bowtie2: Upgrade to 2.3.4.2 and clean up

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

Module Name:	pkgsrc-wip
Committed By:	Jason Bacon <bacon%NetBSD.org@localhost>
Pushed By:	outpaddling
Date:		Fri Sep 14 12:07:45 2018 -0500
Changeset:	39e47ee85c230d829877eb7e24bd20d9b925e314

Modified Files:
	bowtie2/Makefile
	bowtie2/PLIST
	bowtie2/distinfo
	bowtie2/patches/patch-Makefile
Removed Files:
	bowtie2/patches/patch-aligner__result.cpp

Log Message:
bowtie2: Upgrade to 2.3.4.2 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=39e47ee85c230d829877eb7e24bd20d9b925e314

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

diffstat:
 bowtie2/Makefile                          | 10 ++++++----
 bowtie2/PLIST                             |  2 +-
 bowtie2/distinfo                          | 11 +++++------
 bowtie2/patches/patch-Makefile            | 29 +++++++++++++++--------------
 bowtie2/patches/patch-aligner__result.cpp | 11 -----------
 5 files changed, 27 insertions(+), 36 deletions(-)

diffs:
diff --git a/bowtie2/Makefile b/bowtie2/Makefile
index a4617aaf68..ea71d0a67d 100644
--- a/bowtie2/Makefile
+++ b/bowtie2/Makefile
@@ -5,11 +5,11 @@
 #              Wed Mar  2 08:06:07 CST 2016               #
 ###########################################################
 
-DISTNAME=	bowtie2-${PORTVERSION}
+DISTNAME=	bowtie2-${PV}
 CATEGORIES=	biology
 MASTER_SITES=	${MASTER_SITE_GITHUB:=BenLangmead/}
 GITHUB_PROJECT=	bowtie2
-GITHUB_TAG=	v${PORTVERSION}
+GITHUB_TAG=	v${PV}
 
 MAINTAINER=	bacon%NetBSD.org@localhost
 HOMEPAGE=	http://bowtie-bio.sourceforge.net/index.shtml
@@ -21,12 +21,12 @@ USE_TOOLS+=	gmake perl:run pax
 REPLACE_PERL=	scripts/*.pl bowtie2
 REPLACE_PYTHON=	bowtie2-build bowtie2-inspect
 
-PORTVERSION=	2.2.7
+PV=		2.3.4.2
 DATADIR=	${PREFIX}/share/bowtie2
 DOCSDIR=	${PREFIX}/share/doc/bowtie2
 EXAMPLESDIR=	${PREFIX}/share/examples/bowtie2
 
-INSTALLATION_DIRS=	share/bowtie2/doc share/bowtie2/examples share/bowtie2/scripts
+INSTALLATION_DIRS=	share/bowtie2/scripts
 
 post-install:
 	${INSTALL_PROGRAM} \
@@ -45,4 +45,6 @@ post-install:
 	cd ${WRKSRC}/doc && pax -rw * ${DESTDIR}${DOCSDIR}
 
 .include "../../lang/python/application.mk"
+.include "../../wip/tbb/buildlink3.mk"
+.include "../../devel/zlib/buildlink3.mk"
 .include "../../mk/bsd.pkg.mk"
diff --git a/bowtie2/PLIST b/bowtie2/PLIST
index bf65f71c37..ad6020b631 100644
--- a/bowtie2/PLIST
+++ b/bowtie2/PLIST
@@ -36,7 +36,6 @@ share/doc/bowtie2/images/sflogo.png
 share/doc/bowtie2/images/university.small.horizontal.white.png
 share/doc/bowtie2/manual.html
 share/doc/bowtie2/release.txt
-share/doc/bowtie2/strip_markdown.pl
 share/doc/bowtie2/style.css
 share/doc/bowtie2/website/faq.shtml
 share/doc/bowtie2/website/faq.ssi
@@ -59,6 +58,7 @@ share/examples/bowtie2/index/lambda_virus.3.bt2
 share/examples/bowtie2/index/lambda_virus.4.bt2
 share/examples/bowtie2/index/lambda_virus.rev.1.bt2
 share/examples/bowtie2/index/lambda_virus.rev.2.bt2
+share/examples/bowtie2/reads/combined_reads.bam
 share/examples/bowtie2/reads/longreads.fq
 share/examples/bowtie2/reads/reads_1.fq
 share/examples/bowtie2/reads/reads_2.fq
diff --git a/bowtie2/distinfo b/bowtie2/distinfo
index e505473cd8..ea43eee4f8 100644
--- a/bowtie2/distinfo
+++ b/bowtie2/distinfo
@@ -1,8 +1,7 @@
 $NetBSD$
 
