4 files changed, 106 insertions, 14 deletions

diff --git a/biology/cd-hit/Makefile b/biology/cd-hit/Makefile
index b2211b7f1f9a..d7a9b7690069 100644
--- a/biology/cd-hit/Makefile
+++ b/biology/cd-hit/Makefile
@@ -1,33 +1,29 @@
 # $FreeBSD$
 
-PORTNAME=	cd-hit
-PORTVERSION=	4.6.6
-PORTREVISION=	5
+PORTNAME=		cd-hit
 DISTVERSIONPREFIX=	V
-CATEGORIES=	biology
+DISTVERSION=		4.8.1
+CATEGORIES=		biology
 
 MAINTAINER=	jwb@FreeBSD.org
 COMMENT=	Clustering and comparing protein or nucleotide sequences
 
 LICENSE=	GPLv2
 
+USES=		compiler:openmp gmake shebangfix
 USE_GITHUB=	yes
+
 GH_ACCOUNT=	weizhongli
 GH_PROJECT=	cdhit
-
-USES=		compiler:openmp gmake shebangfix
 SHEBANG_FILES=	${WRKSRC}/*.pl
 
 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
+		${WRKSRC}/cd-hit-2d-para.pl \
+		${WRKSRC}/cd-hit-para.pl
 
 post-install:
 	@cd ${STAGEDIR}${PREFIX}/bin && \
diff --git a/biology/cd-hit/distinfo b/biology/cd-hit/distinfo
index 8865a2816460..365f33397544 100644
--- a/biology/cd-hit/distinfo
+++ b/biology/cd-hit/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1482076217
-SHA256 (weizhongli-cdhit-V4.6.6_GH0.tar.gz) = a0c89c969ad338f958620083b12bc69fa30fcba8246a7ec0b6243e5b2ba0365d
-SIZE (weizhongli-cdhit-V4.6.6_GH0.tar.gz) = 1149112
+TIMESTAMP = 1552053543
+SHA256 (weizhongli-cdhit-V4.8.1_GH0.tar.gz) = f8bc3cdd7aebb432fcd35eed0093e7a6413f1e36bbd2a837ebc06e57cdb20b70
+SIZE (weizhongli-cdhit-V4.8.1_GH0.tar.gz) = 945639
diff --git a/biology/cd-hit/files/patch-Makefile b/biology/cd-hit/files/patch-Makefile
new file mode 100644
index 000000000000..cec1eef7f674
--- /dev/null
+++ b/biology/cd-hit/files/patch-Makefile
@@ -0,0 +1,92 @@
+--- Makefile.orig	2019-02-28 20:13:59 UTC
++++ Makefile
+@@ -1,6 +1,6 @@
+-CC = g++ -Wall -ggdb
+-CC = g++ -pg
+-CC = g++
++CXX ?= g++ -Wall -ggdb
++CXX ?= g++ -pg
++CXX ?= g++
+ 
+ # default with OpenMP
+ # with OpenMP
+@@ -47,7 +47,7 @@ PROGS = cd-hit cd-hit-est cd-hit-2d cd-h
+ CCFLAGS := $(CPPFLAGS) $(CCFLAGS) $(CXXFLAGS)
+ 
+ .c++.o:
+-	$(CC) $(CCFLAGS) -c $<
++	$(CXX) $(CCFLAGS) -c $<
+ 
+ all: $(PROGS)
+ 
+@@ -57,52 +57,53 @@ clean:
+ # programs
+ 
+ cd-hit: cdhit-common.o cdhit-utility.o cdhit.o
+-	$(CC) $(CCFLAGS) cdhit.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit
++	$(CXX) $(CCFLAGS) cdhit.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit
+ 
+ cd-hit-2d: cdhit-common.o cdhit-utility.o cdhit-2d.o
+-	$(CC) $(CCFLAGS) cdhit-2d.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-2d
++	$(CXX) $(CCFLAGS) cdhit-2d.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-2d
+ 
+ cd-hit-est: cdhit-common.o cdhit-utility.o cdhit-est.o
+-	$(CC) $(CCFLAGS) cdhit-est.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-est
