671commit hash: 37526bbd4e50616d87f70e1c788ae4895d88d671commit hash: 37526bbd4e50616d87f70e1c788ae4895d88d671commit hash: 37526bbd4e50616d87f70e1c788ae4895d88d671 files touched by this commit
Tobias C. Berner (tcberner) search for other commits by this committer
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 View all of this commit message)
1.7.7
06 Jul 2021 14:56:10
commit hash: e7a0015b134bfa3c85a8922f5968d47bb0dd2337commit hash: e7a0015b134bfa3c85a8922f5968d47bb0dd2337commit hash: e7a0015b134bfa3c85a8922f5968d47bb0dd2337commit hash: e7a0015b134bfa3c85a8922f5968d47bb0dd2337 files touched by this commit
Po-Chuan Hsieh (sunpoet) search for other commits by this committer
biology/p5-Bio-DB-NCBIHelper: Update to 1.7.7

Changes:	https://metacpan.org/dist/Bio-DB-NCBIHelper/changes
1.7.6
06 Apr 2021 14:31:07
commit hash: 305f148f482daf30dcf728039d03d019f88344ebcommit hash: 305f148f482daf30dcf728039d03d019f88344ebcommit hash: 305f148f482daf30dcf728039d03d019f88344ebcommit hash: 305f148f482daf30dcf728039d03d019f88344eb files touched by this commit
Mathieu Arnold (mat) search for other commits by this committer
Remove # $FreeBSD$ from Makefiles.
1.7.6
08 Dec 2019 16:49:25
Revision:519319Original commit files touched by this commit
sunpoet search for other commits by this committer
Add p5-Bio-DB-NCBIHelper 1.7.6

Bio::DB::NCBIHelper provides a single place to setup some common methods for
querying NCBI web databases. This module just centralizes the methods for
constructing a URL for querying NCBI GenBank and NCBI GenPept and the common
HTML stripping done in postprocess_data().

WWW: https://metacpan.org/release/Bio-DB-NCBIHelper

Number of commits found: 7