Import bowtie2-2.2.7 as wip/bowtie2.

To: pkgsrc-wip-changes%NetBSD.org@localhost
Subject: Import bowtie2-2.2.7 as wip/bowtie2.
From: Jason Bacon <bacon4000%gmail.com@localhost>
Date: Wed, 11 May 2016 02:36:00 +0000
Module Name:	pkgsrc-wip
Committed By:	Jason Bacon <bacon4000%gmail.com@localhost>
Pushed By:	outpaddling
Date:		Tue May 10 21:36:00 2016 -0500
Changeset:	0d849f5f8b5b5f986fb5b942f84ca3185d8b330d

Added Files:
	bowtie2/DESCR
	bowtie2/Makefile
	bowtie2/PLIST
	bowtie2/TODO
	bowtie2/distinfo
	bowtie2/files/bowtie2-manual
	bowtie2/patches/patch-Makefile

Log Message:
Import bowtie2-2.2.7 as wip/bowtie2.

Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short
DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp
reads per hour.

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=0d849f5f8b5b5f986fb5b942f84ca3185d8b330d

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

diffstat:
 bowtie2/DESCR                  |  3 ++
 bowtie2/Makefile               | 50 ++++++++++++++++++++++++++++++++
 bowtie2/PLIST                  | 66 ++++++++++++++++++++++++++++++++++++++++++
 bowtie2/TODO                   |  1 +
 bowtie2/distinfo               |  6 ++++
 bowtie2/files/bowtie2-manual   |  4 +++
 bowtie2/patches/patch-Makefile | 24 +++++++++++++++
 7 files changed, 154 insertions(+)

