Index: head/biology/kallisto/Makefile
===================================================================
--- head/biology/kallisto/Makefile	(revision 493809)
+++ head/biology/kallisto/Makefile	(revision 493810)
@@ -1,34 +1,35 @@
 # $FreeBSD$
 
-PORTNAME=	kallisto
+PORTNAME=		kallisto
 DISTVERSIONPREFIX=	v
-DISTVERSION=	0.43.1
-PORTREVISION=	4
-CATEGORIES=	biology
+DISTVERSION=		0.45.1
+CATEGORIES=		biology
 
 MAINTAINER=	jwb@FreeBSD.org
 COMMENT=	Quantify abundances of transcripts from RNA-Seq data
 
 LICENSE=	BSD2CLAUSE
 LICENSE_FILE=	${WRKSRC}/license.txt
 
 LIB_DEPENDS=	libhdf5.so:science/hdf5 \
-		libsz.so:science/szip
+		libsz.so:science/szip \
+		libhts.so:biology/htslib
 
-USES=		cmake compiler:c++11-lang
+USES=		cmake:noninja compiler:c++11-lang
 USE_GITHUB=	yes
 GH_ACCOUNT=	pachterlab
 
 SUB_FILES=	kallisto-test
 
-PORTEXAMPLES=	*
-PLIST_FILES=	bin/kallisto
+PORTEXAMPLES=		*
+PLIST_FILES=		bin/kallisto
 EXAMPLES_PLIST_FILES=	bin/kallisto-test
 
 OPTIONS_DEFINE=	EXAMPLES
+LDFLAGS+=	-L${LOCALBASE}/lib
 
 post-install-EXAMPLES-on:
 	${INSTALL_SCRIPT} ${WRKDIR}/kallisto-test ${STAGEDIR}${PREFIX}/bin
 	cd ${WRKSRC}/test && ${COPYTREE_SHARE} . ${STAGEDIR}${EXAMPLESDIR}
 
 .include <bsd.port.mk>
Index: head/biology/kallisto/distinfo
===================================================================
--- head/biology/kallisto/distinfo	(revision 493809)
+++ head/biology/kallisto/distinfo	(revision 493810)
@@ -1,3 +1,3 @@
-TIMESTAMP = 1512166931
-SHA256 (pachterlab-kallisto-v0.43.1_GH0.tar.gz) = 2164938c2c61c04e338c4c132cf749f56d39e6f0b4c517121bca1fbc218e430e
-SIZE (pachterlab-kallisto-v0.43.1_GH0.tar.gz) = 1067076
+TIMESTAMP = 1551030949
+SHA256 (pachterlab-kallisto-v0.45.1_GH0.tar.gz) = 2c97280c69991f995f77e7c8ab56ae5060329c90f7f0d7e9ca2f01dd50ee378f
+SIZE (pachterlab-kallisto-v0.45.1_GH0.tar.gz) = 2250488

Property changes on: head/biology/kallisto/distinfo
___________________________________________________________________
Modified: fbsd:nokeywords
## -1 +1 ##
-on
\ No newline at end of property
+yes
\ No newline at end of property
Index: head/biology/kallisto/files/kallisto-test.in
===================================================================
--- head/biology/kallisto/files/kallisto-test.in	(revision 493809)
+++ head/biology/kallisto/files/kallisto-test.in	(revision 493810)
@@ -1,48 +1,45 @@
 #!/bin/sh
 
 ##########################################################################
 #   Script description:
+#       Run standard kallisto test data
 #       
-#   Arguments:
-#       
-#   Returns:
-#       
 #   History:
 #   Date        Name        Modification
-#   2016-03-21  Charlie &   Begin
+#   2016-03-21  J Bacon     Begin
 ##########################################################################
 
 usage()
 {
     printf "Usage: $0 test-directory\n"
     exit 1
 }
 
 
 ##########################################################################
 #   Main
 ##########################################################################
 
 if [ $# != 1 ]; then
     usage
 fi
 
 dir="$1"
 if [ -e "$dir" ]; then
     printf "$dir already exists.  Remove it first or choose a different name.\n"
     exit 1
 fi
 
 cp -iR %%EXAMPLESDIR%% "$dir"
 cd "$dir"
 kallisto index -i transcripts.idx transcripts.fasta.gz
 kallisto quant -i transcripts.idx -o output -b 100 reads_1.fastq.gz reads_2.fastq.gz
 ls -l output
 more output/abundance.tsv
 
 cat << EOM
 
 See https://pachterlab.github.io/kallisto/starting.html for instructions
 on interpreting the output above.
 
