From owner-svn-ports-head@freebsd.org Thu Jun 4 18:28:15 2020 Return-Path: Delivered-To: svn-ports-head@mailman.nyi.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mailman.nyi.freebsd.org (Postfix) with ESMTP id 5675432C16E; Thu, 4 Jun 2020 18:28:15 +0000 (UTC) (envelope-from jwb@FreeBSD.org) Received: from mxrelay.nyi.freebsd.org (mxrelay.nyi.freebsd.org [IPv6:2610:1c1:1:606c::19:3]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256 client-signature RSA-PSS (4096 bits) client-digest SHA256) (Client CN "mxrelay.nyi.freebsd.org", Issuer "Let's Encrypt Authority X3" (verified OK)) by mx1.freebsd.org (Postfix) with ESMTPS id 49dDmb1cHMz4VMJ; Thu, 4 Jun 2020 18:28:15 +0000 (UTC) (envelope-from jwb@FreeBSD.org) Received: from repo.freebsd.org (repo.freebsd.org [IPv6:2610:1c1:1:6068::e6a:0]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (Client did not present a certificate) by mxrelay.nyi.freebsd.org (Postfix) with ESMTPS id 3217D23B63; Thu, 4 Jun 2020 18:28:15 +0000 (UTC) (envelope-from jwb@FreeBSD.org) Received: from repo.freebsd.org ([127.0.1.37]) by repo.freebsd.org (8.15.2/8.15.2) with ESMTP id 054ISEA9091809; Thu, 4 Jun 2020 18:28:14 GMT (envelope-from jwb@FreeBSD.org) Received: (from jwb@localhost) by repo.freebsd.org (8.15.2/8.15.2/Submit) id 054ISDoa091800; Thu, 4 Jun 2020 18:28:13 GMT (envelope-from jwb@FreeBSD.org) Message-Id: <202006041828.054ISDoa091800@repo.freebsd.org> X-Authentication-Warning: repo.freebsd.org: jwb set sender to jwb@FreeBSD.org using -f From: "Jason W. Bacon" Date: Thu, 4 Jun 2020 18:28:13 +0000 (UTC) To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r537926 - in head/biology: . vt vt/files X-SVN-Group: ports-head X-SVN-Commit-Author: jwb X-SVN-Commit-Paths: in head/biology: . vt vt/files X-SVN-Commit-Revision: 537926 X-SVN-Commit-Repository: ports MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit X-BeenThere: svn-ports-head@freebsd.org X-Mailman-Version: 2.1.33 Precedence: list List-Id: SVN commit messages for the ports tree for head List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Thu, 04 Jun 2020 18:28:15 -0000 Author: jwb Date: Thu Jun 4 18:28:13 2020 New Revision: 537926 URL: https://svnweb.freebsd.org/changeset/ports/537926 Log: bioloty/vt: Discovers short variants from Next Generation Sequencing data Added: head/biology/vt/ head/biology/vt/Makefile (contents, props changed) head/biology/vt/distinfo (contents, props changed) head/biology/vt/files/ head/biology/vt/files/patch-Makefile (contents, props changed) head/biology/vt/files/patch-lib_Rmath_Make.inc (contents, props changed) head/biology/vt/files/patch-lib_pcre2_Makefile (contents, props changed) head/biology/vt/files/patch-svm__predict.h (contents, props changed) head/biology/vt/files/patch-svm__train.h (contents, props changed) head/biology/vt/pkg-descr (contents, props changed) Modified: head/biology/Makefile Modified: head/biology/Makefile ============================================================================== --- head/biology/Makefile Thu Jun 4 18:25:35 2020 (r537925) +++ head/biology/Makefile Thu Jun 4 18:28:13 2020 (r537926) @@ -173,6 +173,7 @@ SUBDIR += velvet SUBDIR += viennarna SUBDIR += vsearch + SUBDIR += vt SUBDIR += wise .include Added: head/biology/vt/Makefile ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/vt/Makefile Thu Jun 4 18:28:13 2020 (r537926) @@ -0,0 +1,27 @@ +# $FreeBSD$ + +PORTNAME= vt +DISTVERSION= 0.57721 +CATEGORIES= biology + +MAINTAINER= jwb@FreeBSD.org +COMMENT= Discovers short variants from Next Generation Sequencing data + +LICENSE= MIT + +LIB_DEPENDS= libhts.so:biology/htslib \ + libsvm.so:science/libsvm \ + libdeflate.so:archivers/libdeflate \ + libcurl.so:ftp/curl + +USES= gmake ssl +USE_GITHUB= yes + +GH_ACCOUNT= atks + +PLIST_FILES= bin/vt + +do-install: + ${INSTALL_PROGRAM} ${WRKSRC}/vt ${STAGEDIR}${PREFIX}/bin + +.include Added: head/biology/vt/distinfo ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/vt/distinfo Thu Jun 4 18:28:13 2020 (r537926) @@ -0,0 +1,3 @@ +TIMESTAMP = 1591286057 +SHA256 (atks-vt-0.57721_GH0.tar.gz) = 8f06d464ec5458539cfa30f81a034f47fe7f801146fe8ca80c14a3816b704e17 +SIZE (atks-vt-0.57721_GH0.tar.gz) = 20925247 Added: head/biology/vt/files/patch-Makefile ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/vt/files/patch-Makefile Thu Jun 4 18:28:13 2020 (r537926) @@ -0,0 +1,41 @@ +--- Makefile.orig 2018-05-09 00:33:23 UTC ++++ Makefile +@@ -1,7 +1,8 @@ +-OPTFLAG = -O3 +-INCLUDES = -I./lib -I. -I./lib/htslib -I./lib/Rmath -I./lib/pcre2 +-CXXFLAGS = -pipe -std=c++0x $(OPTFLAG) $(INCLUDES) -D__STDC_LIMIT_MACROS +-CXX = g++ ++# ${LOCALBASE}/include must come after bundled dirs ++INCLUDES = -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I${LOCALBASE}/include ++CXXFLAGS ?