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

5 files changed, 64 insertions, 0 deletions

diff --git a/biology/Makefile b/biology/Makefile
index 6832be53ba48..214d40589a06 100644
--- a/biology/Makefile
+++ b/biology/Makefile
@@ -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
diff --git a/biology/p5-Bio-DB-NCBIHelper/Makefile b/biology/p5-Bio-DB-NCBIHelper/Makefile
new file mode 100644
index 000000000000..f28e3dbac39c
--- /dev/null
+++ b/biology/p5-Bio-DB-NCBIHelper/Makefile
@@ -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>
diff --git a/biology/p5-Bio-DB-NCBIHelper/distinfo b/biology/p5-Bio-DB-NCBIHelper/distinfo
new file mode 100644
index 000000000000..89cc3e0ea75c
--- /dev/null
+++ b/biology/p5-Bio-DB-NCBIHelper/distinfo
@@ -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
diff --git a/biology/p5-Bio-DB-NCBIHelper/pkg-descr b/biology/p5-Bio-DB-NCBIHelper/pkg-descr
new file mode 100644
index 000000000000..2fa0d08cfb54
--- /dev/null
+++ b/biology/p5-Bio-DB-NCBIHelper/pkg-descr
@@ -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
diff --git a/biology/p5-Bio-DB-NCBIHelper/pkg-plist b/biology/p5-Bio-DB-NCBIHelper/pkg-plist
new file mode 100644
index 000000000000..1446d4d3f980
--- /dev/null
+++ b/biology/p5-Bio-DB-NCBIHelper/pkg-plist
@@ -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