From owner-svn-ports-all@freebsd.org Sat Sep 19 11:16:53 2015 Return-Path: Delivered-To: svn-ports-all@mailman.ysv.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2001:1900:2254:206a::19:1]) by mailman.ysv.freebsd.org (Postfix) with ESMTP id D246A9CF00F; Sat, 19 Sep 2015 11:16:53 +0000 (UTC) (envelope-from wen@FreeBSD.org) Received: from repo.freebsd.org (repo.freebsd.org [IPv6:2001:1900:2254:2068::e6a:0]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (Client did not present a certificate) by mx1.freebsd.org (Postfix) with ESMTPS id C2F7E1A38; Sat, 19 Sep 2015 11:16:53 +0000 (UTC) (envelope-from wen@FreeBSD.org) Received: from repo.freebsd.org ([127.0.1.70]) by repo.freebsd.org (8.15.2/8.15.2) with ESMTP id t8JBGrUu054116; Sat, 19 Sep 2015 11:16:53 GMT (envelope-from wen@FreeBSD.org) Received: (from wen@localhost) by repo.freebsd.org (8.15.2/8.15.2/Submit) id t8JBGqXG054111; Sat, 19 Sep 2015 11:16:52 GMT (envelope-from wen@FreeBSD.org) Message-Id: <201509191116.t8JBGqXG054111@repo.freebsd.org> X-Authentication-Warning: repo.freebsd.org: wen set sender to wen@FreeBSD.org using -f From: Wen Heping Date: Sat, 19 Sep 2015 11:16:52 +0000 (UTC) To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r397318 - in head/biology: . cd-hit X-SVN-Group: ports-head MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit X-BeenThere: svn-ports-all@freebsd.org X-Mailman-Version: 2.1.20 Precedence: list List-Id: SVN commit messages for the ports tree List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Sat, 19 Sep 2015 11:16:54 -0000 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@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 +# $FreeBSD$ + +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 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