From owner-svn-ports-all@FreeBSD.ORG Tue Jun 17 21:39:45 2014 Return-Path: Delivered-To: svn-ports-all@freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [8.8.178.115]) (using TLSv1 with cipher ADH-AES256-SHA (256/256 bits)) (No client certificate requested) by hub.freebsd.org (Postfix) with ESMTPS id 335F4BF4; Tue, 17 Jun 2014 21:39:45 +0000 (UTC) Received: from svn.freebsd.org (svn.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 141622FD8; Tue, 17 Jun 2014 21:39:45 +0000 (UTC) Received: from svn.freebsd.org ([127.0.1.70]) by svn.freebsd.org (8.14.8/8.14.8) with ESMTP id s5HLdi8O016177; Tue, 17 Jun 2014 21:39:44 GMT (envelope-from rakuco@svn.freebsd.org) Received: (from rakuco@localhost) by svn.freebsd.org (8.14.8/8.14.8/Submit) id s5HLdiRI016174; Tue, 17 Jun 2014 21:39:44 GMT (envelope-from rakuco@svn.freebsd.org) Message-Id: <201406172139.s5HLdiRI016174@svn.freebsd.org> From: Raphael Kubo da Costa Date: Tue, 17 Jun 2014 21:39:44 +0000 (UTC) To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r358183 - in head/biology/velvet: . files 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: 2.1.18 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: Tue, 17 Jun 2014 21:39:45 -0000 Author: rakuco Date: Tue Jun 17 21:39:44 2014 New Revision: 358183 URL: http://svnweb.freebsd.org/changeset/ports/358183 QAT: https://qat.redports.org/buildarchive/r358183/ Log: Update to 1.2.10. PR: 191129 Submitted by: mzaki@m.u-tokyo.ac.jp (maintainer) Modified: head/biology/velvet/Makefile head/biology/velvet/distinfo head/biology/velvet/files/patch-Makefile Modified: head/biology/velvet/Makefile ============================================================================== --- head/biology/velvet/Makefile Tue Jun 17 21:36:06 2014 (r358182) +++ head/biology/velvet/Makefile Tue Jun 17 21:39:44 2014 (r358183) @@ -2,7 +2,7 @@ # $FreeBSD$ PORTNAME= velvet -PORTVERSION= 1.1.04 +PORTVERSION= 1.2.10 CATEGORIES= biology MASTER_SITES= http://www.ebi.ac.uk/~zerbino/velvet/ DISTNAME= ${PORTNAME}_${PORTVERSION} @@ -21,8 +21,9 @@ USES= perl5 gmake USE_PERL5= run BINARIES= velvetg velveth -SCRIPTS= shuffleSequences_fasta.pl shuffleSequences_fastq.pl \ - contrib/VelvetOptimiser-2.1.7/VelvetOptimiser.pl \ +SCRIPTS= contrib/shuffleSequences_fasta/shuffleSequences_fasta.pl \ + contrib/shuffleSequences_fasta/shuffleSequences_fastq.pl \ + contrib/VelvetOptimiser-2.2.4/VelvetOptimiser.pl \ contrib/afg_handling/asmbly_splitter.pl \ contrib/afg_handling/snp_view.pl \ contrib/columbus_scripts/enlarge_exons.pl \ @@ -32,13 +33,14 @@ SCRIPTS= shuffleSequences_fasta.pl shuff contrib/extractContigReads/extractContigReads.pl \ contrib/fasta2agp/fasta2agp.pl \ contrib/observed-insert-length.pl/observed-insert-length.pl \ + contrib/read_prepare/pe_read_prepare.0.1.pl \ contrib/select_paired/select_paired.pl \ contrib/show_repeats/show_repeats.pl -PERLMOD_DIRS= contrib/VelvetOptimiser-2.1.7/VelvetOpt -PERLMOD_FILES= contrib/VelvetOptimiser-2.1.7/VelvetOpt/Assembly.pm \ - contrib/VelvetOptimiser-2.1.7/VelvetOpt/Utils.pm \ - contrib/VelvetOptimiser-2.1.7/VelvetOpt/gwrap.pm \ - contrib/VelvetOptimiser-2.1.7/VelvetOpt/hwrap.pm +PERLMOD_DIRS= contrib/VelvetOptimiser-2.2.4/VelvetOpt +PERLMOD_FILES= contrib/VelvetOptimiser-2.2.4/VelvetOpt/Assembly.pm \ + contrib/VelvetOptimiser-2.2.4/VelvetOpt/Utils.pm \ + contrib/VelvetOptimiser-2.2.4/VelvetOpt/gwrap.pm \ + contrib/VelvetOptimiser-2.2.4/VelvetOpt/hwrap.pm .if !defined(WITHOUT_PYTHON) USE_PYTHON= yes