bowtie: Upgrade to 1.1.2 and clean up

To: pkgsrc-wip-changes%NetBSD.org@localhost
Subject: bowtie: Upgrade to 1.1.2 and clean up
From: Jason Bacon <bacon%NetBSD.org@localhost>
Date: Fri, 14 Sep 2018 16:43:27 +0000
Module Name:	pkgsrc-wip
Committed By:	Jason Bacon <bacon%NetBSD.org@localhost>
Pushed By:	outpaddling
Date:		Fri Sep 14 11:43:27 2018 -0500
Changeset:	f1c68fe9f9a08d7bc0c22d3955f738e421ea6de7

Modified Files:
	bowtie/Makefile
	bowtie/PLIST
	bowtie/distinfo
	bowtie/patches/patch-Makefile
Added Files:
	bowtie/patches/patch-scripts_test_random__bowtie__tests.sh
Removed Files:
	bowtie/patches/patch-scripts_random__bowtie__tests.sh

Log Message:
bowtie: Upgrade to 1.1.2 and clean up

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=f1c68fe9f9a08d7bc0c22d3955f738e421ea6de7

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

diffstat:
 bowtie/Makefile                                    | 24 +++++--------
 bowtie/PLIST                                       | 40 +++++++++++++++++++---
 bowtie/distinfo                                    | 12 +++----
 bowtie/patches/patch-Makefile                      | 34 +++---------------
 .../patches/patch-scripts_random__bowtie__tests.sh | 13 -------
 .../patch-scripts_test_random__bowtie__tests.sh    | 20 +++++++++++
 6 files changed, 76 insertions(+), 67 deletions(-)

diffs:
diff --git a/bowtie/Makefile b/bowtie/Makefile
index 74c69da469..3afdbe0f04 100644
--- a/bowtie/Makefile
+++ b/bowtie/Makefile
@@ -10,9 +10,8 @@
 # .if ${ARCH} == i386
 # MAKE_ENV+=	POPCNT_CAPABILITY=0
 # .endif
-# .include <bsd.port.post.mk>
 
-DISTNAME=	bowtie-1.0.1
+DISTNAME=	bowtie-1.1.2
 CATEGORIES=	biology
 MASTER_SITES=	${MASTER_SITE_GITHUB:=BenLangmead/}
 GITHUB_TAG=	v${PKGVERSION_NOREV}
@@ -21,38 +20,33 @@ MAINTAINER=	bacon%NetBSD.org@localhost
 COMMENT=	Ultrafast, memory-efficient short read aligner
 LICENSE=	artistic
 
-# 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:run pax
+REPLACE_PYTHON=	bowtie bowtie-build bowtie-inspect
 REPLACE_PERL=	scripts/*.pl
 
-# Adapt REINPLACE commands to SUBST:
 SUBST_CLASSES+=		lock_guard
 SUBST_STAGE.lock_guard=	post-patch
 SUBST_FILES.lock_guard=	hit.h log.h
 SUBST_SED.lock_guard=	-e 's|lock_guard<MUTEX_T>|tthread::lock_guard<MUTEX_T>|g'
 
 DATADIR=	${PREFIX}/share/bowtie
+DOCSDIR=	${PREFIX}/share/docs/bowtie
 
-AUTO_MKDIRS=	yes
+INSTALLATION_DIRS=	bin share/bowtie share/docs/bowtie
 
 do-install:
-	${INSTALL_PROGRAM} \
+	${INSTALL_PROGRAM} ${WRKSRC}/bowtie-*-[ls] ${DESTDIR}${PREFIX}/bin
+	${INSTALL_SCRIPT} \
 		${WRKSRC}/bowtie \
 		${WRKSRC}/bowtie-build \
 		${WRKSRC}/bowtie-inspect \
-		${DESTDIR}${PREFIX}/bin
-	${INSTALL_SCRIPT} \
 		${WRKSRC}/scripts/*.sh \
 		${WRKSRC}/scripts/*.pl \
 		${DESTDIR}${PREFIX}/bin
 	${MKDIR} ${DESTDIR}${DATADIR}
-	cd ${WRKSRC} && ${PAX} -wr genomes indexes reads \
-		${DESTDIR}${DATADIR}
-	cd ${WRKSRC}/doc && ${PAX} -wr * \
-		${DESTDIR}${DOCSDIR}
+	(cd ${WRKSRC} && ${PAX} -wr genomes indexes reads ${DESTDIR}${DATADIR})
+	(cd ${WRKSRC}/doc && ${PAX} -wr * ${DESTDIR}${DOCSDIR})
 