diffs:
diff --git a/bowtie2/DESCR b/bowtie2/DESCR
new file mode 100644
index 0000000..79b1d21
--- /dev/null
+++ b/bowtie2/DESCR
@@ -0,0 +1,3 @@
+Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short
+DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp
+reads per hour.
diff --git a/bowtie2/Makefile b/bowtie2/Makefile
new file mode 100644
index 0000000..14e24e8
--- /dev/null
+++ b/bowtie2/Makefile
@@ -0,0 +1,50 @@
+# $NetBSD$
+#
+###########################################################
+#                  Generated by fbsd2pkg                  #
+#              Wed Mar  2 08:06:07 CST 2016               #
+###########################################################
+
+DISTNAME=	bowtie2-${PORTVERSION}
+CATEGORIES=	biology
+MASTER_SITES=	${MASTER_SITE_GITHUB:=BenLangmead/}
+GITHUB_PROJECT=	bowtie2
+GITHUB_TAG=	v${PORTVERSION}
+
+MAINTAINER=	bacon4000%gmail.com@localhost
+HOMEPAGE=	http://bowtie-bio.sourceforge.net/index.shtml
+COMMENT=	Ultrafast, memory-efficient short read aligner
+LICENSE=	artistic
+
+USE_LANGUAGES=	c c++
+USE_TOOLS+=	gmake perl:run pax
+REPLACE_PERL=	scripts/*.pl bowtie2
+REPLACE_PYTHON=	bowtie2-build bowtie2-inspect
+
+FETCH_USING=	curl
+
+PORTVERSION=	2.2.7
+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
+
+post-install:
+	${INSTALL_PROGRAM} \
+		${WRKSRC}/bowtie2*-s \
+		${WRKSRC}/bowtie2*-l \
+		${DESTDIR}${PREFIX}/bin
+	${INSTALL_SCRIPT} \
+		${WRKSRC}/scripts/*.sh \
+		${WRKSRC}/scripts/*.pl \
+		${DESTDIR}${DATADIR}/scripts
+	${INSTALL_SCRIPT} \
+		${FILESDIR}/bowtie2-manual \
+		${DESTDIR}${PREFIX}/bin
+	cd ${WRKSRC}/example && pax -rw index reads reference \
+		${DESTDIR}${EXAMPLESDIR}
+	cd ${WRKSRC}/doc && pax -rw * ${DESTDIR}${DOCSDIR}
+
+.include "../../lang/python/application.mk"
+.include "../../mk/bsd.pkg.mk"
diff --git a/bowtie2/PLIST b/bowtie2/PLIST
new file mode 100644
index 0000000..585f2bc
--- /dev/null
+++ b/bowtie2/PLIST
@@ -0,0 +1,66 @@
+@comment $NetBSD$
+bin/bowtie2
+bin/bowtie2-align-l
+bin/bowtie2-align-s
+bin/bowtie2-build
+bin/bowtie2-build-l
+bin/bowtie2-build-s
+bin/bowtie2-inspect
+bin/bowtie2-inspect-l
+bin/bowtie2-inspect-s
+bin/bowtie2-manual
+share/bowtie2/scripts/convert_quals.pl
+share/bowtie2/scripts/gen_2b_occ_lookup.pl
+share/bowtie2/scripts/gen_occ_lookup.pl
+share/bowtie2/scripts/gen_solqual_lookup.pl
+share/bowtie2/scripts/infer_fraglen.pl
+share/bowtie2/scripts/make_a_thaliana_tair.sh
+share/bowtie2/scripts/make_b_taurus_UMD3.sh
+share/bowtie2/scripts/make_canFam2.sh
+share/bowtie2/scripts/make_c_elegans.sh
+share/bowtie2/scripts/make_d_melanogaster.sh
+share/bowtie2/scripts/make_e_coli.sh
+share/bowtie2/scripts/make_hg18.sh
+share/bowtie2/scripts/make_hg19.sh
+share/bowtie2/scripts/make_h_sapiens_ncbi36.sh
+share/bowtie2/scripts/make_h_sapiens_ncbi37.sh
+share/bowtie2/scripts/make_mm10.sh
+share/bowtie2/scripts/make_mm9.sh
+share/bowtie2/scripts/make_m_musculus_ncbi37.sh
+share/bowtie2/scripts/make_rn4.sh
+share/bowtie2/scripts/make_s_cerevisiae.sh
+share/doc/bowtie2/images/bowtie_logo.png
+share/doc/bowtie2/images/osi-certified.gif
+share/doc/bowtie2/images/sflogo.png
+share/doc/bowtie2/images/university.small.horizontal.white.png
+share/doc/bowtie2/manual.html
+share/doc/bowtie2/README
+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
+share/doc/bowtie2/website/foot.ssi
+share/doc/bowtie2/website/index.html
+share/doc/bowtie2/website/index.shtml
+share/doc/bowtie2/website/manual.shtml
+share/doc/bowtie2/website/manual.ssi
+share/doc/bowtie2/website/news.shtml
+share/doc/bowtie2/website/old_news.ssi
+share/doc/bowtie2/website/other_tools.shtml
+share/doc/bowtie2/website/push_images.sh
+share/doc/bowtie2/website/push.sh
+share/doc/bowtie2/website/recent_news.ssi
+share/doc/bowtie2/website/rhsidebar.ssi
+share/doc/bowtie2/website/top.ssi
+share/examples/bowtie2/index/lambda_virus.1.bt2
+share/examples/bowtie2/index/lambda_virus.2.bt2
+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/longreads.fq
+share/examples/bowtie2/reads/reads_1.fq
+share/examples/bowtie2/reads/reads_2.fq
+share/examples/bowtie2/reads/simulate.pl
+share/examples/bowtie2/reference/lambda_virus.fa
diff --git a/bowtie2/TODO b/bowtie2/TODO
new file mode 100644
index 0000000..b2e3b56
--- /dev/null
+++ b/bowtie2/TODO
@@ -0,0 +1 @@
+Clean up and test.
diff --git a/bowtie2/distinfo b/bowtie2/distinfo
new file mode 100644
index 0000000..ed09e3e
--- /dev/null
+++ b/bowtie2/distinfo
@@ -0,0 +1,6 @@
+$NetBSD$
+
+SHA1 (bowtie2-2.2.7.tar.gz) = 001784d8a9e9fa06d705b2171af1309c30cf13e9
+RMD160 (bowtie2-2.2.7.tar.gz) = bf7af50df878a98ea84df70f3b1196d9b7ed5948
+Size (bowtie2-2.2.7.tar.gz) = 5813850 bytes
+SHA1 (patch-Makefile) = de7328796af0997784e6ba37d3770aa57a149076
diff --git a/bowtie2/files/bowtie2-manual b/bowtie2/files/bowtie2-manual
new file mode 100644
index 0000000..65f05a0
--- /dev/null
+++ b/bowtie2/files/bowtie2-manual
@@ -0,0 +1,4 @@
+#!/bin/sh
+
+webbrowser file:///usr/local/share/doc/bowtie/manual.html
+
diff --git a/bowtie2/patches/patch-Makefile b/bowtie2/patches/patch-Makefile
new file mode 100644
index 0000000..79175f2
--- /dev/null
+++ b/bowtie2/patches/patch-Makefile
@@ -0,0 +1,24 @@
+$NetBSD$
+
+--- Makefile.orig	2016-02-11 17:20:57.000000000 +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
+ 
+ INC =
+ GCC_PREFIX = $(shell dirname `which gcc`)
+@@ -169,7 +169,7 @@ 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
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