bio-mocha: Bcftools plugin for mosaic chromosomal alteration analysis

To: pkgsrc-wip-changes%NetBSD.org@localhost
Subject: bio-mocha: Bcftools plugin for mosaic chromosomal alteration analysis
From: Jason Bacon <bacon%NetBSD.org@localhost>
Date: Tue, 27 Dec 2022 19:33:36 +0000
Module Name:	pkgsrc-wip
Committed By:	Jason Bacon <bacon%NetBSD.org@localhost>
Pushed By:	outpaddling
Date:		Tue Dec 27 13:33:36 2022 -0600
Changeset:	4e347bd3301e288f8890121503d39ea8a07e2ce8

Modified Files:
	Makefile
Added Files:
	bio-mocha/DESCR
	bio-mocha/Makefile
	bio-mocha/PLIST
	bio-mocha/distinfo
	bio-mocha/patches/patch-Makefile
	bio-mocha/patches/patch-configure.ac

Log Message:
bio-mocha: Bcftools plugin for mosaic chromosomal alteration analysis

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=4e347bd3301e288f8890121503d39ea8a07e2ce8

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

diffstat:
 Makefile                             |  1 +
 bio-mocha/DESCR                      |  6 ++++
 bio-mocha/Makefile                   | 58 ++++++++++++++++++++++++++++++++++++
 bio-mocha/PLIST                      |  1 +
 bio-mocha/distinfo                   |  7 +++++
 bio-mocha/patches/patch-Makefile     | 35 ++++++++++++++++++++++
 bio-mocha/patches/patch-configure.ac | 13 ++++++++
 7 files changed, 121 insertions(+)