 EOM

Property changes on: head/biology/kallisto/files/kallisto-test.in
___________________________________________________________________
Modified: fbsd:nokeywords
## -1 +1 ##
-on
\ No newline at end of property
+yes
\ No newline at end of property
Deleted: svn:keywords
## -1 +0,0 ##
-FreeBSD=%H
\ No newline at end of property
Index: head/biology/kallisto/files/patch-CMakeLists.txt
===================================================================
--- head/biology/kallisto/files/patch-CMakeLists.txt	(nonexistent)
+++ head/biology/kallisto/files/patch-CMakeLists.txt	(revision 493810)
@@ -0,0 +1,25 @@
+--- CMakeLists.txt.orig	2018-12-20 14:20:05 UTC
++++ CMakeLists.txt
+@@ -34,22 +34,6 @@ ELSE(LINK MATCHES shared)
+     message("shared build")
+ ENDIF(LINK MATCHES static)
+ 
+-
+-include(ExternalProject)
+-ExternalProject_Add(htslib
+-    PREFIX ${PROJECT_SOURCE_DIR}/ext/htslib
+-    SOURCE_DIR ${PROJECT_SOURCE_DIR}/ext/htslib
+-    BUILD_IN_SOURCE 1
+-    CONFIGURE_COMMAND autoheader && autoconf && ${PROJECT_SOURCE_DIR}/ext/htslib/configure 
+-        --prefix=${PREFIX} --disable-bz2 --disable-lzma --disable-libcurl
+-    BUILD_COMMAND make lib-static
+-    INSTALL_COMMAND ""
+-)
+-
+-include_directories(${htslib_PREFIX}/src/htslib)
+-
+-
+-
+ # add_compile_options(-Wdeprecated-register)
+ 
+ add_subdirectory(src)

Property changes on: head/biology/kallisto/files/patch-CMakeLists.txt
___________________________________________________________________
Added: fbsd:nokeywords
## -0,0 +1 ##
+yes
\ No newline at end of property
Added: svn:eol-style
## -0,0 +1 ##
+native
\ No newline at end of property
Added: svn:mime-type
## -0,0 +1 ##
+text/plain
\ No newline at end of property
Index: head/biology/kallisto/files/patch-src_CMakeLists.txt
===================================================================
--- head/biology/kallisto/files/patch-src_CMakeLists.txt	(nonexistent)
+++ head/biology/kallisto/files/patch-src_CMakeLists.txt	(revision 493810)
@@ -0,0 +1,26 @@
+--- src/CMakeLists.txt.orig	2018-10-17 23:58:22 UTC
++++ src/CMakeLists.txt
+@@ -3,15 +3,13 @@ file(GLOB headers *.h *.hpp)
+ 
+ list(REMOVE_ITEM sources main.cpp)
+ 
+-include_directories(../ext/htslib)
+-
+ add_library(kallisto_core ${sources} ${headers})
+ target_include_directories(kallisto_core PUBLIC ${CMAKE_CURRENT_SOURCE_DIR})
+ 
+ add_executable(kallisto main.cpp)
+ 
+ find_package( Threads REQUIRED )
+-target_link_libraries(kallisto kallisto_core pthread ${CMAKE_CURRENT_SOURCE_DIR}/../ext/htslib/libhts.a)
++target_link_libraries(kallisto kallisto_core pthread hts)
+ 
+ if(LINK MATCHES static)
+     set(BUILD_SHARED_LIBS OFF)
+@@ -56,4 +54,4 @@ else()
+ endif(LINK MATCHES static)
+ 
+ 
+-install(TARGETS kallisto DESTINATION "${CMAKE_INSTALL_BINDIR}")
+\ No newline at end of file
++install(TARGETS kallisto DESTINATION "${CMAKE_INSTALL_BINDIR}")

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