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samtools0119: Sync to newer revision from private repo

Module Name:	pkgsrc-wip
Committed By:	Jason Bacon <bacon@centosdev.local>
Pushed By:	outpaddling
Date:		Thu Mar 30 20:35:32 2017 -0500
Changeset:	6cd7aee408a580fe64bf392b18f77a816e26b20a

Modified Files:
	samtools0119/Makefile
	samtools0119/PLIST
	samtools0119/buildlink3.mk
	samtools0119/distinfo
	samtools0119/patches/patch-Makefile

Log Message:
samtools0119: Sync to newer revision from private repo

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=6cd7aee408a580fe64bf392b18f77a816e26b20a

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

diffstat:
 samtools0119/Makefile               | 77 ++++++++++++++----------------
 samtools0119/PLIST                  | 94 ++++++++++++++++++-------------------
 samtools0119/buildlink3.mk          | 10 ++--
 samtools0119/distinfo               |  3 +-
 samtools0119/patches/patch-Makefile |  4 +-
 5 files changed, 93 insertions(+), 95 deletions(-)

diffs:
diff --git a/samtools0119/Makefile b/samtools0119/Makefile
index d911107a87..096c0836ed 100644
--- a/samtools0119/Makefile
+++ b/samtools0119/Makefile
@@ -1,68 +1,63 @@
-# $NetBSD: Makefile,v 1.1 2014/09/04 21:46:49 outpaddling Exp $
+# $NetBSD$
 
 ###########################################################
 #               Generated by fbsd2pkg                     #
 ###########################################################
 
-###################################
-# Unconverted FreeBSD port syntax:
-
-# # Created by: Jason Bacon <bacon%sculpin.jbacon.dyndns.org@localhost>
-# # $FreeBSD$
-# # FIXME: Check complete deps
-# # Just for speed: Recent GCC has better optimizer
-# USE_GCC=	yes
-# USES=	shebangfix
-# SHEBANG_FILES=	misc/*.pl
-# # FIXME: Find expl and logl somewhere to avoid reducing precision
-# post-patch:
-# 	${REINPLACE_CMD} -e 's|expl|exp|g' -e 's|logl|log|g' \
-# 		${WRKSRC}/errmod.c ${WRKSRC}/bcftools/prob1.c
-# 	${REINPLACE_CMD} -e "s|/software/bin/python|${LOCALBASE}/bin/python|g" \
-# 		${WRKSRC}/misc/*.py
-# .include <bsd.port.mk>
-
-DISTNAME=	samtools-0.1.19
+DISTNAME=	samtools-${PORTVERSION}
+PKGNAME=	samtools01-${PORTVERSION}
 CATEGORIES=	biology
 MASTER_SITES=	${MASTER_SITE_SOURCEFORGE:=samtools/}
 EXTRACT_SUFX=	.tar.bz2
 
 MAINTAINER=	bacon4000%gmail.com@localhost
 
+PORTVERSION=	0.1.19
+
 COMMENT=	Generic format for storing large nucleotide sequence alignments
 # LICENSE=	
 
-# Pessimistic assumption.  Test and change if possible.
-MAKE_JOBS_SAFE=	no
+USE_TOOLS+=	gmake perl
+USE_ZLIB=	yes
+
+REPLACE_PERL=	misc/export2sam.pl misc/plot-bamcheck
+REPLACE_PYTHON=	misc/varfilter.py
+
+# No REPLACE_LUAJIT available at this time
+SUBST_CLASSES+=		luajit
+SUBST_STAGE.luajit=	post-patch
+SUBST_SED.luajit=	-e 's|/usr/bin/env luajit|${PREFIX}/bin/luajit|g'
+SUBST_FILES.luajit=	misc/r2plot.lua misc/vcfutils.lua
+
+LDFLAGS+=	${COMPILER_RPATH_FLAG}${PREFIX}/lib
 
-# Just assuming C and C++: Adjust this!
-USE_LANGUAGES=	c c++
-USE_TOOLS+=	 gmake perl
+SAMPREFIX=	${PREFIX}/samtools0119
 
 do-build:
-	cd ${WRKSRC} && ${MAKE_PROGRAM}  all-recur razip
+	cd ${WRKSRC} && ${MAKE_PROGRAM} LDFLAGS="${LDFLAGS}" all-recur razip
 
