biology/bowtie2: import bowtie2-2.4.2

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.

6 files changed, 131 insertions, 0 deletions

diff --git a/biology/bowtie2/DESCR b/biology/bowtie2/DESCR
new file mode 100644
index 00000000000..79b1d218f58
--- /dev/null
+++ b/biology/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/biology/bowtie2/Makefile b/biology/bowtie2/Makefile
new file mode 100644
index 00000000000..b020cef4e4e
--- /dev/null
+++ b/biology/bowtie2/Makefile
@@ -0,0 +1,37 @@
+# $NetBSD: Makefile,v 1.1 2021/01/21 17:30:12 bacon Exp $
+
+DISTNAME=	bowtie2-2.4.2
+CATEGORIES=	biology
+MASTER_SITES=	${MASTER_SITE_GITHUB:=BenLangmead/}
+GITHUB_TAG=	v${PKGVERSION_NOREV}
+
+MAINTAINER=	bacon@NetBSD.org
+HOMEPAGE=	https://github.com/BenLangmead/bowtie2
+COMMENT=	Ultrafast, memory-efficient short read aligner
+LICENSE=	gnu-gpl-v3
+
+USE_LANGUAGES=	c c++
+USE_TOOLS+=	gmake pax:build perl:run
+REPLACE_PERL=	scripts/*.pl bowtie2
+REPLACE_PYTHON=	bowtie2-build bowtie2-inspect
+REPLACE_SH=	scripts/bowtie2-hbb.sh
+
+# Use onetbb on supported platforms when a package is available
+MAKE_FLAGS+=	NO_TBB=1
+
+DATADIR=	${PREFIX}/share/bowtie2
+EXAMPLESDIR=	${PREFIX}/share/examples/bowtie2
+
+INSTALLATION_DIRS=	share/bowtie2/scripts share/examples/bowtie2
+
+post-install:
+	${INSTALL_PROGRAM} ${WRKSRC}/bowtie2*-s ${WRKSRC}/bowtie2*-l \
+		${DESTDIR}${PREFIX}/bin
+	${INSTALL_SCRIPT} ${WRKSRC}/scripts/*.sh ${WRKSRC}/scripts/*.pl \
+		${DESTDIR}${DATADIR}/scripts
+	(cd ${WRKSRC}/example && pax -rw index reads reference \
+		${DESTDIR}${EXAMPLESDIR})
+
+.include "../../lang/python/application.mk"
+.include "../../devel/zlib/buildlink3.mk"
+.include "../../mk/bsd.pkg.mk"
diff --git a/biology/bowtie2/PLIST b/biology/bowtie2/PLIST
new file mode 100644
index 00000000000..249ae7dddfe
--- /dev/null
+++ b/biology/bowtie2/PLIST
@@ -0,0 +1,44 @@
+@comment $NetBSD: PLIST,v 1.1 2021/01/21 17:30:12 bacon Exp $
+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
+share/bowtie2/scripts/bowtie2-hbb.sh
+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_c_elegans.sh
+share/bowtie2/scripts/make_canFam2.sh
+share/bowtie2/scripts/make_d_melanogaster.sh
+share/bowtie2/scripts/make_e_coli.sh
+share/bowtie2/scripts/make_h_sapiens_ncbi36.sh
+share/bowtie2/scripts/make_h_sapiens_ncbi37.sh
+share/bowtie2/scripts/make_hg18.sh
+share/bowtie2/scripts/make_hg19.sh
+share/bowtie2/scripts/make_m_musculus_ncbi37.sh
+share/bowtie2/scripts/make_mm10.sh
+share/bowtie2/scripts/make_mm9.sh
+share/bowtie2/scripts/make_rn4.sh
+share/bowtie2/scripts/make_s_cerevisiae.sh
+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/combined_reads.bam
+share/examples/bowtie2/reads/conversion_utilities.sh
+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/biology/bowtie2/distinfo b/biology/bowtie2/distinfo
new file mode 100644
index 00000000000..bb68b8505c0
--- /dev/null
+++ b/biology/bowtie2/distinfo
@@ -0,0 +1,8 @@
+$NetBSD: distinfo,v 1.1 2021/01/21 17:30:12 bacon Exp $
+
+SHA1 (bowtie2-2.4.2.tar.gz) = b8eb8158828459412586003b6051d79ed123fc82
+RMD160 (bowtie2-2.4.2.tar.gz) = 0c6c5fe29a40f913e3810d1fe022b948403dfb09
+SHA512 (bowtie2-2.4.2.tar.gz) = f8bb74aaec7557bcd1bc4b5ec5e2a3b141d78c88b04f39cdcc417d15f058bdb48b15d159c4ab569b4d655e3d1bd0cf8152343f05b9a20d5d29680c3e8c2f1a05
+Size (bowtie2-2.4.2.tar.gz) = 10590144 bytes
+SHA1 (patch-Makefile) = 00aa2794474478aa578f6aee5cdb319dfa132ae1
+SHA1 (patch-scripts_bowtie2-hbb.sh) = d360774cfef0675b4c1cdd1175b394d2cf7f761a
diff --git a/biology/bowtie2/patches/patch-Makefile b/biology/bowtie2/patches/patch-Makefile
new file mode 100644
index 00000000000..23e15f3f6b9
--- /dev/null
+++ b/biology/bowtie2/patches/patch-Makefile
@@ -0,0 +1,24 @@
+$NetBSD: patch-Makefile,v 1.1 2021/01/21 17:30:12 bacon Exp $
+
+# Respect PREFIX and CXXFLAGS
+
+--- Makefile.orig	2020-10-06 03:46:41.000000000 +0000
++++ Makefile
+@@ -21,7 +21,7 @@
+ # Makefile for bowtie, bowtie2-build, bowtie2-inspect
+ #
+ 
+-PREFIX := /usr/local
++PREFIX ?= /usr/local
+ bindir := $(PREFIX)/bin
+ 
+ ARCH := $(shell uname -m)
+@@ -234,7 +234,7 @@ ifeq (32,$(BITS))
+ endif
+ 
+ DEBUG_FLAGS    := -O0 -g3 $(SSE_FLAG)
+-RELEASE_FLAGS  := -O3 $(SSE_FLAG) -funroll-loops -g3
++# RELEASE_FLAGS  := -O3 $(SSE_FLAG) -funroll-loops -g3
+ NOASSERT_FLAGS := -DNDEBUG
+ FILE_FLAGS     := -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE
+ DEBUG_DEFS     = -DCOMPILER_OPTIONS="\"$(DEBUG_FLAGS) $(CXXFLAGS)\""
diff --git a/biology/bowtie2/patches/patch-scripts_bowtie2-hbb.sh b/biology/bowtie2/patches/patch-scripts_bowtie2-hbb.sh
new file mode 100644
index 00000000000..2a9ef93e68a
--- /dev/null
+++ b/biology/bowtie2/patches/patch-scripts_bowtie2-hbb.sh
@@ -0,0 +1,15 @@
+$NetBSD: patch-scripts_bowtie2-hbb.sh,v 1.1 2021/01/21 17:30:12 bacon Exp $
+
+# Eliminate bash dependency
+
+--- scripts/bowtie2-hbb.sh.orig	2020-10-06 03:46:41.000000000 +0000
++++ scripts/bowtie2-hbb.sh
+@@ -11,7 +11,7 @@ while getopts "sb:" opt; do
+ done
+ shift $(($OPTIND - 1))
+ 
+-if [ "$branch" == "" ] ; then
++if [ "$branch" = "" ] ; then
+     branch="master"
+ fi
+