New port: biology/bowtie.

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.

WWW: http://bowtie-bio.sourceforge.net/index.shtml

PR:		206939
Submitted by:	Jason Bacon <bacon4000@gmail.com>

6 files changed, 194 insertions, 0 deletions

diff --git a/biology/Makefile b/biology/Makefile
index c2c7b80c4489..25eb27f25ddd 100644
--- a/biology/Makefile
+++ b/biology/Makefile
@@ -12,6 +12,7 @@
     SUBDIR += biococoa
     SUBDIR += biojava
     SUBDIR += blat
+    SUBDIR += bowtie
     SUBDIR += bwa
     SUBDIR += cd-hit
     SUBDIR += cdbfasta
diff --git a/biology/bowtie/Makefile b/biology/bowtie/Makefile
new file mode 100644
index 000000000000..5f3e404bf3ac
--- /dev/null
+++ b/biology/bowtie/Makefile
@@ -0,0 +1,45 @@
+# Created by: Jason Bacon <bacon4000@gmail.com>
+# $FreeBSD$
+
+PORTNAME=		bowtie
+PORTVERSION=		1.1.2
+DISTVERSIONPREFIX=	v
+CATEGORIES=		biology
+
+MAINTAINER=	bacon4000@gmail.com
+COMMENT=	Ultrafast, memory-efficient short read aligner
+
+LICENSE=	ART10
+
+# May also work on other 64-bit platforms, but untested
+ONLY_FOR_ARCHS=	amd64
+# FIXME: bowtie-align intermittently dumps core when compiled with clang
+# GCC 4.2 does not provide good performance
+USE_GCC=	yes
+USES=		gmake perl5 shebangfix
+USE_PERL5=	run
+SHEBANG_FILES=	scripts/*.pl
+
+USE_GITHUB=	yes
+GH_ACCOUNT=	BenLangmead
+
+post-install:
+	${MKDIR} ${STAGEDIR}${DATADIR}/scripts
+	${INSTALL_SCRIPT} \
+		${WRKSRC}/bowtie \
+		${WRKSRC}/bowtie-build \
+		${WRKSRC}/bowtie-inspect \
+		${STAGEDIR}${PREFIX}/bin
+	${INSTALL_SCRIPT} \
+		${WRKSRC}/scripts/*.sh \
+		${WRKSRC}/scripts/*.pl \
+		${STAGEDIR}${DATADIR}/scripts
+	cd ${WRKSRC} && ${COPYTREE_SHARE} \
+		'genomes indexes reads' \
+		${STAGEDIR}${DATADIR}
+	cd ${WRKSRC}/doc && ${COPYTREE_SHARE} \
+		\* \
+		${STAGEDIR}${DOCSDIR}
+	${STRIP_CMD} ${STAGEDIR}${PREFIX}/bin/*-[sl]
+
+.include <bsd.port.mk>
diff --git a/biology/bowtie/distinfo b/biology/bowtie/distinfo
new file mode 100644
index 000000000000..ffacca889d6c
--- /dev/null
+++ b/biology/bowtie/distinfo
@@ -0,0 +1,2 @@
+SHA256 (BenLangmead-bowtie-v1.1.2_GH0.tar.gz) = 717145f12d599e9b3672981f5444fbbdb8e02bfde2a80eba577e28baa4125ba7
+SIZE (BenLangmead-bowtie-v1.1.2_GH0.tar.gz) = 7831346
diff --git a/biology/bowtie/files/patch-Makefile b/biology/bowtie/files/patch-Makefile
new file mode 100644
index 000000000000..8f3a35cf59f5
--- /dev/null
+++ b/biology/bowtie/files/patch-Makefile
@@ -0,0 +1,52 @@
+--- Makefile.orig	2015-06-23 16:32:51 UTC