 do-install:
-	${MKDIR} ${DESTDIR}${PREFIX}/bin
-	${INSTALL_PROGRAM} ${WRKSRC}/samtools ${DESTDIR}${PREFIX}/bin
-	${INSTALL_PROGRAM} ${WRKSRC}/razip ${DESTDIR}${PREFIX}/bin
-	${INSTALL_PROGRAM} ${WRKSRC}/bcftools/bcftools ${DESTDIR}${PREFIX}/bin
+	${MKDIR} ${DESTDIR}${SAMPREFIX}/bin
+	${INSTALL_PROGRAM} ${WRKSRC}/samtools ${DESTDIR}${SAMPREFIX}/bin
+	${INSTALL_PROGRAM} ${WRKSRC}/razip ${DESTDIR}${SAMPREFIX}/bin
+	${INSTALL_PROGRAM} ${WRKSRC}/bcftools/bcftools ${DESTDIR}${SAMPREFIX}/bin
 .for f in ace2sam bamcheck maq2sam-long maq2sam-short md5fa md5sum-lite wgsim
-	${INSTALL_PROGRAM} ${WRKSRC}/misc/${f} ${DESTDIR}${PREFIX}/bin
+	${INSTALL_PROGRAM} ${WRKSRC}/misc/${f} ${DESTDIR}${SAMPREFIX}/bin
 .endfor
 	${INSTALL_SCRIPT} ${WRKSRC}/misc/*.pl ${WRKSRC}/misc/plot-bamcheck \
-		${DESTDIR}${PREFIX}/bin
-	${INSTALL_SCRIPT} ${WRKSRC}/misc/*.py ${DESTDIR}${PREFIX}/bin
-	${INSTALL_SCRIPT} ${WRKSRC}/misc/*.lua ${DESTDIR}${PREFIX}/bin
-	${MKDIR} ${DESTDIR}${PREFIX}/lib
-	${INSTALL_DATA} ${WRKSRC}/libbam.a ${DESTDIR}${PREFIX}/lib
-	${MKDIR} ${DESTDIR}${PREFIX}/man/man1
-	${INSTALL_MAN} ${WRKSRC}/samtools.1 ${DESTDIR}${PREFIX}/man/man1
-	${MKDIR} ${DESTDIR}${PREFIX}/include/bam
-	${INSTALL_DATA} ${WRKSRC}/*.h ${DESTDIR}${PREFIX}/include/bam
+		${DESTDIR}${SAMPREFIX}/bin
+	${INSTALL_SCRIPT} ${WRKSRC}/misc/*.py ${DESTDIR}${SAMPREFIX}/bin
+	${INSTALL_SCRIPT} ${WRKSRC}/misc/*.lua ${DESTDIR}${SAMPREFIX}/bin
+	${MKDIR} ${DESTDIR}${SAMPREFIX}/lib
+	${INSTALL_DATA} ${WRKSRC}/libbam.a ${DESTDIR}${SAMPREFIX}/lib
+	${MKDIR} ${DESTDIR}${SAMPREFIX}/man/man1
+	${INSTALL_MAN} ${WRKSRC}/samtools.1 ${DESTDIR}${SAMPREFIX}/man/man1
+	${MKDIR} ${DESTDIR}${SAMPREFIX}/include/bam
+	${INSTALL_DATA} ${WRKSRC}/*.h ${DESTDIR}${SAMPREFIX}/include/bam
 
