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Add p5-Bio-DB-NCBIHelper 1.7.6

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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
This commit is contained in:
Sunpoet Po-Chuan Hsieh 2019-12-08 16:49:25 +00:00
parent 876817898e
commit 2b9ee80386
Notes: svn2git 2021-03-31 03:12:20 +00:00 
svn path=/head/; revision=519319
5 changed files with 64 additions and 0 deletions
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1
biology/Makefile
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@ -87,6 +87,7 @@
SUBDIR += p5-Bio-Cluster
SUBDIR += p5-Bio-Coordinate
SUBDIR += p5-Bio-DB-EMBL
SUBDIR += p5-Bio-DB-NCBIHelper
SUBDIR += p5-Bio-Das
SUBDIR += p5-Bio-Das-Lite
SUBDIR += p5-Bio-FeatureIO

36
biology/p5-Bio-DB-NCBIHelper/Makefile Normal file
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@ -0,0 +1,36 @@
# Created by: Po-Chuan Hsieh <sunpoet@FreeBSD.org>
# $FreeBSD$
PORTNAME= Bio-DB-NCBIHelper
PORTVERSION= 1.7.6
CATEGORIES= biology perl5
MASTER_SITES= CPAN
PKGNAMEPREFIX= p5-
MAINTAINER= sunpoet@FreeBSD.org
COMMENT= Collection of routines useful for queries to NCBI databases
LICENSE= ART10 GPLv1+
LICENSE_COMB= dual
LICENSE_FILE= ${WRKSRC}/LICENSE
BUILD_DEPENDS= ${RUN_DEPENDS}
RUN_DEPENDS= p5-Bio-ASN1-EntrezGene>=0:biology/p5-Bio-ASN1-EntrezGene \
p5-BioPerl>=1.007007:biology/p5-BioPerl \
p5-CGI>=0:www/p5-CGI \
p5-Cache-Cache>=0:devel/p5-Cache-Cache \
p5-HTTP-Message>=0:www/p5-HTTP-Message \
p5-LWP-Protocol-https>=0:www/p5-LWP-Protocol-https \
p5-URI>=0:net/p5-URI \
p5-XML-Twig>=0:textproc/p5-XML-Twig \
p5-libwww>=0:www/p5-libwww
TEST_DEPENDS= p5-Test-Exception>=0:devel/p5-Test-Exception \
p5-Test-Most>=0:devel/p5-Test-Most \
p5-Test-RequiresInternet>=0:devel/p5-Test-RequiresInternet
USES= perl5
USE_PERL5= configure
NO_ARCH= yes
.include <bsd.port.mk>

3
biology/p5-Bio-DB-NCBIHelper/distinfo Normal file
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@ -0,0 +1,3 @@
TIMESTAMP = 1575793785
SHA256 (Bio-DB-NCBIHelper-1.7.6.tar.gz) = 6475fef8475e9491fec352b4fe3a6249be7b0bee92e7bad62c3f81ca31e3bcc7
SIZE (Bio-DB-NCBIHelper-1.7.6.tar.gz) = 45150

6
biology/p5-Bio-DB-NCBIHelper/pkg-descr Normal file
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@ -0,0 +1,6 @@
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

18
biology/p5-Bio-DB-NCBIHelper/pkg-plist Normal file
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@ -0,0 +1,18 @@
bin/bp_biofetch_genbank_proxy
bin/bp_download_query_genbank
bin/bp_query_entrez_taxa
%%SITE_PERL%%/Bio/DB/EntrezGene.pm
%%SITE_PERL%%/Bio/DB/GenBank.pm
%%SITE_PERL%%/Bio/DB/GenPept.pm
%%SITE_PERL%%/Bio/DB/NCBIHelper.pm
%%SITE_PERL%%/Bio/DB/Query/GenBank.pm
%%SITE_PERL%%/Bio/DB/Taxonomy/entrez.pm
%%PERL5_MAN1%%/bp_biofetch_genbank_proxy.1.gz
%%PERL5_MAN1%%/bp_download_query_genbank.1.gz
%%PERL5_MAN1%%/bp_query_entrez_taxa.1.gz
%%PERL5_MAN3%%/Bio::DB::EntrezGene.3.gz
%%PERL5_MAN3%%/Bio::DB::GenBank.3.gz
%%PERL5_MAN3%%/Bio::DB::GenPept.3.gz
%%PERL5_MAN3%%/Bio::DB::NCBIHelper.3.gz
%%PERL5_MAN3%%/Bio::DB::Query::GenBank.3.gz
%%PERL5_MAN3%%/Bio::DB::Taxonomy::entrez.3.gz