4 files changed, 80 insertions, 0 deletions

diff --git a/biology/cd-hit/Makefile b/biology/cd-hit/Makefile
new file mode 100644
index 000000000000..e3cd02127edf
--- /dev/null
+++ b/biology/cd-hit/Makefile
@@ -0,0 +1,41 @@
+# Created by: Jason Bacon <jwbacon@tds.net>
+# $FreeBSD$
+
+PORTNAME=	cd-hit
+PORTVERSION=	4.6.4
+DISTVERSIONPREFIX=	V
+CATEGORIES=	biology
+
+MAINTAINER=	jwbacon@tds.net
+COMMENT=	Clustering and comparing protein or nucleotide sequences
+
+LICENSE=	GPLv2
+
+USE_GITHUB=	yes
+GH_ACCOUNT=	weizhongli
+GH_PROJECT=	cdhit
+
+USES=		gmake shebangfix
+WRKSRC=		${WRKDIR}/cdhit-${PORTVERSION}
+# Only for OpenMP
+USE_GCC=	yes
+SHEBANG_FILES=	${WRKSRC}/*.pl
+
+#MAKEFILE=	makefile
+MAKE_FLAGS=	openmp=yes
+
+post-patch:
+	@${REINPLACE_CMD} \
+		-e 's|g++|${CXX}|g' \
+		-e 's|\$$(PREFIX)|$${DESTDIR}$${PREFIX}/bin|g' \
+		${WRKSRC}/${MAKEFILE}
+	@${REINPLACE_CMD} \
+		-e 's|/bin/bash|${LOCALBASE}/bin/bash|g' \
+		${WRKSRC}/*.pl
+
+post-stage:
+	@cd ${STAGEDIR}${PREFIX}/bin && \
+		${STRIP_CMD} cd-hit cd-hit-2d cd-hit-454 \
+		cd-hit-div cd-hit-est cd-hit-est-2d
+
+.include <bsd.port.mk>
diff --git a/biology/cd-hit/distinfo b/biology/cd-hit/distinfo
new file mode 100644
index 000000000000..db221603beb2
--- /dev/null
+++ b/biology/cd-hit/distinfo
@@ -0,0 +1,2 @@
+SHA256 (weizhongli-cdhit-V4.6.4_GH0.tar.gz) = b170108147ec91d8b5f9d10b9e8d5fd971e7aef3af6ec1e5542cbaf10d54b2fc
+SIZE (weizhongli-cdhit-V4.6.4_GH0.tar.gz) = 1148426
diff --git a/biology/cd-hit/pkg-descr b/biology/cd-hit/pkg-descr
new file mode 100644
index 000000000000..1ee003c9c3ba
--- /dev/null
+++ b/biology/cd-hit/pkg-descr
@@ -0,0 +1,4 @@
+CD-HIT is a very widely used program for clustering and comparing protein or
+nucleotide sequences.
+
+WWW: http://weizhong-lab.ucsd.edu/cd-hit/
diff --git a/biology/cd-hit/pkg-plist b/biology/cd-hit/pkg-plist
new file mode 100644
index 000000000000..265308f03170
--- /dev/null
+++ b/biology/cd-hit/pkg-plist
@@ -0,0 +1,33 @@
+bin/cd-hit
+bin/cd-hit-2d
+bin/cd-hit-2d-para.pl
+bin/cd-hit-454
+bin/cd-hit-div
+bin/cd-hit-div.pl
+bin/cd-hit-est
+bin/cd-hit-est-2d
+bin/cd-hit-para.pl
+bin/clstr2tree.pl
+bin/clstr2txt.pl
+bin/clstr2xml.pl
+bin/clstr_cut.pl
+bin/clstr_merge.pl
+bin/clstr_merge_noorder.pl
+bin/clstr_quality_eval.pl
+bin/clstr_quality_eval_by_link.pl
+bin/clstr_reduce.pl
+bin/clstr_renumber.pl
+bin/clstr_rep.pl
+bin/clstr_reps_faa_rev.pl
+bin/clstr_rev.pl
+bin/clstr_select.pl
+bin/clstr_select_rep.pl
+bin/clstr_size_histogram.pl
+bin/clstr_size_stat.pl
+bin/clstr_sort_by.pl
+bin/clstr_sort_prot_by.pl
+bin/clstr_sql_tbl.pl
+bin/clstr_sql_tbl_sort.pl
+bin/make_multi_seq.pl
+bin/plot_2d.pl
+bin/plot_len1.pl