+.include "../../lang/python/application.mk"
 .include "../../mk/bsd.pkg.mk"
diff --git a/bowtie/PLIST b/bowtie/PLIST
index b9174b93b2..26a0cc5a02 100644
--- a/bowtie/PLIST
+++ b/bowtie/PLIST
@@ -1,8 +1,14 @@
-@comment $NetBSD: PLIST,v 1.2 2015/01/28 16:21:48 outpaddling Exp $
+@comment $NetBSD$
 bin/best_verify.pl
 bin/bowtie
+bin/bowtie-align-l
+bin/bowtie-align-s
 bin/bowtie-build
+bin/bowtie-build-l
+bin/bowtie-build-s
 bin/bowtie-inspect
+bin/bowtie-inspect-l
+bin/bowtie-inspect-s
 bin/bs_mapability.pl
 bin/build_test.sh
 bin/colorize_fasta.pl
@@ -32,9 +38,6 @@ bin/make_rn4.sh
 bin/make_s_cerevisiae.sh
 bin/mapability.pl
 bin/pe_verify.pl
-bin/random_bowtie_tests.pl
-bin/random_bowtie_tests.sh
-bin/random_bowtie_tests_p.sh
 bin/reconcile_alignments.pl
 bin/reconcile_alignments_pe.pl
 share/bowtie/genomes/.cvsignore
@@ -56,3 +59,32 @@ share/bowtie/reads/e_coli_1000_1.fa
 share/bowtie/reads/e_coli_1000_1.fq
 share/bowtie/reads/e_coli_1000_2.fa
 share/bowtie/reads/e_coli_1000_2.fq
+share/docs/bowtie/README
+share/docs/bowtie/manual.html
+share/docs/bowtie/release.txt
+share/docs/bowtie/strip_markdown.pl
+share/docs/bowtie/style.css
+share/docs/bowtie/website/css/style.css
+share/docs/bowtie/website/foot.ssi
+share/docs/bowtie/website/images/bowtie_logo.png
+share/docs/bowtie/website/images/osi-certified.gif
+share/docs/bowtie/website/images/sflogo.png
+share/docs/bowtie/website/images/university.small.horizontal.white.png
+share/docs/bowtie/website/index.html
+share/docs/bowtie/website/index.shtml
+share/docs/bowtie/website/latest-version.txt
+share/docs/bowtie/website/manual.html
+share/docs/bowtie/website/manual.shtml
+share/docs/bowtie/website/manual.ssi
+share/docs/bowtie/website/md5s.shtml
+share/docs/bowtie/website/md5s.ssi
+share/docs/bowtie/website/news.shtml
+share/docs/bowtie/website/old_news.ssi
+share/docs/bowtie/website/other_tools.shtml
+share/docs/bowtie/website/other_tools.ssi
+share/docs/bowtie/website/push_langmead.sh
+share/docs/bowtie/website/recent_news.ssi
+share/docs/bowtie/website/rhsidebar.ssi
+share/docs/bowtie/website/top.ssi
+share/docs/bowtie/website/tutorial.html
+share/docs/bowtie/website/tutorial.shtml
diff --git a/bowtie/distinfo b/bowtie/distinfo
index 6a324b0215..ad757d302f 100644
--- a/bowtie/distinfo
+++ b/bowtie/distinfo
@@ -1,8 +1,8 @@
 $NetBSD$
 
-SHA1 (bowtie-1.0.1.tar.gz) = c816271844b063f5440bcb7cb3dab09fd1613f00
-RMD160 (bowtie-1.0.1.tar.gz) = 85fc6253a3386b24894056db3b29ec5c65595c94
-SHA512 (bowtie-1.0.1.tar.gz) = 98f7d6075b696765b73452a07b84a24d89e4050763abaa1fa7336fc8a20337636006653967c281d6082649c1428ebe615ef355e16dcbe22e4b5ad7c8f5960de7
-Size (bowtie-1.0.1.tar.gz) = 7818119 bytes
-SHA1 (patch-Makefile) = 384bf98cf8312aaa7af2bb8d059f86684a8b146f
-SHA1 (patch-scripts_random__bowtie__tests.sh) = 999abd0f6f092b24957c343a4bdac9d3d7cc4003
+SHA1 (bowtie-1.1.2.tar.gz) = 4ab22146626a1661d690afed3daa7a3b59bb8c62
+RMD160 (bowtie-1.1.2.tar.gz) = 723f8cc273c6db3031c2dc4b8bd7fab70fbd78f2
+SHA512 (bowtie-1.1.2.tar.gz) = 81f8df4b292b70d57a545b3d485d166b92cdd68be144f7fe60215de1175a85c815c584559f647c097fc03eccfa24eff91c816a6db8b11ea162287a3a8e500701
+Size (bowtie-1.1.2.tar.gz) = 7831346 bytes
+SHA1 (patch-Makefile) = f38c82018fc458511bf40bb6baf0e6b1bd6c7faf
+SHA1 (patch-scripts_test_random__bowtie__tests.sh) = aaa2911d4b5e15082eb0857f00c8f53c4508688c
diff --git a/bowtie/patches/patch-Makefile b/bowtie/patches/patch-Makefile
index 4da2fda8a8..a754534e7f 100644
--- a/bowtie/patches/patch-Makefile
+++ b/bowtie/patches/patch-Makefile
@@ -1,42 +1,18 @@
-$NetBSD: patch-Makefile,v 1.2 2015/01/28 16:21:48 outpaddling Exp $
+$NetBSD$
 