++++ Makefile
+@@ -8,9 +8,13 @@ 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 = $(wildcard *.h)
+ BOWTIE_MM = 1
+ BOWTIE_SHARED_MEM = 1
+@@ -90,10 +94,10 @@ PREFETCH_LOCALITY = 2
+ PREF_DEF = -DPREFETCH_LOCALITY=$(PREFETCH_LOCALITY)
+ 
+ ifeq (1,$(WITH_TBB))
+-	LIBS = $(PTHREAD_LIB) -ltbb -ltbbmalloc_proxy
++	LIBS = ${LDFLAGS} $(PTHREAD_LIB) -ltbb -ltbbmalloc_proxy
+ 	EXTRA_FLAGS += -DWITH_TBB
+ else
+-	LIBS = $(PTHREAD_LIB)
++	LIBS = ${LDFLAGS} $(PTHREAD_LIB)
+ endif
+ 
+ SEARCH_LIBS = 
+@@ -123,7 +127,7 @@ SEARCH_FRAGMENTS = $(wildcard search_*_p
+ VERSION = $(shell cat VERSION)
+ 
+ BITS=32
+-ifeq (x86_64,$(shell uname -m))
++ifeq (amd64,$(shell uname -m))
+ 	BITS=64
+ endif
+ # msys will always be 32 bit so look at the cpu arch instead.
+@@ -143,8 +147,8 @@ ifeq (32,$(BITS))
+     $(error bowtie2 compilation requires a 64-bit platform )
+ endif
+ 
+-DEBUG_FLAGS = -O0 -g3 -m64
+-RELEASE_FLAGS = -O3 -m64
++DEBUG_FLAGS = -O0 -g3
++RELEASE_FLAGS = -O
+ NOASSERT_FLAGS = -DNDEBUG
+ FILE_FLAGS = -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE
+ 
diff --git a/biology/bowtie/pkg-descr b/biology/bowtie/pkg-descr
new file mode 100644
index 000000000000..03d1a2c4269f
--- /dev/null
+++ b/biology/bowtie/pkg-descr
@@ -0,0 +1,5 @@
+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.
+
+WWW: http://bowtie-bio.sourceforge.net/index.shtml
diff --git a/biology/bowtie/pkg-plist b/biology/bowtie/pkg-plist
new file mode 100644
index 000000000000..e0e8c2056459
--- /dev/null
+++ b/biology/bowtie/pkg-plist
@@ -0,0 +1,89 @@
+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
+%%DATADIR%%/genomes/.cvsignore
+%%DATADIR%%/genomes/NC_008253.fna
+%%DATADIR%%/indexes/e_coli.1.ebwt
+%%DATADIR%%/indexes/e_coli.2.ebwt
+%%DATADIR%%/indexes/e_coli.3.ebwt
+%%DATADIR%%/indexes/e_coli.4.ebwt
+%%DATADIR%%/indexes/e_coli.README
+%%DATADIR%%/indexes/e_coli.rev.1.ebwt
+%%DATADIR%%/indexes/e_coli.rev.2.ebwt
+%%DATADIR%%/reads/e_coli_1000.fa
+%%DATADIR%%/reads/e_coli_1000.fq
+%%DATADIR%%/reads/e_coli_1000.raw
+%%DATADIR%%/reads/e_coli_10000snp.csfasta
+%%DATADIR%%/reads/e_coli_10000snp.fa
+%%DATADIR%%/reads/e_coli_10000snp.fq
+%%DATADIR%%/reads/e_coli_1000_1.fa
+%%DATADIR%%/reads/e_coli_1000_1.fq
+%%DATADIR%%/reads/e_coli_1000_2.fa
+%%DATADIR%%/reads/e_coli_1000_2.fq
+%%DATADIR%%/scripts/best_verify.pl
+%%DATADIR%%/scripts/bs_mapability.pl
+%%DATADIR%%/scripts/build_test.sh
+%%DATADIR%%/scripts/colorize_fasta.pl
