From 633c71fbf74172270dbd775c00b3b6f7e46f4ed1 Mon Sep 17 00:00:00 2001
From: "Jason W. Bacon" <jwb@FreeBSD.org>
Date: Tue, 23 Mar 2021 16:32:29 +0000
Subject: biology/vcf2hap: Generate .hap file from VCF for haplohseq

vcf2hap is a simple tool for generating a .hap file from a VCF. The .hap file
is required by haplohseq.  vcf2hap is extremely fast and requires a trivial
amount of memory regardless of the size of the VCF file.
---
 biology/Makefile          |  1 +
 biology/vcf2hap/Makefile  | 26 ++++++++++++++++++++++++++
 biology/vcf2hap/distinfo  |  3 +++
 biology/vcf2hap/pkg-descr |  5 +++++
 4 files changed, 35 insertions(+)
 create mode 100644 biology/vcf2hap/Makefile
 create mode 100644 biology/vcf2hap/distinfo
 create mode 100644 biology/vcf2hap/pkg-descr

(limited to 'biology')

diff --git a/biology/Makefile b/biology/Makefile
index 260d2763d896..3ef12bfb358a 100644
--- a/biology/Makefile
+++ b/biology/Makefile
@@ -181,6 +181,7 @@
     SUBDIR += trimmomatic
     SUBDIR += ugene
     SUBDIR += vcf-split
+    SUBDIR += vcf2hap
     SUBDIR += vcflib
     SUBDIR += vcftools
     SUBDIR += velvet
diff --git a/biology/vcf2hap/Makefile b/biology/vcf2hap/Makefile
new file mode 100644
index 000000000000..bb4a4bd88103
--- /dev/null
+++ b/biology/vcf2hap/Makefile
@@ -0,0 +1,26 @@
+# $FreeBSD$
+
+PORTNAME=	vcf2hap
+DISTVERSION=	0.1.2
+CATEGORIES=	biology
+
+MAINTAINER=	jwb@FreeBSD.org
+COMMENT=	Generate .hap file from VCF for haplohseq
+
+LICENSE=	BSD2CLAUSE
+LICENSE_FILE=	${WRKSRC}/LICENSE
+
+BUILD_DEPENDS=	biolibc>=0.1.1:biology/biolibc
+
+USE_GITHUB=	yes
+GH_ACCOUNT=	auerlab
+
+PLIST_FILES=	bin/vcf2hap man/man1/vcf2hap.1.gz
+
+pre-build:
+	(cd ${WRKSRC} && ${MAKE} LOCALBASE=${LOCALBASE} depend)
+
+do-test:
+	(cd ${WRKSRC}/Test && ./run-test.sh)
+
+.include <bsd.port.mk>
diff --git a/biology/vcf2hap/distinfo b/biology/vcf2hap/distinfo
new file mode 100644
index 000000000000..7b288bf922c7
--- /dev/null
+++ b/biology/vcf2hap/distinfo
@@ -0,0 +1,3 @@
+TIMESTAMP = 1616515046
+SHA256 (auerlab-vcf2hap-0.1.2_GH0.tar.gz) = 69804e605bdf646582cbc33bb2839387da5cb2e8a3f83a8a03b5a464d01348f1
+SIZE (auerlab-vcf2hap-0.1.2_GH0.tar.gz) = 197782
diff --git a/biology/vcf2hap/pkg-descr b/biology/vcf2hap/pkg-descr
new file mode 100644
index 000000000000..540a5393a487
--- /dev/null
+++ b/biology/vcf2hap/pkg-descr
@@ -0,0 +1,5 @@
+vcf2hap is a simple tool for generating a .hap file from a VCF. The .hap file
+is required by haplohseq.  vcf2hap is extremely fast and requires a trivial
+amount of memory regardless of the size of the VCF file.
+
+WWW: https://github.com/auerlab/vcf2hap
-- 
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