-# Guess based on FreeBSD USE_PYTHON_RUN=yes
 .include "../../lang/python/application.mk"
+.include "../../lang/lua/application.mk"
+.include "../../lang/LuaJIT2/buildlink3.mk"
 .include "../../devel/zlib/buildlink3.mk"
 .include "../../devel/ncurses/buildlink3.mk"
 .include "../../mk/bsd.pkg.mk"
diff --git a/samtools0119/PLIST b/samtools0119/PLIST
index 949ec2c814..a4434c45b5 100644
--- a/samtools0119/PLIST
+++ b/samtools0119/PLIST
@@ -1,47 +1,47 @@
-@comment $NetBSD: PLIST,v 1.1 2014/09/04 21:46:49 outpaddling Exp $
-bin/ace2sam
-bin/bamcheck
-bin/bcftools
-bin/blast2sam.pl
-bin/bowtie2sam.pl
-bin/export2sam.pl
-bin/interpolate_sam.pl
-bin/maq2sam-long
-bin/maq2sam-short
-bin/md5fa
-bin/md5sum-lite
-bin/novo2sam.pl
-bin/plot-bamcheck
-bin/psl2sam.pl
-bin/r2plot.lua
-bin/razip
-bin/sam2vcf.pl
-bin/samtools
-bin/samtools.pl
-bin/soap2sam.pl
-bin/varfilter.py
-bin/vcfutils.lua
-bin/wgsim
-bin/wgsim_eval.pl
-bin/zoom2sam.pl
-include/bam/bam.h
-include/bam/bam2bcf.h
-include/bam/bam_endian.h
-include/bam/bam_tview.h
-include/bam/bgzf.h
-include/bam/errmod.h
-include/bam/faidx.h
-include/bam/kaln.h
-include/bam/khash.h
-include/bam/klist.h
-include/bam/knetfile.h
-include/bam/kprobaln.h
-include/bam/kseq.h
-include/bam/ksort.h
-include/bam/kstring.h
-include/bam/razf.h
-include/bam/sam.h
-include/bam/sam_header.h
-include/bam/sample.h
-lib/libbam.a
-man/man1/samtools.1
+@comment $NetBSD$
+samtools0119/bin/ace2sam
+samtools0119/bin/bamcheck
+samtools0119/bin/bcftools
+samtools0119/bin/blast2sam.pl
+samtools0119/bin/bowtie2sam.pl
+samtools0119/bin/export2sam.pl
+samtools0119/bin/interpolate_sam.pl
+samtools0119/bin/maq2sam-long
+samtools0119/bin/maq2sam-short
+samtools0119/bin/md5fa
+samtools0119/bin/md5sum-lite
+samtools0119/bin/novo2sam.pl
+samtools0119/bin/plot-bamcheck
+samtools0119/bin/psl2sam.pl
+samtools0119/bin/r2plot.lua
+samtools0119/bin/razip
+samtools0119/bin/sam2vcf.pl
+samtools0119/bin/samtools
+samtools0119/bin/samtools.pl
+samtools0119/bin/soap2sam.pl
+samtools0119/bin/varfilter.py
+samtools0119/bin/vcfutils.lua
+samtools0119/bin/wgsim
+samtools0119/bin/wgsim_eval.pl
+samtools0119/bin/zoom2sam.pl
+samtools0119/include/bam/bam2bcf.h
+samtools0119/include/bam/bam_endian.h
+samtools0119/include/bam/bam.h
+samtools0119/include/bam/bam_tview.h
+samtools0119/include/bam/bgzf.h
+samtools0119/include/bam/errmod.h
+samtools0119/include/bam/faidx.h
+samtools0119/include/bam/kaln.h
+samtools0119/include/bam/khash.h
+samtools0119/include/bam/klist.h
+samtools0119/include/bam/knetfile.h
+samtools0119/include/bam/kprobaln.h
+samtools0119/include/bam/kseq.h
+samtools0119/include/bam/ksort.h
+samtools0119/include/bam/kstring.h
+samtools0119/include/bam/razf.h
+samtools0119/include/bam/sam.h
+samtools0119/include/bam/sam_header.h
+samtools0119/include/bam/sample.h
+samtools0119/lib/libbam.a
+samtools0119/man/man1/samtools.1
diff --git a/samtools0119/buildlink3.mk b/samtools0119/buildlink3.mk
index 2dfded7970..1217a7f6f5 100644
--- a/samtools0119/buildlink3.mk
+++ b/samtools0119/buildlink3.mk
@@ -1,12 +1,12 @@
-# $NetBSD: buildlink3.mk,v 1.2 2014/09/05 15:01:33 outpaddling Exp $
+# $NetBSD$
 
-BUILDLINK_TREE+=	samtools
+BUILDLINK_TREE+=	samtools01
 
 .if !defined(SAMTOOLS_BUILDLINK3_MK)
 SAMTOOLS_BUILDLINK3_MK:=
 
-BUILDLINK_API_DEPENDS.samtools+=	samtools>=0.1.19
-BUILDLINK_PKGSRCDIR.samtools?=	../../wip/samtools
+BUILDLINK_API_DEPENDS.samtools01+=	samtools01>=0.1.19
+BUILDLINK_PKGSRCDIR.samtools01?=	../../uwm-pkgsrc-wip/samtools0119
 .endif	# SAMTOOLS_BUILDLINK3_MK
 
-BUILDLINK_TREE+=	-samtools
+BUILDLINK_TREE+=	-samtools01
diff --git a/samtools0119/distinfo b/samtools0119/distinfo
index 72296b58f1..014e25e5e4 100644
--- a/samtools0119/distinfo
+++ b/samtools0119/distinfo
@@ -1,5 +1,6 @@
-$NetBSD: distinfo,v 1.1 2014/09/04 21:46:49 outpaddling Exp $
+$NetBSD$
 
 SHA1 (samtools-0.1.19.tar.bz2) = ff3f4cf40612d4c2ad26e6fcbfa5f8af84cbe881
 RMD160 (samtools-0.1.19.tar.bz2) = 4e74858d3762f785452d1c9507bd127de9791894
 Size (samtools-0.1.19.tar.bz2) = 514507 bytes
+SHA1 (patch-Makefile) = 9ae9b0f04a3dad5d8f470b6fc132ba20d30e065d
diff --git a/samtools0119/patches/patch-Makefile b/samtools0119/patches/patch-Makefile
index ebe35cec3b..b26807c248 100644
--- a/samtools0119/patches/patch-Makefile
+++ b/samtools0119/patches/patch-Makefile
@@ -1,5 +1,7 @@
 --- Makefile.orig	2013-03-19 02:48:09.000000000 -0500
 +++ Makefile	2014-05-21 19:07:53.000000000 -0500
+--- Makefile.orig	2013-03-19 07:48:09.000000000 +0000
++++ Makefile
 @@ -1,6 +1,7 @@
 -CC=			gcc
 -CFLAGS=		-g -Wall -O2
@@ -11,7 +13,7 @@
  DFLAGS=		-D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1
  KNETFILE_O=	knetfile.o
  LOBJS=		bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o	\
-@@ -41,7 +42,8 @@
+@@ -41,7 +42,8 @@ all:$(PROG)
  lib:libbam.a
  
  libbam.a:$(LOBJS)
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