Add samtools0119

To: pkgsrc-wip-changes%NetBSD.org@localhost
Subject: Add samtools0119
From: Jason Bacon <jwbacon%tds.net@localhost>
Date: Sat, 19 Mar 2016 14:03:06 +0000
Module Name:	pkgsrc-wip
Committed By:	Jason Bacon <jwbacon%tds.net@localhost>
Pushed By:	outpaddling
Date:		Sat Mar 19 09:03:06 2016 -0500
Changeset:	dbdb0fd331d4cf8f29b2eaec11778b6a4d3da3a4

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

Log Message:
Add samtools0119

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=dbdb0fd331d4cf8f29b2eaec11778b6a4d3da3a4

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

diffstat:
 samtools0119/DESCR                  |  3 ++
 samtools0119/Makefile               | 68 +++++++++++++++++++++++++++++++++++++
 samtools0119/PLIST                  | 47 +++++++++++++++++++++++++
 samtools0119/buildlink3.mk          | 12 +++++++
 samtools0119/distinfo               |  5 +++
 samtools0119/patches/patch-Makefile | 23 +++++++++++++
 webbrowser/Makefile                 |  1 +
 webbrowser/distinfo                 |  8 ++---
 8 files changed, 163 insertions(+), 4 deletions(-)

diffs:
diff --git a/samtools0119/DESCR b/samtools0119/DESCR
new file mode 100644
index 0000000..dcebc45
--- /dev/null
+++ b/samtools0119/DESCR
@@ -0,0 +1,3 @@
+[description of the port]
+
+WWW: http://port.home.page/
diff --git a/samtools0119/Makefile b/samtools0119/Makefile
new file mode 100644
index 0000000..1b40791
--- /dev/null
+++ b/samtools0119/Makefile
@@ -0,0 +1,68 @@
+# $NetBSD: Makefile,v 1.1 2014/09/04 21:46:49 outpaddling Exp $
+
+###########################################################
+#               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
+CATEGORIES=	biology
+MASTER_SITES=	${MASTER_SITE_SOURCEFORGE:=samtools/}
+EXTRACT_SUFX=	.tar.bz2
+
+MAINTAINER=	jwbacon%tds.net@localhost
+
+COMMENT=	Generic format for storing large nucleotide sequence alignments
+# LICENSE=	
+
+# Pessimistic assumption.  Test and change if possible.
+MAKE_JOBS_SAFE=	no
+
+# Just assuming C and C++: Adjust this!
+USE_LANGUAGES=	c c++
+USE_TOOLS+=	 gmake perl
+
+do-build:
+	cd ${WRKSRC} && ${MAKE_PROGRAM}  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
+.for f in ace2sam bamcheck maq2sam-long maq2sam-short md5fa md5sum-lite wgsim
+	${INSTALL_PROGRAM} ${WRKSRC}/misc/${f} ${DESTDIR}${PREFIX}/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
+
+# Guess based on FreeBSD USE_PYTHON_RUN=yes
+.include "../../lang/python/application.mk"
+.include "../../devel/zlib/buildlink3.mk"
+.include "../../devel/ncurses/buildlink3.mk"
+.include "../../mk/bsd.pkg.mk"
diff --git a/samtools0119/PLIST b/samtools0119/PLIST
new file mode 100644
index 0000000..949ec2c
--- /dev/null
+++ b/samtools0119/PLIST
@@ -0,0 +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
diff --git a/samtools0119/buildlink3.mk b/samtools0119/buildlink3.mk
new file mode 100644
index 0000000..2dfded7
--- /dev/null
+++ b/samtools0119/buildlink3.mk
@@ -0,0 +1,12 @@
+# $NetBSD: buildlink3.mk,v 1.2 2014/09/05 15:01:33 outpaddling Exp $
+
+BUILDLINK_TREE+=	samtools
+
+.if !defined(SAMTOOLS_BUILDLINK3_MK)
+SAMTOOLS_BUILDLINK3_MK:=
+
+BUILDLINK_API_DEPENDS.samtools+=	samtools>=0.1.19
+BUILDLINK_PKGSRCDIR.samtools?=	../../wip/samtools
+.endif	# SAMTOOLS_BUILDLINK3_MK
+
+BUILDLINK_TREE+=	-samtools
diff --git a/samtools0119/distinfo b/samtools0119/distinfo
new file mode 100644
index 0000000..72296b5
--- /dev/null
+++ b/samtools0119/distinfo
@@ -0,0 +1,5 @@
+$NetBSD: distinfo,v 1.1 2014/09/04 21:46:49 outpaddling Exp $
+
+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
diff --git a/samtools0119/patches/patch-Makefile b/samtools0119/patches/patch-Makefile
new file mode 100644
index 0000000..ebe35ce
--- /dev/null
+++ b/samtools0119/patches/patch-Makefile
@@ -0,0 +1,23 @@
+--- Makefile.orig	2013-03-19 02:48:09.000000000 -0500
++++ Makefile	2014-05-21 19:07:53.000000000 -0500
+@@ -1,6 +1,7 @@
+-CC=			gcc
+-CFLAGS=		-g -Wall -O2
+-#LDFLAGS=		-Wl,-rpath,\$$ORIGIN/../lib
++CC?=		gcc
++CFLAGS?=	-g -Wall -O2
++RANLIB?=	/usr/bin/ranlib
++#LDFLAGS=	-Wl,-rpath,\$$ORIGIN/../lib
+ 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 @@
+ lib:libbam.a
+ 
+ libbam.a:$(LOBJS)
+-		$(AR) -csru $@ $(LOBJS)
++		$(AR) cr $@ $(LOBJS)
++		$(RANLIB) $@
+ 
+ samtools:lib-recur $(AOBJS)
+ 		$(CC) $(CFLAGS) -o $@ $(AOBJS) $(LDFLAGS) libbam.a -Lbcftools -lbcf $(LIBPATH) $(LIBCURSES) -lm -lz -lpthread
diff --git a/webbrowser/Makefile b/webbrowser/Makefile
index bb3fc56..30757b0 100644
--- a/webbrowser/Makefile
+++ b/webbrowser/Makefile
@@ -4,6 +4,7 @@
 DISTNAME=	webbrowser-0.3
 CATEGORIES=	www
 MASTER_SITES=	http://acadix.biz/Ports/distfiles/
+EXTRACT_SUFX=	.tar.xz
 
 MAINTAINER=	jwbacon%tds.net@localhost
 HOMEPAGE=	http://acadix.biz/Ports/distfiles/
diff --git a/webbrowser/distinfo b/webbrowser/distinfo
index 040de9e..6ad6e60 100644
--- a/webbrowser/distinfo
+++ b/webbrowser/distinfo
@@ -1,5 +1,5 @@
-$NetBSD: distinfo,v 1.1 2013/08/14 01:13:50 outpaddling Exp $
+$NetBSD$
 
-SHA1 (webbrowser-0.3.tar.gz) = 822496a2eab4beefef30c955731754b2660c2d93
-RMD160 (webbrowser-0.3.tar.gz) = 6215cdfd5985c5ebbb6ceb34402e73fb23e98b36
-Size (webbrowser-0.3.tar.gz) = 1916 bytes
+SHA1 (webbrowser-0.3.tar.xz) = c3101bc2afc2a9ef7cb29a7f8d47a17e461ec616
+RMD160 (webbrowser-0.3.tar.xz) = 28fd4efebcc1dbdc8cdb35e2c9e4ca605857484d
+Size (webbrowser-0.3.tar.xz) = 1656 bytes
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