svn commit: r537926 - in head/biology: . vt vt/files
Jason W. Bacon
jwb at FreeBSD.org
Thu Jun 4 18:28:15 UTC 2020
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 <bsd.port.subdir.mk>
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 at 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 <bsd.port.mk>
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 <svm.h>
+
+ 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 <svm.h>
+ #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
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