git: 68c12d4ad402 - main - biology/bcf-score: Bcftools plugins for GWAS-VCF summary statistics

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From: Jason W. Bacon <jwb_at_FreeBSD.org>
Date: Sat, 25 Feb 2023 14:27:48 UTC
The branch main has been updated by jwb:

URL: https://cgit.FreeBSD.org/ports/commit/?id=68c12d4ad402d885c078499f05c4a3919276398b

commit 68c12d4ad402d885c078499f05c4a3919276398b
Author:     Jason W. Bacon <jwb@FreeBSD.org>
AuthorDate: 2023-02-25 14:27:17 +0000
Commit:     Jason W. Bacon <jwb@FreeBSD.org>
CommitDate: 2023-02-25 14:27:46 +0000

    biology/bcf-score: Bcftools plugins for GWAS-VCF summary statistics
    
    Score is a set of tools in the form of a bcftools plugin, for handling
    and converting summary statistics files following the GWAS-VCF
    specification.
---
 biology/Makefile                           |  1 +
 biology/bcf-score/Makefile                 | 51 ++++++++++++++++++++++++++++++
 biology/bcf-score/distinfo                 |  5 +++
 biology/bcf-score/files/patch-Makefile     | 33 +++++++++++++++++++
 biology/bcf-score/files/patch-configure.ac | 11 +++++++
 biology/bcf-score/pkg-descr                |  3 ++
 biology/bcf-score/pkg-plist                |  6 ++++
 7 files changed, 110 insertions(+)

