bcf-score: Bcftools plugin for mosaic chromosomal alteration analysis

To: pkgsrc-wip-changes%NetBSD.org@localhost
Subject: bcf-score: Bcftools plugin for mosaic chromosomal alteration analysis
From: Jason W. Bacon <bacon%NetBSD.org@localhost>
Date: Mon, 30 Sep 2024 11:53:19 +0000
Module Name:	pkgsrc-wip
Committed By:	Jason W. Bacon <bacon%NetBSD.org@localhost>
Pushed By:	outpaddling
Date:		Mon Sep 30 06:52:54 2024 -0500
Changeset:	c07b6c79a4f8beaceb89a690c6066d671c235fb2

Modified Files:
	Makefile
Added Files:
	bcf-score/DESCR
	bcf-score/Makefile
	bcf-score/PLIST
	bcf-score/PLIST.new
	bcf-score/distinfo
	bcf-score/patches/patch-Makefile

Log Message:
bcf-score: Bcftools plugin for mosaic chromosomal alteration analysis

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.

Also add missing bcftools to wip/Makefile

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=c07b6c79a4f8beaceb89a690c6066d671c235fb2

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

diffstat:
 Makefile                         |  2 ++
 bcf-score/DESCR                  |  3 ++
 bcf-score/Makefile               | 73 ++++++++++++++++++++++++++++++++++++++++
 bcf-score/PLIST                  |  8 +++++
 bcf-score/PLIST.new              |  3 ++
 bcf-score/distinfo               |  9 +++++
 bcf-score/patches/patch-Makefile | 23 +++++++++++++
 7 files changed, 121 insertions(+)