-# Respect build env
-
---- Makefile.orig	2014-03-20 13:52:20.000000000 -0500
-+++ Makefile	2014-05-22 08:16:29.000000000 -0500
-@@ -5,9 +5,13 @@
+# Respect env
+--- Makefile.orig	2018-09-14 16:04:25.976840223 +0000
++++ Makefile
+@@ -8,9 +8,9 @@ bindir = $(prefix)/bin
  SEQAN_DIR = SeqAn-1.1
  SEQAN_INC = -I $(SEQAN_DIR)
  INC = $(SEQAN_INC) -I third_party
 -CPP = g++
 -CXX = $(CPP)
 -CC = gcc
-+
-+# Use ?= to allow environment CPP, CC, CXX to take precedence.  This avoids
-+# the need to modify the Makefile on different platforms.  Package managers
-+# such as FreeBSD ports, MacPorts, etc. set these variables automatically.
 +CPP ?= g++
 +CXX ?= $(CPP)
 +CC ?= gcc
  HEADERS = $(wildcard *.h)
  BOWTIE_MM = 1
  BOWTIE_SHARED_MEM = 1
-@@ -124,13 +128,16 @@
-     EXTRA_FLAGS += -Wl,-macosx_version_min,10.6
- endif
- 
-+# This is unnecessary on most platforms.  The compiler will default
-+# to the native architecture.  Could this be wrapped in a check for
-+# just the platforms that require it?
- # Convert BITS=?? to a -m flag
- BITS_FLAG =
- ifeq (32,$(BITS))
--    BITS_FLAG = -m32
-+    #BITS_FLAG = -m32
- endif
- ifeq (64,$(BITS))
--    BITS_FLAG = -m64
-+    #BITS_FLAG = -m64
- endif
- 
- DEBUG_FLAGS = -O0 -g3 $(BITS_FLAG)
diff --git a/bowtie/patches/patch-scripts_random__bowtie__tests.sh b/bowtie/patches/patch-scripts_random__bowtie__tests.sh
deleted file mode 100644
index e14b068701..0000000000
--- a/bowtie/patches/patch-scripts_random__bowtie__tests.sh
+++ /dev/null
@@ -1,13 +0,0 @@
-$NetBSD: patch-scripts_random__bowtie__tests.sh,v 1.1 2013/09/01 15:56:45 asau Exp $
-
---- scripts/random_bowtie_tests.sh.orig	2013-04-18 19:33:39.000000000 +0000
-+++ scripts/random_bowtie_tests.sh
-@@ -7,7 +7,7 @@ else
- 	shift
- fi
- 
--if [ "$1" == "-c" ] ; then
-+if [ "$1" = "-c" ] ; then
- 	rm -f bowtie bowtie-debug bowtie-build-debug bowtie-inspect-debug
- 	shift
- fi
diff --git a/bowtie/patches/patch-scripts_test_random__bowtie__tests.sh b/bowtie/patches/patch-scripts_test_random__bowtie__tests.sh
new file mode 100644
index 0000000000..61dd92127d
--- /dev/null
+++ b/bowtie/patches/patch-scripts_test_random__bowtie__tests.sh
@@ -0,0 +1,20 @@
+$NetBSD$
+
+# Remove bashisms
+--- scripts/test/random_bowtie_tests.sh.orig	2018-09-14 16:08:02.613191531 +0000
++++ scripts/test/random_bowtie_tests.sh
+@@ -1,4 +1,4 @@
+-#!/bin/bash
++#!/bin/sh
+ 
+ PREFIX=${0%/*}
+ 
+@@ -9,7 +9,7 @@ else
+ 	shift
+ fi
+ 
+-if [ "$1" == "-c" ] ; then
++if [ "$1" = "-c" ] ; then
+ 	make clean
+ 	shift
+ fi
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