bio-mocha: Fix build, generare plist

[Jason W. Bacon <bacon%NetBSD.org@localhost>]

Module Name:	pkgsrc-wip
Committed By:	Jason W. Bacon <bacon%NetBSD.org@localhost>
Pushed By:	outpaddling
Date:		Sun Sep 29 07:24:31 2024 -0500
Changeset:	e56ec7b21e66d9c6cf33d2c5f1039af644e5b515

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

Log Message:
bio-mocha: Fix build, generare plist

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=e56ec7b21e66d9c6cf33d2c5f1039af644e5b515

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

diffstat:
 bio-mocha/Makefile                   | 22 ++++++++++++++--------
 bio-mocha/PLIST                      |  6 ++++++
 bio-mocha/distinfo                   |  6 ++++--
 bio-mocha/patches/patch-Makefile     | 26 +++++++-------------------
 bio-mocha/patches/patch-configure.ac | 13 -------------
 5 files changed, 31 insertions(+), 42 deletions(-)

diffs:
diff --git a/bio-mocha/Makefile b/bio-mocha/Makefile
index f91c0b08f0..1d8805af41 100644
--- a/bio-mocha/Makefile
+++ b/bio-mocha/Makefile
@@ -5,6 +5,7 @@ CATEGORIES=	biology
 MASTER_SITES=	https://software.broadinstitute.org/software/mocha/
 MASTER_SITES+=	${MASTER_SITE_GITHUB:=samtools/}
 DISTFILES+=	bio-mocha_1.20-20240505.tar.gz
+DISTFILES+=	bcftools-1.21.tar.bz2
 GITHUB_PROJECT=	bcftools
 GITHUB_TAG=	1.21
 
@@ -13,10 +14,15 @@ 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
+REPLACE_INTERPRETER+=   R
+REPLACE.R.old=          /usr/bin/env Rscript
+REPLACE.R.new=          ${PREFIX}/bin/Rscript
+REPLACE_FILES.R=        MoCha/*.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:../../shells/bash
 DEPENDS+=	bcftools>=1.16:../../biology/bcftools
@@ -25,13 +31,15 @@ USE_TOOLS+=	autoconf automake autoreconf gmake perl pax
 GNU_CONFIGURE=	yes
 REPLACE_PERL=	misc/* test/test.pl
 
+WRKSRC=		${WRKDIR}/bcftools-${GITHUB_TAG}
+
 DATADIR=		${PREFIX}/share/bio-mocha
 INSTALLATION_DIRS=	libexec/bcftools
 
 post-extract:
-	@${MV} ${WRKDIR}/*.c ${WRKDIR}/*.h ${WRKSRC}/plugins
+	@${CP} ${WRKDIR}/*.c ${WRKDIR}/*.h ${WRKSRC}/plugins
 	@${MKDIR} ${WRKSRC}/MoCha
-	@${MV} ${WRKDIR}/*.R ${WRKSRC}/MoCha
+	@${CP} ${WRKDIR}/*.R ${WRKSRC}/MoCha
 
 pre-configure:
 	cd ${WRKSRC} && autoreconf -if
@@ -44,8 +52,6 @@ do-install:
 		${DESTDIR}${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"
diff --git a/bio-mocha/PLIST b/bio-mocha/PLIST
index 48d96a5493..71f59b5d08 100644
--- a/bio-mocha/PLIST
+++ b/bio-mocha/PLIST
@@ -1 +1,7 @@
 @comment $NetBSD$
+libexec/bcftools/extendFMT.so
+libexec/bcftools/mocha.so
+libexec/bcftools/mochatools.so
+share/bio-mocha/mocha_plot.R
+share/bio-mocha/pileup_plot.R
+share/bio-mocha/summary_plot.R
diff --git a/bio-mocha/distinfo b/bio-mocha/distinfo
index ebfd65b197..7e5997c007 100644
--- a/bio-mocha/distinfo
+++ b/bio-mocha/distinfo
@@ -1,7 +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 (bio-mocha_1.20-20240505.tar.gz) = 318b02176dfff73b88da45f7bd754921027307696ce4a124a934090539529efe
 SHA512 (bio-mocha_1.20-20240505.tar.gz) = 1aeeffb2383f7e6d223129ca58ca55823444275b0d0d759f9c8842dc5f3f4ff493af106c68bdc2c43840098691a357a53e18af4914f78584aad34edb58851991
 Size (bio-mocha_1.20-20240505.tar.gz) = 66752 bytes
-SHA1 (patch-Makefile) = 9b79aadea58ccfd7e393a792c0517f13b2d84818
-SHA1 (patch-configure.ac) = 552e295688c35821183caf2cf454959a2b5510fa
+SHA1 (patch-Makefile) = 9dfe7b5dcf77deac6d248d7612440780ec8a3731
diff --git a/bio-mocha/patches/patch-Makefile b/bio-mocha/patches/patch-Makefile
index 0b07454bb2..c1cae450ea 100644
--- a/bio-mocha/patches/patch-Makefile
+++ b/bio-mocha/patches/patch-Makefile
@@ -1,21 +1,18 @@
-$NetBSD$
+$NetBSD: patch-Makefile,v 1.4 2022/02/26 23:14:33 bacon Exp $
 
---- Makefile.orig	2021-03-17 09:16:18 UTC
+# Respect pkgsrc env
+
+--- Makefile.orig	2021-03-19 17:42:33.842623449 +0000
 +++ Makefile
-@@ -58,13 +58,14 @@ pluginpath  = $(plugindir)
- # Installation location for $(MISC_PROGRAMS) and $(MISC_SCRIPTS)
- misc_bindir = $(bindir)
+@@ -60,11 +60,11 @@ misc_bindir = $(bindir)
  
--MKDIR_P = mkdir -p
--INSTALL = install -p
+ 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}
@@ -24,12 +21,3 @@ $NetBSD$
  
  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
deleted file mode 100644
index 057f63ee3a..0000000000
--- a/bio-mocha/patches/patch-configure.ac
+++ /dev/null
@@ -1,13 +0,0 @@
-$NetBSD$
-
---- 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])