= -pipe -std=c++0x $(OPTFLAG) $(INCLUDES) -D__STDC_LIMIT_MACROS ++CXXFLAGS += -std=c++0x $(INCLUDES) -D__STDC_LIMIT_MACROS ++CXX ?= g++ + + SOURCESONLY = + +@@ -139,11 +140,11 @@ SOURCESONLY = main.cpp + TARGET = vt + TOOLSRC = $(SOURCES:=.cpp) $(SOURCESONLY) + TOOLOBJ = $(TOOLSRC:.cpp=.o) +-LIBDEFLATE = lib/libdeflate/libdeflate.a +-LIBHTS = lib/htslib/libhts.a ++LIBDEFLATE = -ldeflate ++LIBHTS = -lhts + LIBRMATH = lib/Rmath/libRmath.a + LIBPCRE2 = lib/pcre2/libpcre2.a +-LIBSVM = lib/libsvm/libsvm.a ++LIBSVM = -lsvm + + all : $(TARGET) + +@@ -165,8 +166,8 @@ ${LIBSVM} : + version : + git rev-parse HEAD | cut -c 1-8 | awk '{print "#define VERSION \"0.5772-"$$0"\""}' > version.h; + +-$(TARGET) : ${LIBHTS} ${LIBRMATH} ${LIBPCRE2} ${LIBSVM} $(TOOLOBJ) +- $(CXX) $(CXXFLAGS) -o $@ $(TOOLOBJ) $(LIBHTS) $(LIBRMATH) ${LIBPCRE2} ${LIBDEFLATE} -lz -lpthread -lbz2 -llzma -lcurl -lcrypto ++$(TARGET) : ${LIBRMATH} ${LIBPCRE2} $(TOOLOBJ) ++ $(CXX) $(CXXFLAGS) -o $@ $(TOOLOBJ) -L${LOCALBASE}/lib $(LIBHTS) $(LIBRMATH) ${LIBPCRE2} ${LIBDEFLATE} -lz -lpthread -lbz2 -llzma -lcurl -lcrypto + + $(TOOLOBJ): $(HEADERSONLY) + Added: head/biology/vt/files/patch-lib_Rmath_Make.inc ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/vt/files/patch-lib_Rmath_Make.inc Thu Jun 4 18:28:13 2020 (r537926) @@ -0,0 +1,31 @@ +--- lib/Rmath/Make.inc.orig 2020-06-04 16:21:07 UTC ++++ lib/Rmath/Make.inc +@@ -3,21 +3,21 @@ + OS = $(shell uname) + ARCH = $(shell uname -m) + +-FC = gfortran +-FFLAGS-add += -O3 ++FC ?= gfortran ++# FFLAGS-add += -O3 + +-USEGCC = 1 +-USECLANG = 0 ++USEGCC = 0 ++USECLANG = 1 + +-CFLAGS-add += -Wall -O3 ++# CFLAGS-add += -Wall -O3 + + ifeq ($(USECLANG),1) + USEGCC = 0 +-CC = clang ++CC ?= clang + endif + + ifeq ($(USEGCC),1) +-CC = gcc ++CC ?= gcc + endif + AR = ar + Added: head/biology/vt/files/patch-lib_pcre2_Makefile ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/vt/files/patch-lib_pcre2_Makefile Thu Jun 4 18:28:13 2020 (r537926) @@ -0,0 +1,11 @@ +--- lib/pcre2/Makefile.orig 2020-06-04 16:13:50 UTC ++++ lib/pcre2/Makefile +@@ -28,7 +28,7 @@ TOOLSRC = $(SOURCES:=.c) + TOOLOBJ = $(TOOLSRC:.c=.o) + + .c.o : +- gcc -g -O3 -DHAVE_CONFIG_H -DPCRE2_CODE_UNIT_WIDTH=8 -I. -o $@ -c $*.c ++ ${CC} ${CFLAGS} -DHAVE_CONFIG_H -DPCRE2_CODE_UNIT_WIDTH=8 -I. -o $@ -c $*.c + + libpcre2.a: $(TOOLOBJ) + @-rm -f $@ Added: head/biology/vt/files/patch-svm__predict.h ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/vt/files/patch-svm__predict.h Thu Jun 4 18:28:13 2020 (r537926) @@ -0,0 +1,14 @@ +--- svm_predict.h.orig 2020-06-04 16:33:17 UTC ++++ svm_predict.h +@@ -25,8 +25,8 @@ + #define SVM_PREDICT_H + + #include "program.h" +-#include "libsvm/svm.h" ++#include + + void svm_predict(int argc, char ** argv); + +-#endif +\ No newline at end of file ++#endif Added: head/biology/vt/files/patch-svm__train.h ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/vt/files/patch-svm__train.h Thu Jun 4 18:28:13 2020 (r537926) @@ -0,0 +1,15 @@ +--- svm_train.h.orig 2020-06-04 16:32:44 UTC ++++ svm_train.h +@@ -25,9 +25,9 @@ + #define SVM_TRAIN_H + + #include "program.h" +-#include "libsvm/svm.h" ++#include + #include "Rmath/Rmath.h" + + void svm_train(int argc, char ** argv); + +-#endif +\ No newline at end of file ++#endif Added: head/biology/vt/pkg-descr ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/vt/pkg-descr Thu Jun 4 18:28:13 2020 (r537926) @@ -0,0 +1,4 @@ +vt is a variant tool set that discovers short variants from Next Generation +Sequencing data. + +WWW: https://genome.sph.umich.edu/wiki/Vt