-SHA1 (bowtie2-2.2.7.tar.gz) = 001784d8a9e9fa06d705b2171af1309c30cf13e9
-RMD160 (bowtie2-2.2.7.tar.gz) = bf7af50df878a98ea84df70f3b1196d9b7ed5948
-SHA512 (bowtie2-2.2.7.tar.gz) = 5dc34d7fc9f31af0a648d2b6ec16e4a45679cf40569fdb69ba2f909aeed0b99b9cd364cbc8cfff8a7d011726fc53e7e7665f466cffaa27dd74ba5acd41b17d8d
-Size (bowtie2-2.2.7.tar.gz) = 5813850 bytes
-SHA1 (patch-Makefile) = de7328796af0997784e6ba37d3770aa57a149076
-SHA1 (patch-aligner__result.cpp) = 1c7ed81fdd4ac2decb27eac898286fc2284ddbae
+SHA1 (bowtie2-2.3.4.2.tar.gz) = 492434eac513cc480902b9ded2f3e70f0887f100
+RMD160 (bowtie2-2.3.4.2.tar.gz) = 582f4518db7a2eeb9178a404747586c2eb5b408b
+SHA512 (bowtie2-2.3.4.2.tar.gz) = eeb12569f3af9b45c702f47cf72e765cb060865365745e29a884b14df4ada33cf7d0b25f9e1c2680c12cbc0ab84d9d14b0910e53f992613508ede00edf14611e
+Size (bowtie2-2.3.4.2.tar.gz) = 10571530 bytes
+SHA1 (patch-Makefile) = 9b229a672d083deeb1be2ba8a42bcf342eb301c9
diff --git a/bowtie2/patches/patch-Makefile b/bowtie2/patches/patch-Makefile
index 79175f2f99..dac0ce9a9e 100644
--- a/bowtie2/patches/patch-Makefile
+++ b/bowtie2/patches/patch-Makefile
@@ -1,24 +1,25 @@
 $NetBSD$
 
---- Makefile.orig	2016-02-11 17:20:57.000000000 +0000
+# Respect env
+--- Makefile.orig	2018-09-14 16:46:59.124139009 +0000
 +++ Makefile
 @@ -21,8 +21,8 @@
  # Makefile for bowtie, bowtie2-build, bowtie2-inspect
  #
  
--prefix = /usr/local
--bindir = $(prefix)/bin
+-prefix := /usr/local
+-bindir := $(prefix)/bin
 +PREFIX ?= /usr/local
-+bindir = $(PREFIX)/bin
++bindir := $(PREFIX)/bin
  
- INC =
- GCC_PREFIX = $(shell dirname `which gcc`)
-@@ -169,7 +169,7 @@ SSE_FLAG=-msse2 
+ LDLIBS := -lz
+ GCC_PREFIX := $(shell dirname `which gcc`)
+@@ -187,7 +187,7 @@ endif
+ SSE_FLAG := -msse2
  
- DEBUG_FLAGS    = -O0 -g3 -m64 $(SSE_FLAG)
- DEBUG_DEFS     = -DCOMPILER_OPTIONS="\"$(DEBUG_FLAGS) $(EXTRA_FLAGS)\""
--RELEASE_FLAGS  = -O3 -m64 $(SSE_FLAG) -funroll-loops -g3
-+RELEASE_FLAGS  = ${CXXFLAGS} $(SSE_FLAG) -funroll-loops
- RELEASE_DEFS   = -DCOMPILER_OPTIONS="\"$(RELEASE_FLAGS) $(EXTRA_FLAGS)\""
- NOASSERT_FLAGS = -DNDEBUG
- FILE_FLAGS     = -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE
+ DEBUG_FLAGS    := -O0 -g3 -m64 $(SSE_FLAG)
+-RELEASE_FLAGS  := -O3 -m64 $(SSE_FLAG) -funroll-loops -g3
++RELEASE_FLAGS  := $(CXXFLAGS)
+ NOASSERT_FLAGS := -DNDEBUG
+ FILE_FLAGS     := -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE
+ DEBUG_DEFS     = -DCOMPILER_OPTIONS="\"$(DEBUG_FLAGS) $(CXXFLAGS)\""
diff --git a/bowtie2/patches/patch-aligner__result.cpp b/bowtie2/patches/patch-aligner__result.cpp
deleted file mode 100644
index 70e515da16..0000000000
--- a/bowtie2/patches/patch-aligner__result.cpp
+++ /dev/null
@@ -1,11 +0,0 @@
---- aligner_result.cpp.orig	2017-02-19 18:40:54.398991000 -0600
-+++ aligner_result.cpp	2017-02-19 18:41:14.093250000 -0600
-@@ -1130,7 +1130,7 @@ bool AlnFlags::printYF(BTString& o, bool
- 	else if(!nfilt_  ) flag = "NS";
- 	else if(!scfilt_ ) flag = "SC";
- 	else if(!qcfilt_ ) flag = "QC";
--	if(flag > 0) {
-+	if(*flag != '\0') {
- 		if(!first) o.append('\t');
- 		o.append("YF:Z:");
- 		o.append(flag);