diffs:
diff --git a/Makefile b/Makefile
index 9496658ba3..49aeb6c3c4 100644
--- a/Makefile
+++ b/Makefile
@@ -289,6 +289,8 @@ SUBDIR+=	basic-stats
 SUBDIR+=	bastard
 SUBDIR+=	bats-core
 SUBDIR+=	bazel
+SUBDIR+=	bcf-score
+SUBDIR+=	bcftools
 SUBDIR+=	bcryptcpp
 SUBDIR+=	be
 SUBDIR+=	beast
diff --git a/bcf-score/DESCR b/bcf-score/DESCR
new file mode 100644
index 0000000000..2d926613d7
--- /dev/null
+++ b/bcf-score/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/bcf-score/Makefile b/bcf-score/Makefile
new file mode 100644
index 0000000000..399ec601f4
--- /dev/null
+++ b/bcf-score/Makefile
@@ -0,0 +1,73 @@
+# $NetBSD$
+
+DISTNAME=	bcf-score-1.20
+CATEGORIES=	biology
+# Can't get ${MASTER_SITE_GITHUB:=samtools/} to work with additional distfile
+MASTER_SITES=	https://software.broadinstitute.org/software/score/
+MASTER_SITES+=	https://github.com/samtools/bcftools/releases/download/${GH_TAG}/
+DISTFILES+=	score_1.20-20240505.tar.gz
+DISTFILES+=	bcftools-1.21.tar.bz2
+GH_TAG=		1.21
+
+OWNER=		bacon%NetBSD.org@localhost
+HOMEPAGE=	https://software.broadinstitute.org/software/score/
+COMMENT=	Bcftools plugin for mosaic chromosomal alteration analysis
+LICENSE=	mit
+
+REPLACE_INTERPRETER+=	R
+REPLACE.R.old=		/usr/bin/env Rscript
+REPLACE.R.new=		${PREFIX}/bin/Rscript
+REPLACE_FILES.R=	bcf-score/*.R
+
+SUBST_CLASSES+=		version
+SUBST_STAGE.version=	pre-configure
+SUBST_SED.version=	-e "s|m4_esyscmd_s(\[./version.sh 2>/dev/null\])|[${PKGVERSION_NOREV}]|"
+SUBST_FILES.version=	configure.ac
+
+DEPENDS=	bash>=0:../../shells/bash
+DEPENDS+=	bcftools>=1.16:../../biology/bcftools
+
+USE_TOOLS+=	autoconf automake autoreconf gmake perl pax
+GNU_CONFIGURE=	yes
+REPLACE_PERL=	misc/* test/test.pl
+
+WRKSRC=		${WRKDIR}/bcftools-${GH_TAG}
+
+CFLAGS+=	-isystem ${LOCALBASE}/include/suitesparse
+LDFLAGS+=	-lcholmod
+
+DATADIR=		${PREFIX}/share/bcf-score
+INSTALLATION_DIRS=	libexec/bcftools
+
+post-extract:
+	${CP} ${WRKDIR}/*.c ${WRKDIR}/*.h ${WRKSRC}/plugins
+	${MKDIR} ${WRKSRC}/bcf-score
+	${CP} ${WRKDIR}/*.R ${WRKSRC}/bcf-score
+
+pre-configure:
+	cd ${WRKSRC} && autoreconf -if
+
+# One .so for each .c in the score distfile
+do-install:
+	${MKDIR} ${DESTDIR}${PREFIX}/libexec/bcftools
+	${INSTALL_PROGRAM} ${WRKSRC}/plugins/blup.so \
+		${DESTDIR}${PREFIX}/libexec/bcftools
+	${INSTALL_PROGRAM} ${WRKSRC}/plugins/liftover.so \
+		${DESTDIR}${PREFIX}/libexec/bcftools
+	${INSTALL_PROGRAM} ${WRKSRC}/plugins/metal.so \
+		${DESTDIR}${PREFIX}/libexec/bcftools
+	${INSTALL_PROGRAM} ${WRKSRC}/plugins/munge.so \
+		${DESTDIR}${PREFIX}/libexec/bcftools
+	${INSTALL_PROGRAM} ${WRKSRC}/plugins/pgs.so \
+		${DESTDIR}${PREFIX}/libexec/bcftools
+	${INSTALL_PROGRAM} ${WRKSRC}/plugins/score.so \
+		${DESTDIR}${PREFIX}/libexec/bcftools
+	(cd ${WRKSRC}/bcf-score && pax -rw . ${DESTDIR}${DATADIR})
+
+.include "../../devel/zlib/buildlink3.mk"
+.include "../../archivers/bzip2/buildlink3.mk"
+.include "../../archivers/xz/buildlink3.mk"
+.include "../../math/suitesparse/buildlink3.mk"
+.include "../../lang/python/application.mk"
+.include "../../wip/htslib/buildlink3.mk"
+.include "../../mk/bsd.pkg.mk"
diff --git a/bcf-score/PLIST b/bcf-score/PLIST
new file mode 100644
index 0000000000..7c789ff6bd
--- /dev/null
+++ b/bcf-score/PLIST
@@ -0,0 +1,8 @@
+@comment $NetBSD$
+libexec/bcftools/blup.so
+libexec/bcftools/liftover.so
+libexec/bcftools/metal.so
+libexec/bcftools/munge.so
+libexec/bcftools/pgs.so
+libexec/bcftools/score.so
+share/bcf-score/assoc_plot.R
diff --git a/bcf-score/PLIST.new b/bcf-score/PLIST.new
new file mode 100644
index 0000000000..5f0515ac04
--- /dev/null
+++ b/bcf-score/PLIST.new
@@ -0,0 +1,3 @@
+@comment $NetBSD$
+share/bcf-score/assoc_plot.R
+@pkgdir libexec/bcftools
diff --git a/bcf-score/distinfo b/bcf-score/distinfo
new file mode 100644
index 0000000000..5c7fffbbb0
--- /dev/null
+++ b/bcf-score/distinfo
@@ -0,0 +1,9 @@
+$NetBSD$
+
+BLAKE2s (bcftools-1.21.tar.bz2) = 517b73f84870fa967e6f7f6241c446131cc54229e7ee446110955e39dfbe2563
+SHA512 (bcftools-1.21.tar.bz2) = f8fb2e50a1a9e7a7e8a4f71d71d052f6019d54c60ae060d0abfbd01ab61a2c44e04e069c479ea9f6156513b54a611a9a46930a0ff4454019bb715fdb9558d07d
+Size (bcftools-1.21.tar.bz2) = 7982173 bytes
+BLAKE2s (score_1.20-20240505.tar.gz) = 01791f1c3127f575f34d36fe344b838e4a55b8733791ed4ea44bcf75c2666001
+SHA512 (score_1.20-20240505.tar.gz) = 6e3da79138c83a81d6392a991836c9ba6f92e13fcd1b418647eb83b83952ba79169e6ddc781700f33d9daacbef8731ba0a6f40387bfd93ce0783f78c25d9dd76
+Size (score_1.20-20240505.tar.gz) = 96852 bytes
+SHA1 (patch-Makefile) = 9dfe7b5dcf77deac6d248d7612440780ec8a3731
diff --git a/bcf-score/patches/patch-Makefile b/bcf-score/patches/patch-Makefile
new file mode 100644
index 0000000000..c1cae450ea
--- /dev/null
+++ b/bcf-score/patches/patch-Makefile
@@ -0,0 +1,23 @@
+$NetBSD: patch-Makefile,v 1.4 2022/02/26 23:14:33 bacon Exp $
+
+# Respect pkgsrc env
+
+--- Makefile.orig	2021-03-19 17:42:33.842623449 +0000
++++ Makefile
+@@ -60,11 +60,11 @@ 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)
++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 = \
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