++	$(CXX) $(CCFLAGS) cdhit-est.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-est
+ 
+ cd-hit-est-2d: cdhit-common.o cdhit-utility.o cdhit-est-2d.o
+-	$(CC) $(CCFLAGS) cdhit-est-2d.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-est-2d
++	$(CXX) $(CCFLAGS) cdhit-est-2d.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-est-2d
+ 
+ cd-hit-div: cdhit-common.o cdhit-utility.o cdhit-div.o
+-	$(CC) $(CCFLAGS) cdhit-div.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-div
++	$(CXX) $(CCFLAGS) cdhit-div.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-div
+ 
+ cd-hit-454: cdhit-common.o cdhit-utility.o cdhit-454.o
+-	$(CC) $(CCFLAGS) cdhit-454.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-454
++	$(CXX) $(CCFLAGS) cdhit-454.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-454
+ 
+ # objects
+ cdhit-common.o: cdhit-common.c++ cdhit-common.h
+-	$(CC) $(CCFLAGS) cdhit-common.c++ -c
++	$(CXX) $(CCFLAGS) cdhit-common.c++ -c
+ 
+ cdhit-utility.o: cdhit-utility.c++ cdhit-utility.h
+-	$(CC) $(CCFLAGS) cdhit-utility.c++ -c
++	$(CXX) $(CCFLAGS) cdhit-utility.c++ -c
+ 
+ cdhit.o: cdhit.c++ cdhit-utility.h
+-	$(CC) $(CCFLAGS) cdhit.c++ -c
++	$(CXX) $(CCFLAGS) cdhit.c++ -c
+ 
+ cdhit-2d.o: cdhit-2d.c++ cdhit-utility.h
+-	$(CC) $(CCFLAGS) cdhit-2d.c++ -c
++	$(CXX) $(CCFLAGS) cdhit-2d.c++ -c
+ 
+ cdhit-est.o: cdhit-est.c++ cdhit-utility.h
+-	$(CC) $(CCFLAGS) cdhit-est.c++ -c
++	$(CXX) $(CCFLAGS) cdhit-est.c++ -c
+ 
+ cdhit-est-2d.o: cdhit-est-2d.c++ cdhit-utility.h
+-	$(CC) $(CCFLAGS) cdhit-est-2d.c++ -c
++	$(CXX) $(CCFLAGS) cdhit-est-2d.c++ -c
+ 
+ cdhit-div.o: cdhit-div.c++ cdhit-common.h
+-	$(CC) $(CCFLAGS) cdhit-div.c++ -c
++	$(CXX) $(CCFLAGS) cdhit-div.c++ -c
+ 
+ cdhit-454.o: cdhit-454.c++ cdhit-common.h
+-	$(CC) $(CCFLAGS) cdhit-454.c++ -c
++	$(CXX) $(CCFLAGS) cdhit-454.c++ -c
+ 
+-PREFIX ?= /usr/local/bin
++PREFIX ?= /usr/local
+ 
+ install:
++	mkdir -p $(DESTDIR)$(PREFIX)/bin
+ 	for prog in $(PROGS); do \
+-		install -m 0755 $$prog $(PREFIX); \
++		install -m 0755 $$prog $(DESTDIR)$(PREFIX)/bin; \
+ 	done
+-	install -m 0755 *.pl $(PREFIX);
++	install -m 0755 *.pl $(DESTDIR)$(PREFIX)/bin
diff --git a/biology/cd-hit/pkg-plist b/biology/cd-hit/pkg-plist
index 265308f03170..f7e45a239860 100644
--- a/biology/cd-hit/pkg-plist
+++ b/biology/cd-hit/pkg-plist
@@ -1,7 +1,9 @@
+bin/FET.pl
 bin/cd-hit
 bin/cd-hit-2d
 bin/cd-hit-2d-para.pl
 bin/cd-hit-454
+bin/cd-hit-clstr_2_blm8.pl
 bin/cd-hit-div
 bin/cd-hit-div.pl
 bin/cd-hit-est
@@ -11,6 +13,8 @@ bin/clstr2tree.pl
 bin/clstr2txt.pl
 bin/clstr2xml.pl
 bin/clstr_cut.pl
+bin/clstr_list.pl
+bin/clstr_list_sort.pl
 bin/clstr_merge.pl
 bin/clstr_merge_noorder.pl
 bin/clstr_quality_eval.pl