Modified: head/biology/velvet/distinfo ============================================================================== --- head/biology/velvet/distinfo Tue Jun 17 21:36:06 2014 (r358182) +++ head/biology/velvet/distinfo Tue Jun 17 21:39:44 2014 (r358183) @@ -1,2 +1,2 @@ -SHA256 (velvet_1.1.04.tgz) = 7ae9855c3eabd1d222815a7132cdc9eeb387d83132390d020fc78491e6dcc9d6 -SIZE (velvet_1.1.04.tgz) = 7744134 +SHA256 (velvet_1.2.10.tgz) = 884dd488c2d12f1f89cdc530a266af5d3106965f21ab9149e8cb5c633c977640 +SIZE (velvet_1.2.10.tgz) = 18818559 Modified: head/biology/velvet/files/patch-Makefile ============================================================================== --- head/biology/velvet/files/patch-Makefile Tue Jun 17 21:36:06 2014 (r358182) +++ head/biology/velvet/files/patch-Makefile Tue Jun 17 21:39:44 2014 (r358183) @@ -1,47 +1,33 @@ ---- Makefile.orig 2011-03-30 14:34:09.000000000 +0900 -+++ Makefile 2011-06-02 20:28:04.000000000 +0900 -@@ -1,18 +1,18 @@ +--- Makefile.orig 2013-10-18 01:03:39.000000000 +0900 ++++ Makefile 2014-06-17 21:34:34.000000000 +0900 +@@ -1,15 +1,15 @@ -CC = gcc -CFLAGS = -Wall +CC ?= gcc +CFLAGS += -Wall DEBUG = -g --LDFLAGS = -lm + LIBS = -lm -OPT = -O3 -MAXKMERLENGTH=31 -CATEGORIES=2 -+#LDFLAGS = -lm +#OPT = -O3 +MAXKMERLENGTH?=31 +CATEGORIES?=2 DEF = -D MAXKMERLENGTH=$(MAXKMERLENGTH) -D CATEGORIES=$(CATEGORIES) - - Z_LIB_DIR=third-party/zlib-1.2.3 - Z_LIB_FILES=$(Z_LIB_DIR)/*.o + PDFLATEX_VERSION := $(shell pdflatex --version 2> /dev/null) # Mac OS users: uncomment the following lines --# Z_LIB_FILES= --# LDFLAGS = -lm -lz -+Z_LIB_FILES= -+LDFLAGS += -lm -lz - # CFLAGS = -Wall -m64 +-CFLAGS = -Wall -m64 ++#CFLAGS = -Wall -m64 # Sparc/Solaris users: uncomment the following line -@@ -35,7 +35,7 @@ - OBJ = obj/tightString.o obj/run.o obj/splay.o obj/splayTable.o obj/graph.o obj/run2.o obj/fibHeap.o obj/fib.o obj/concatenatedGraph.o obj/passageMarker.o obj/graphStats.o obj/correctedGraph.o obj/dfib.o obj/dfibHeap.o obj/recycleBin.o obj/readSet.o obj/shortReadPairs.o obj/locallyCorrectedGraph.o obj/graphReConstruction.o obj/roadMap.o obj/preGraph.o obj/preGraphConstruction.o obj/concatenatedPreGraph.o obj/readCoherentGraph.o obj/utility.o obj/kmer.o obj/scaffold.o obj/kmerOccurenceTable.o obj/allocArray.o + # CFLAGS = -Wall -m64 +@@ -40,7 +40,7 @@ + OBJ = obj/tightString.o obj/run.o obj/splay.o obj/splayTable.o obj/graph.o obj/run2.o obj/fibHeap.o obj/fib.o obj/concatenatedGraph.o obj/passageMarker.o obj/graphStats.o obj/correctedGraph.o obj/dfib.o obj/dfibHeap.o obj/recycleBin.o obj/readSet.o obj/binarySequences.o obj/shortReadPairs.o obj/locallyCorrectedGraph.o obj/graphReConstruction.o obj/roadMap.o obj/preGraph.o obj/preGraphConstruction.o obj/concatenatedPreGraph.o obj/readCoherentGraph.o obj/utility.o obj/kmer.o obj/scaffold.o obj/kmerOccurenceTable.o obj/allocArray.o obj/autoOpen.o OBJDBG = $(subst obj,obj/dbg,$(OBJ)) -default : cleanobj zlib obj velveth velvetg doc +default : cleanobj zlib obj velveth velvetg - clean : + clean : clean-zlib -rm obj/*.o obj/dbg/*.o ./velvet* -@@ -47,7 +47,7 @@ - -rm obj/*.o obj/dbg/*.o - - zlib : -- cd $(Z_LIB_DIR); ./configure; make; rm minigzip.o; rm example.o -+# cd $(Z_LIB_DIR); ./configure; make; rm minigzip.o; rm example.o - - velveth : obj - $(CC) $(CFLAGS) $(OPT) $(LDFLAGS) -o velveth obj/tightString.o obj/run.o obj/recycleBin.o obj/splay.o obj/splayTable.o obj/readSet.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o $(Z_LIB_FILES)