+%%DATADIR%%/scripts/colorize_fastq.pl
+%%DATADIR%%/scripts/convert_quals.pl
+%%DATADIR%%/scripts/fastq_to_tabbed.pl
+%%DATADIR%%/scripts/gen_2b_occ_lookup.pl
+%%DATADIR%%/scripts/gen_dnamasks2colormask.pl
+%%DATADIR%%/scripts/gen_occ_lookup.pl
+%%DATADIR%%/scripts/gen_solqual_lookup.pl
+%%DATADIR%%/scripts/infer_fraglen.pl
+%%DATADIR%%/scripts/make_a_thaliana_tair.sh
+%%DATADIR%%/scripts/make_b_taurus_UMD3.sh
+%%DATADIR%%/scripts/make_c_elegans.sh
+%%DATADIR%%/scripts/make_canFam2.sh
+%%DATADIR%%/scripts/make_d_melanogaster.sh
+%%DATADIR%%/scripts/make_e_coli.sh
+%%DATADIR%%/scripts/make_galGal3.sh
+%%DATADIR%%/scripts/make_h_sapiens_ncbi36.sh
+%%DATADIR%%/scripts/make_h_sapiens_ncbi37.sh
+%%DATADIR%%/scripts/make_hg18.sh
+%%DATADIR%%/scripts/make_hg19.sh
+%%DATADIR%%/scripts/make_m_musculus_ncbi37.sh
+%%DATADIR%%/scripts/make_mm8.sh
+%%DATADIR%%/scripts/make_mm9.sh
+%%DATADIR%%/scripts/make_rn4.sh
+%%DATADIR%%/scripts/make_s_cerevisiae.sh
+%%DATADIR%%/scripts/mapability.pl
+%%DATADIR%%/scripts/pe_verify.pl
+%%DATADIR%%/scripts/reconcile_alignments.pl
+%%DATADIR%%/scripts/reconcile_alignments_pe.pl
+%%PORTDOCS%%%%DOCSDIR%%/README
+%%PORTDOCS%%%%DOCSDIR%%/manual.html
+%%PORTDOCS%%%%DOCSDIR%%/release.txt
+%%PORTDOCS%%%%DOCSDIR%%/strip_markdown.pl
+%%PORTDOCS%%%%DOCSDIR%%/style.css
+%%PORTDOCS%%%%DOCSDIR%%/website/css/style.css
+%%PORTDOCS%%%%DOCSDIR%%/website/foot.ssi
+%%PORTDOCS%%%%DOCSDIR%%/website/images/bowtie_logo.png
+%%PORTDOCS%%%%DOCSDIR%%/website/images/osi-certified.gif
+%%PORTDOCS%%%%DOCSDIR%%/website/images/sflogo.png
+%%PORTDOCS%%%%DOCSDIR%%/website/images/university.small.horizontal.white.png
+%%PORTDOCS%%%%DOCSDIR%%/website/index.html
+%%PORTDOCS%%%%DOCSDIR%%/website/index.shtml
+%%PORTDOCS%%%%DOCSDIR%%/website/latest-version.txt
+%%PORTDOCS%%%%DOCSDIR%%/website/manual.html
+%%PORTDOCS%%%%DOCSDIR%%/website/manual.shtml
+%%PORTDOCS%%%%DOCSDIR%%/website/manual.ssi
+%%PORTDOCS%%%%DOCSDIR%%/website/md5s.shtml
+%%PORTDOCS%%%%DOCSDIR%%/website/md5s.ssi
+%%PORTDOCS%%%%DOCSDIR%%/website/news.shtml
+%%PORTDOCS%%%%DOCSDIR%%/website/old_news.ssi
+%%PORTDOCS%%%%DOCSDIR%%/website/other_tools.shtml
+%%PORTDOCS%%%%DOCSDIR%%/website/other_tools.ssi
+%%PORTDOCS%%%%DOCSDIR%%/website/push_langmead.sh
+%%PORTDOCS%%%%DOCSDIR%%/website/recent_news.ssi
+%%PORTDOCS%%%%DOCSDIR%%/website/rhsidebar.ssi
+%%PORTDOCS%%%%DOCSDIR%%/website/top.ssi
+%%PORTDOCS%%%%DOCSDIR%%/website/tutorial.html
+%%PORTDOCS%%%%DOCSDIR%%/website/tutorial.shtml