diff --git a/biology/Makefile b/biology/Makefile
index 43439e1f4a89..927e88c08f00 100644
--- a/biology/Makefile
+++ b/biology/Makefile
@@ -11,6 +11,7 @@
     SUBDIR += bamutil
     SUBDIR += barrnap
     SUBDIR += bbmap
+    SUBDIR += bcf-score
     SUBDIR += bcftools
     SUBDIR += bedtools
     SUBDIR += bfc
diff --git a/biology/bcf-score/Makefile b/biology/bcf-score/Makefile
new file mode 100644
index 000000000000..96207e1f8f84
--- /dev/null
+++ b/biology/bcf-score/Makefile
@@ -0,0 +1,51 @@
+PORTNAME=	bcf-score
+DISTVERSION=	1.16
+CATEGORIES=	biology
+MASTER_SITES=	https://software.broadinstitute.org/software/score/
+DISTFILES+=	score_${DISTVERSION}-20221221.tar.gz
+
+MAINTAINER=	jwb@FreeBSD.org
+COMMENT=	Bcftools plugins for GWAS-VCF summary statistics files
+WWW=		https://software.broadinstitute.org/software/score/
+
+LICENSE=	MIT
+
+LIB_DEPENDS=	libhts.so:biology/htslib
+BUILD_DEPENDS=	bash:shells/bash
+RUN_DEPENDS=	bcftools>=${PORTVERSION}:biology/bcftools
+
+USES=		autoreconf gmake localbase perl5 python:env shebangfix
+USE_GITHUB=	yes
+USE_PERL5=	test
+
+GH_ACCOUNT=	samtools
+GH_PROJECT=	bcftools
+GH_TAGNAME=	1.17
+GNU_CONFIGURE=	yes
+SHEBANG_FILES=	misc/* test/test.pl
+
+post-extract:
+	@${CP} ${WRKDIR}/*.c ${WRKDIR}/*.h ${WRKSRC}/plugins
+	@${MKDIR} ${WRKSRC}/bcf-score
+	@${CP} ${WRKDIR}/*.R ${WRKSRC}/bcf-score
+
+pre-configure:
+	@${REINPLACE_CMD} -e 's|@PORTVERSION@|${PORTVERSION}|g' \
+		${WRKSRC}/configure.ac
+
+# One .so for each .c in the score distfile
+do-install:
+	${MKDIR} ${STAGEDIR}${PREFIX}/libexec/bcftools
+	${INSTALL_PROGRAM} ${WRKSRC}/plugins/blupx.so \
+		${STAGEDIR}${PREFIX}/libexec/bcftools
+	${INSTALL_PROGRAM} ${WRKSRC}/plugins/liftover.so \
+		${STAGEDIR}${PREFIX}/libexec/bcftools
+	${INSTALL_PROGRAM} ${WRKSRC}/plugins/metal.so \
+		${STAGEDIR}${PREFIX}/libexec/bcftools
+	${INSTALL_PROGRAM} ${WRKSRC}/plugins/munge.so \
+		${STAGEDIR}${PREFIX}/libexec/bcftools
+	${INSTALL_PROGRAM} ${WRKSRC}/plugins/score.so \
+		${STAGEDIR}${PREFIX}/libexec/bcftools
+	(cd ${WRKSRC}/bcf-score && ${COPYTREE_SHARE} . ${STAGEDIR}${DATADIR})
+
+.include <bsd.port.mk>
diff --git a/biology/bcf-score/distinfo b/biology/bcf-score/distinfo
new file mode 100644
index 000000000000..d343300fb841
--- /dev/null
+++ b/biology/bcf-score/distinfo
@@ -0,0 +1,5 @@
+TIMESTAMP = 1677335027
+SHA256 (score_1.16-20221221.tar.gz) = f5f7331f2f670ea26cbc48a924e1467ac13c69aaf3b2a56599e3decda9375c0b
+SIZE (score_1.16-20221221.tar.gz) = 61927
+SHA256 (samtools-bcftools-1.16-1.17_GH0.tar.gz) = e6fdb4c94b531671ea8a0b00cb9245aa2602f6c4480621e45dac76338f590b9e
+SIZE (samtools-bcftools-1.16-1.17_GH0.tar.gz) = 3481344
diff --git a/biology/bcf-score/files/patch-Makefile b/biology/bcf-score/files/patch-Makefile
new file mode 100644
index 000000000000..3299954ae45b
--- /dev/null
+++ b/biology/bcf-score/files/patch-Makefile
@@ -0,0 +1,33 @@
+--- Makefile.orig	2021-03-17 09:16:18 UTC
++++ Makefile
+@@ -58,13 +58,14 @@ pluginpath  = $(plugindir)
+ # Installation location for $(MISC_PROGRAMS) and $(MISC_SCRIPTS)
+ misc_bindir = $(bindir)
+ 
+-MKDIR_P = mkdir -p
+-INSTALL = install -p
+-INSTALL_DATA    = $(INSTALL) -m 644
+-INSTALL_DIR     = $(MKDIR_P) -m 755
+-INSTALL_MAN     = $(INSTALL_DATA)
+-INSTALL_PROGRAM = $(INSTALL)
+-INSTALL_SCRIPT  = $(INSTALL_PROGRAM)
++# Use BSD_INSTALL_PROGRAM to strip when WITH_DEBUG not set
++MKDIR_P 	= mkdir -p
++INSTALL 	= install -p
++INSTALL_DATA    = ${BSD_INSTALL_DATA}
++INSTALL_DIR     = $(MKDIR_P)
++INSTALL_MAN     = ${BSD_INSTALL_MAN}
++INSTALL_PROGRAM = ${BSD_INSTALL_PROGRAM}
++INSTALL_SCRIPT  = ${BSD_INSTALL_SCRIPT}
+ 
+ PROGRAMS = bcftools
+ MISC_SCRIPTS = \
+@@ -142,7 +143,7 @@ print-version:
+ ifdef USE_GPL
+     main.o : EXTRA_CPPFLAGS += -DUSE_GPL
+     OBJS += polysomy.o peakfit.o
+-    GSL_LIBS ?= -lgsl -lcblas
++    GSL_LIBS ?= -lgslcblas
+ endif
+ 
+ print-%:
diff --git a/biology/bcf-score/files/patch-configure.ac b/biology/bcf-score/files/patch-configure.ac
new file mode 100644
index 000000000000..ca845d2ad85f
--- /dev/null
+++ b/biology/bcf-score/files/patch-configure.ac
@@ -0,0 +1,11 @@
+--- configure.ac.orig	2018-07-18 08:34:29 UTC
++++ configure.ac
+@@ -23,7 +23,7 @@
+ # DEALINGS IN THE SOFTWARE.
+ 
+ dnl Process this file with autoconf to produce a configure script
+-AC_INIT([BCFtools], m4_esyscmd_s([./version.sh 2>/dev/null]),
++AC_INIT([BCFtools], [@PORTVERSION@],
+         [samtools-help@lists.sourceforge.net], [], [http://www.htslib.org/])
+ AC_PREREQ([2.63])  dnl This version introduced 4-argument AC_CHECK_HEADER
+ AC_CONFIG_SRCDIR([main.c])
diff --git a/biology/bcf-score/pkg-descr b/biology/bcf-score/pkg-descr
new file mode 100644
index 000000000000..2d926613d77b
--- /dev/null
+++ b/biology/bcf-score/pkg-descr
@@ -0,0 +1,3 @@
+Score is a set of tools in the form of a bcftools plugin, for handling
+and converting summary statistics files following the GWAS-VCF
+specification.
diff --git a/biology/bcf-score/pkg-plist b/biology/bcf-score/pkg-plist
new file mode 100644
index 000000000000..719a907bf251
--- /dev/null
+++ b/biology/bcf-score/pkg-plist
@@ -0,0 +1,6 @@
+libexec/bcftools/blupx.so
+libexec/bcftools/liftover.so
+libexec/bcftools/metal.so
+libexec/bcftools/munge.so
+libexec/bcftools/score.so
+%%DATADIR%%/assoc_plot.R