bioloty/vt: Discovers short variants from Next Generation Sequencing data

9 files changed, 147 insertions, 0 deletions

diff --git a/biology/Makefile b/biology/Makefile
index 553b36986d8e..31478fdfcb0c 100644
--- a/biology/Makefile
+++ b/biology/Makefile
@@ -173,6 +173,7 @@
     SUBDIR += velvet
     SUBDIR += viennarna
     SUBDIR += vsearch
+    SUBDIR += vt
     SUBDIR += wise
 
 .include <bsd.port.subdir.mk>
diff --git a/biology/vt/Makefile b/biology/vt/Makefile
new file mode 100644
index 000000000000..ac37321e25e3
--- /dev/null
+++ b/biology/vt/Makefile
@@ -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 <bsd.port.mk>
diff --git a/biology/vt/distinfo b/biology/vt/distinfo
new file mode 100644
index 000000000000..1889a65759ef
--- /dev/null
+++ b/biology/vt/distinfo
@@ -0,0 +1,3 @@
+TIMESTAMP = 1591286057
+SHA256 (atks-vt-0.57721_GH0.tar.gz) = 8f06d464ec5458539cfa30f81a034f47fe7f801146fe8ca80c14a3816b704e17
+SIZE (atks-vt-0.57721_GH0.tar.gz) = 20925247
diff --git a/biology/vt/files/patch-Makefile b/biology/vt/files/patch-Makefile
new file mode 100644
index 000000000000..c0f74422f5c7
--- /dev/null
+++ b/biology/vt/files/patch-Makefile
@@ -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)
+ 
diff --git a/biology/vt/files/patch-lib_Rmath_Make.inc b/biology/vt/files/patch-lib_Rmath_Make.inc
new file mode 100644
index 000000000000..8935c0618117
--- /dev/null
+++ b/biology/vt/files/patch-lib_Rmath_Make.inc
@@ -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
+ 
diff --git a/biology/vt/files/patch-lib_pcre2_Makefile b/biology/vt/files/patch-lib_pcre2_Makefile
new file mode 100644
index 000000000000..05179b0f9934
--- /dev/null
+++ b/biology/vt/files/patch-lib_pcre2_Makefile
@@ -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 $@
diff --git a/biology/vt/files/patch-svm__predict.h b/biology/vt/files/patch-svm__predict.h
new file mode 100644
index 000000000000..b5f62014ffec
--- /dev/null
+++ b/biology/vt/files/patch-svm__predict.h
@@ -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
diff --git a/biology/vt/files/patch-svm__train.h b/biology/vt/files/patch-svm__train.h
new file mode 100644
index 000000000000..3b0ffa9b5d55
--- /dev/null
+++ b/biology/vt/files/patch-svm__train.h
@@ -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
diff --git a/biology/vt/pkg-descr b/biology/vt/pkg-descr
new file mode 100644
index 000000000000..054cdd2824e9
--- /dev/null
+++ b/biology/vt/pkg-descr
@@ -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