Remove samtools: Renamed to samtools0119

To: pkgsrc-wip-changes%NetBSD.org@localhost
Subject: Remove samtools: Renamed to samtools0119
From: Jason Bacon <jwbacon%tds.net@localhost>
Date: Sat, 19 Mar 2016 14:13:57 +0000
Module Name:	pkgsrc-wip
Committed By:	Jason Bacon <jwbacon%tds.net@localhost>
Pushed By:	outpaddling
Date:		Sat Mar 19 09:13:57 2016 -0500
Changeset:	aa3d647fc99f4aa0282c8adcf2d4de733c89d26a

Removed Files:
	samtools/DESCR
	samtools/Makefile
	samtools/PLIST
	samtools/buildlink3.mk
	samtools/distinfo
	samtools/patches/patch-Makefile

Log Message:
Remove samtools: Renamed to samtools0119

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=aa3d647fc99f4aa0282c8adcf2d4de733c89d26a

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

diffstat:
 samtools/DESCR                  |  3 --
 samtools/Makefile               | 68 -----------------------------------------
 samtools/PLIST                  | 47 ----------------------------
 samtools/buildlink3.mk          | 12 --------
 samtools/distinfo               |  5 ---
 samtools/patches/patch-Makefile | 23 --------------
 6 files changed, 158 deletions(-)

diffs:
diff --git a/samtools/DESCR b/samtools/DESCR
deleted file mode 100644
index dcebc45..0000000
--- a/samtools/DESCR
+++ /dev/null
@@ -1,3 +0,0 @@
-[description of the port]
-
-WWW: http://port.home.page/
diff --git a/samtools/Makefile b/samtools/Makefile
deleted file mode 100644
index 1b40791..0000000
--- a/samtools/Makefile
+++ /dev/null
@@ -1,68 +0,0 @@
-# $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/samtools/PLIST b/samtools/PLIST
deleted file mode 100644
index 949ec2c..0000000
--- a/samtools/PLIST
+++ /dev/null
@@ -1,47 +0,0 @@
-@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/samtools/buildlink3.mk b/samtools/buildlink3.mk
deleted file mode 100644
index 2dfded7..0000000
--- a/samtools/buildlink3.mk
+++ /dev/null
@@ -1,12 +0,0 @@
-# $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/samtools/distinfo b/samtools/distinfo
deleted file mode 100644
index 72296b5..0000000
--- a/samtools/distinfo
+++ /dev/null
@@ -1,5 +0,0 @@
-$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/samtools/patches/patch-Makefile b/samtools/patches/patch-Makefile
deleted file mode 100644
index ebe35ce..0000000
--- a/samtools/patches/patch-Makefile
+++ /dev/null
@@ -1,23 +0,0 @@
---- 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
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