svn commit: r397318 - in head/biology: . cd-hit

[Wen Heping]

Author: wen
Date: Sat Sep 19 11:16:51 2015
New Revision: 397318
URL: https://svnweb.freebsd.org/changeset/ports/397318

Log:
  CD-HIT is a very widely used program for clustering and comparing protein or
  nucleotide sequences.
  
  WWW: http://weizhong-lab.ucsd.edu/cd-hit/
  
  PR:		203183
  Submitted by:	jwbacon at tds.net

Added:
  head/biology/cd-hit/
  head/biology/cd-hit/Makefile   (contents, props changed)
  head/biology/cd-hit/distinfo   (contents, props changed)
  head/biology/cd-hit/pkg-descr   (contents, props changed)
  head/biology/cd-hit/pkg-plist   (contents, props changed)
Modified:
  head/biology/Makefile

Modified: head/biology/Makefile
==============================================================================
--- head/biology/Makefile	Sat Sep 19 11:05:37 2015	(r397317)
+++ head/biology/Makefile	Sat Sep 19 11:16:51 2015	(r397318)
@@ -11,6 +11,7 @@
     SUBDIR += biococoa
     SUBDIR += biojava
     SUBDIR += blat
+    SUBDIR += cd-hit
     SUBDIR += chemeq
     SUBDIR += clustalw
     SUBDIR += consed

Added: head/biology/cd-hit/Makefile
==============================================================================
--- /dev/null	00:00:00 1970	(empty, because file is newly added)
+++ head/biology/cd-hit/Makefile	Sat Sep 19 11:16:51 2015	(r397318)
@@ -0,0 +1,41 @@
+# Created by: Jason Bacon <jwbacon at tds.net>
+# $FreeBSD$
+
+PORTNAME=	cd-hit
+PORTVERSION=	4.6.4
+DISTVERSIONPREFIX=	V
+CATEGORIES=	biology
+
+MAINTAINER=	jwbacon at 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>

Added: head/biology/cd-hit/distinfo
==============================================================================
--- /dev/null	00:00:00 1970	(empty, because file is newly added)
+++ head/biology/cd-hit/distinfo	Sat Sep 19 11:16:51 2015	(r397318)
@@ -0,0 +1,2 @@
+SHA256 (weizhongli-cdhit-V4.6.4_GH0.tar.gz) = b170108147ec91d8b5f9d10b9e8d5fd971e7aef3af6ec1e5542cbaf10d54b2fc
+SIZE (weizhongli-cdhit-V4.6.4_GH0.tar.gz) = 1148426

Added: head/biology/cd-hit/pkg-descr
==============================================================================
--- /dev/null	00:00:00 1970	(empty, because file is newly added)
+++ head/biology/cd-hit/pkg-descr	Sat Sep 19 11:16:51 2015	(r397318)
@@ -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/

Added: head/biology/cd-hit/pkg-plist
==============================================================================
--- /dev/null	00:00:00 1970	(empty, because file is newly added)
+++ head/biology/cd-hit/pkg-plist	Sat Sep 19 11:16:51 2015	(r397318)
@@ -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