diffs:
diff --git a/Makefile b/Makefile
index 9fa1ade738..ca6910a7ff 100644
--- a/Makefile
+++ b/Makefile
@@ -283,6 +283,7 @@ SUBDIR+=	bindgraph
 SUBDIR+=	binutils-gold-git
 SUBDIR+=	biolibc
 SUBDIR+=	biolibc-tools
+SUBDIR+=	bio-mocha
 SUBDIR+=	bioruby
 SUBDIR+=	bip
 SUBDIR+=	bitkeeper
diff --git a/bio-mocha/DESCR b/bio-mocha/DESCR
new file mode 100644
index 0000000000..0ab93cdde4
--- /dev/null
+++ b/bio-mocha/DESCR
@@ -0,0 +1,6 @@
+MoChA is a bcftools plugin released under the MIT license for mosaic
+chromosomal alteration detection and analysis from DNA microarray or
+whole genome sequence data. It can be used both with Illumina and
+Affymetrix data. It can also be used for detection of germline copy
+number variants. Data can be prepared in usable file formats using the
+gtc2vcf plugin.
diff --git a/bio-mocha/Makefile b/bio-mocha/Makefile
new file mode 100644
index 0000000000..29020ea3be
--- /dev/null
+++ b/bio-mocha/Makefile
@@ -0,0 +1,58 @@
+# $NetBSD$
+#
+###########################################################
+#                  Generated by fbsd2pkg                  #
+#              Tue Dec 27 12:57:33 CST 2022               #
+###########################################################
+
+DISTNAME=	bio-mocha-1.16
+CATEGORIES=	biology
+MASTER_SITES=	https://software.broadinstitute.org/software/mocha/
+MASTER_SITES+=	${MASTER_SITE_GITHUB:=samtools/}
+DISTFILES+=	bio-mocha_1.16-20221221.tar.gz
+GITHUB_PROJECT=	bcftools
+GITHUB_TAG=	1.16
+
+MAINTAINER=	bacon%NetBSD.org@localhost
+HOMEPAGE=	https://software.broadinstitute.org/software/mocha/
+COMMENT=	Bcftools plugin for mosaic chromosomal alteration analysis
+LICENSE=	mit
+
+SUBST_CLASSES+=	1
+SUBST_STAGE.1=	pre-configure
+SUBST_SED.1+=	-e 's|@PV@|${PV}|g'
+SUBST_FILES.1+=	${WRKSRC}/configure.ac
+
+DEPENDS=	bash:../../shells/bash
+DEPENDS+=	bcftools>=1.16:../../wip/bcftools
+
+USE_TOOLS+=	autoconf automake autoreconf gmake perl pax
+GNU_CONFIGURE=	yes
+REPLACE_PERL=	misc/* test/test.pl
+
+DATADIR=		${PREFIX}/share/bio-mocha
+INSTALLATION_DIRS=	libexec/bcftools
+
+post-extract:
+	@${MV} ${WRKDIR}/*.c ${WRKDIR}/*.h ${WRKSRC}/plugins
+	@${MKDIR} ${WRKSRC}/MoCha
+	@${MV} ${WRKDIR}/*.R ${WRKSRC}/MoCha
+
+pre-configure:
+	cd ${WRKSRC} && autoreconf -if
+
+# One .so for each .c in the mocha distfile
+do-install:
+	${INSTALL_PROGRAM} ${WRKSRC}/plugins/extendFMT.so \
+		${DESTDIR}${PREFIX}/libexec/bcftools
+	${INSTALL_PROGRAM} ${WRKSRC}/plugins/mocha.so \
+		${DESTDIR}${PREFIX}/libexec/bcftools
+	${INSTALL_PROGRAM} ${WRKSRC}/plugins/mochatools.so \
+		${DESTDIR}${PREFIX}/libexec/bcftools
+	${INSTALL_PROGRAM} ${WRKSRC}/plugins/trio-phase.so \
+		${DESTDIR}${PREFIX}/libexec/bcftools
+	(cd ${WRKSRC}/MoCha && pax -rw . ${DESTDIR}${DATADIR})
+
+.include "../../wip/htslib/buildlink3.mk"
+.include "../../lang/python/application.mk"
+.include "../../mk/bsd.pkg.mk"
diff --git a/bio-mocha/PLIST b/bio-mocha/PLIST
new file mode 100644
index 0000000000..48d96a5493
--- /dev/null
+++ b/bio-mocha/PLIST
@@ -0,0 +1 @@
+@comment $NetBSD$
diff --git a/bio-mocha/distinfo b/bio-mocha/distinfo
new file mode 100644
index 0000000000..71309ae590
--- /dev/null
+++ b/bio-mocha/distinfo
@@ -0,0 +1,7 @@
+$NetBSD$
+
+BLAKE2s (bio-mocha_1.16-20221221.tar.gz) = ccd280a4da3ab957af9f74acb9892fe380b37885349e4a967968ed6b0fe68f74
+SHA512 (bio-mocha_1.16-20221221.tar.gz) = 0989db22b56853acd5e6d42cd2585daadd18277bc2b850d83352399d016cf553220be52849acfbc4efc8bb2d51698c848a6f1c5c21a5009f4fb82b599e55aa4a
+Size (bio-mocha_1.16-20221221.tar.gz) = 68625 bytes
+SHA1 (patch-Makefile) = 9b79aadea58ccfd7e393a792c0517f13b2d84818
+SHA1 (patch-configure.ac) = 552e295688c35821183caf2cf454959a2b5510fa
diff --git a/bio-mocha/patches/patch-Makefile b/bio-mocha/patches/patch-Makefile
new file mode 100644
index 0000000000..0b07454bb2
--- /dev/null
+++ b/bio-mocha/patches/patch-Makefile
@@ -0,0 +1,35 @@
+$NetBSD$
+
+--- 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  = ${BSD_INSTALL_SCRIPT}
+ 
+ PROGRAMS = bcftools
+ MISC_SCRIPTS = \
+@@ -142,7 +143,7 @@ print-version:
+ ifdef USE_GPL
+     main.o : EXTRA_CPPFLAGS += -DUSE_GPL
+     OBJS += polysomy.o peakfit.o
+-    GSL_LIBS ?= -lgsl -lcblas
++    GSL_LIBS ?= -lgslcblas
+ endif
+ 
+ print-%:
diff --git a/bio-mocha/patches/patch-configure.ac b/bio-mocha/patches/patch-configure.ac
new file mode 100644
index 0000000000..057f63ee3a
--- /dev/null
+++ b/bio-mocha/patches/patch-configure.ac
@@ -0,0 +1,13 @@
+$NetBSD$
+
+--- 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@localhost], [], [http://www.htslib.org/])
+ AC_PREREQ([2.63])  dnl This version introduced 4-argument AC_CHECK_HEADER
+ AC_CONFIG_SRCDIR([main.c])
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