svn commit: r519319 - in head/biology: . p5-Bio-DB-NCBIHelper
Sunpoet Po-Chuan Hsieh
sunpoet at FreeBSD.org
Sun Dec 8 16:49:27 UTC 2019
Author: sunpoet
Date: Sun Dec 8 16:49:25 2019
New Revision: 519319
URL: https://svnweb.freebsd.org/changeset/ports/519319
Log:
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
Added:
head/biology/p5-Bio-DB-NCBIHelper/
head/biology/p5-Bio-DB-NCBIHelper/Makefile (contents, props changed)
head/biology/p5-Bio-DB-NCBIHelper/distinfo (contents, props changed)
head/biology/p5-Bio-DB-NCBIHelper/pkg-descr (contents, props changed)
head/biology/p5-Bio-DB-NCBIHelper/pkg-plist (contents, props changed)
Modified:
head/biology/Makefile
Modified: head/biology/Makefile
==============================================================================
--- head/biology/Makefile Sun Dec 8 16:49:19 2019 (r519318)
+++ head/biology/Makefile Sun Dec 8 16:49:25 2019 (r519319)
@@ -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
Added: head/biology/p5-Bio-DB-NCBIHelper/Makefile
==============================================================================
--- /dev/null 00:00:00 1970 (empty, because file is newly added)
+++ head/biology/p5-Bio-DB-NCBIHelper/Makefile Sun Dec 8 16:49:25 2019 (r519319)
@@ -0,0 +1,36 @@
+# Created by: Po-Chuan Hsieh <sunpoet at FreeBSD.org>
+# $FreeBSD$
+
+PORTNAME= Bio-DB-NCBIHelper
+PORTVERSION= 1.7.6
+CATEGORIES= biology perl5
+MASTER_SITES= CPAN
+PKGNAMEPREFIX= p5-
+
+MAINTAINER= sunpoet at 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>
Added: head/biology/p5-Bio-DB-NCBIHelper/distinfo
==============================================================================
--- /dev/null 00:00:00 1970 (empty, because file is newly added)
+++ head/biology/p5-Bio-DB-NCBIHelper/distinfo Sun Dec 8 16:49:25 2019 (r519319)
@@ -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
Added: head/biology/p5-Bio-DB-NCBIHelper/pkg-descr
==============================================================================
--- /dev/null 00:00:00 1970 (empty, because file is newly added)
+++ head/biology/p5-Bio-DB-NCBIHelper/pkg-descr Sun Dec 8 16:49:25 2019 (r519319)
@@ -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
Added: head/biology/p5-Bio-DB-NCBIHelper/pkg-plist
==============================================================================
--- /dev/null 00:00:00 1970 (empty, because file is newly added)
+++ head/biology/p5-Bio-DB-NCBIHelper/pkg-plist Sun Dec 8 16:49:25 2019 (r519319)
@@ -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
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