Index: head/biology/cufflinks/Makefile
===================================================================
--- head/biology/cufflinks/Makefile	(revision 529952)
+++ head/biology/cufflinks/Makefile	(revision 529953)
@@ -1,41 +1,43 @@
 # $FreeBSD$
 
 PORTNAME=	cufflinks
 DISTVERSIONPREFIX=	v
-DISTVERSION=	2.2.1-83
-DISTVERSIONSUFFIX=	-gb4fa050
-PORTREVISION=	2
+DISTVERSION=	2.2.1-89
+DISTVERSIONSUFFIX=	-gdc3b0cb
 CATEGORIES=	biology
+
+PATCH_SITES=	https://github.com/${GH_ACCOUNT}/${PORTNAME}/commit/
+PATCHFILES+=	ea4671149f3054c773d99cea521db75bf7b0658f.patch:-p1 # https://github.com/cole-trapnell-lab/cufflinks/pull/127
 
 MAINTAINER=	yuri@FreeBSD.org
 COMMENT=	Cufflinks assembles transcripts, estimates their abundance, etc
 
 LICENSE=	BSL
 LICENSE_FILE=	${WRKSRC}/LICENSE
 
 LIB_DEPENDS=	libboost_system.so:devel/boost-libs \
 		libhts.so:biology/htslib
 
 USES=		autoreconf eigen:3 gmake python shebangfix
 SHEBANG_FILES=	src/cuffmerge
 GNU_CONFIGURE=	yes
 USE_GITHUB=	yes
 GH_ACCOUNT=	cole-trapnell-lab
 
 CXXFLAGS+=	-I${LOCALBASE}/include/eigen3
 CFLAGS+=	-I${LOCALBASE}/include/eigen3 # https://github.com/cole-trapnell-lab/cufflinks/issues/113
 
 PLIST_FILES=	bin/compress_gtf \
 		bin/cuffcompare \
 		bin/cuffdiff \
 		bin/cufflinks \
 		bin/cuffmerge \
 		bin/cuffnorm \
 		bin/cuffquant \
 		bin/gffread \
 		bin/gtf_to_sam
 
 post-patch: # https://github.com/cole-trapnell-lab/cufflinks/issues/116
 	@${GREP} -rl 'fabs(' ${WRKSRC} | ${GREP} "\.cpp$$" | ${XARGS} ${REINPLACE_CMD} 's|std::fabs(|fabs(| ; s|fabs(|::fabs(|'
 
 .include <bsd.port.mk>
Index: head/biology/cufflinks/distinfo
===================================================================
--- head/biology/cufflinks/distinfo	(revision 529952)
+++ head/biology/cufflinks/distinfo	(revision 529953)
@@ -1,3 +1,5 @@
-TIMESTAMP = 1558818522
-SHA256 (cole-trapnell-lab-cufflinks-v2.2.1-83-gb4fa050_GH0.tar.gz) = 0b26b02c080115d4262d466503bdc43db5ff5583d8122e77355782dc7cbe0522
-SIZE (cole-trapnell-lab-cufflinks-v2.2.1-83-gb4fa050_GH0.tar.gz) = 8804967
+TIMESTAMP = 1585636520
+SHA256 (cole-trapnell-lab-cufflinks-v2.2.1-89-gdc3b0cb_GH0.tar.gz) = 3947a7266b4f58a92b3944b8e205c8875a7c0ce9ea19b394ea82ff77b91999be
+SIZE (cole-trapnell-lab-cufflinks-v2.2.1-89-gdc3b0cb_GH0.tar.gz) = 8807044
+SHA256 (ea4671149f3054c773d99cea521db75bf7b0658f.patch) = d64446bab1b683dbdb51b33992694bbbc6511aa4eacd2b95812da75e090dff47
+SIZE (ea4671149f3054c773d99cea521db75bf7b0658f.patch) = 3779
Index: head/biology/cufflinks/files/patch-src_biascorrection.h
===================================================================
--- head/biology/cufflinks/files/patch-src_biascorrection.h	(revision 529952)
+++ head/biology/cufflinks/files/patch-src_biascorrection.h	(nonexistent)
@@ -1,11 +0,0 @@
---- src/biascorrection.h.orig	2019-05-25 21:22:56 UTC
-+++ src/biascorrection.h
-@@ -15,7 +15,7 @@
- #include <vector>
- #include <list>
- #include <string>
--#include <boost/tr1/unordered_map.hpp>
-+#include <boost/unordered_map.hpp>
- #include <boost/thread.hpp>
- #include "common.h"
- 

Property changes on: head/biology/cufflinks/files/patch-src_biascorrection.h
___________________________________________________________________
Deleted: fbsd:nokeywords
## -1 +0,0 ##
-yes
\ No newline at end of property
Deleted: svn:eol-style
## -1 +0,0 ##
-native
\ No newline at end of property
Deleted: svn:mime-type
## -1 +0,0 ##
-text/plain
\ No newline at end of property