Index: head/biology/kallisto/Makefile
===================================================================
--- head/biology/kallisto/Makefile	(revision 544076)
+++ head/biology/kallisto/Makefile	(revision 544077)
@@ -1,40 +1,41 @@
 # $FreeBSD$
 
 PORTNAME=		kallisto
 DISTVERSIONPREFIX=	v
-DISTVERSION=		0.46.2
-PORTREVISION=		1
+DISTVERSION=		0.46.1
+PORTEPOCH=		1
 CATEGORIES=		biology
 
 MAINTAINER=	jwb@FreeBSD.org
 COMMENT=	Quantify abundances of transcripts from RNA-Seq data
 
 LICENSE=	BSD2CLAUSE
 LICENSE_FILE=	${WRKSRC}/license.txt
 
+BUILD_DEPENDS=	autoconf>=0:devel/autoconf
 LIB_DEPENDS=	libhdf5.so:science/hdf5 \
-		libsz.so:science/szip \
-		libhts.so:biology/htslib
+		libsz.so:science/szip
 
-USES=		cmake:noninja compiler:c++11-lang localbase:ldflags
+USES=		cmake:noninja compiler:c++11-lang gmake localbase:ldflags
 USE_GITHUB=	yes
 GH_ACCOUNT=	pachterlab
 
 SUB_FILES=	kallisto-test
 
 PORTEXAMPLES=		*
 PLIST_FILES=		bin/kallisto
 EXAMPLES_PLIST_FILES=	bin/kallisto-test
 
-# hdf5 is being phased out and is no longer build in by default, but is still
-# required for Sleuth and other downstream tools.  Remove this after Sleuth
-# et all catch up.
-CMAKE_ARGS+=	-DUSE_HDF5:BOOL=ON
+# hdf5 is being phased out and is no longer built in by default, but is still
+# required for Sleuth (requires kallisto bootstrap estimates) and other
+# downstream tools.  Remove this after Sleuth et all catch up.
+CMAKE_ARGS+=		-DUSE_HDF5:BOOL=ON
+MAKE_JOBS_UNSAFE=	yes
 
 OPTIONS_DEFINE=	EXAMPLES
 
 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 544076)
+++ head/biology/kallisto/distinfo	(revision 544077)
@@ -1,3 +1,3 @@
-TIMESTAMP = 1581611719
-SHA256 (pachterlab-kallisto-v0.46.2_GH0.tar.gz) = 10bab0c2929d8c345750e02735b305bbbfa89e8a48f42c4b9af44f3d44ff4c82
-SIZE (pachterlab-kallisto-v0.46.2_GH0.tar.gz) = 2693857
+TIMESTAMP = 1595454023
+SHA256 (pachterlab-kallisto-v0.46.1_GH0.tar.gz) = 492ef081395e8858fcd9832aceb8b61c79358f00afb45e6709146c0fb51dd231
+SIZE (pachterlab-kallisto-v0.46.1_GH0.tar.gz) = 2254560
Index: head/biology/kallisto/files/patch-src_CMakeLists.txt
===================================================================
--- head/biology/kallisto/files/patch-src_CMakeLists.txt	(revision 544076)
+++ head/biology/kallisto/files/patch-src_CMakeLists.txt	(nonexistent)
@@ -1,26 +0,0 @@
---- 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
___________________________________________________________________
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
Index: head/biology/kallisto/files/patch-CMakeLists.txt
===================================================================
--- head/biology/kallisto/files/patch-CMakeLists.txt	(revision 544076)
+++ head/biology/kallisto/files/patch-CMakeLists.txt	(revision 544077)
@@ -1,25 +1,11 @@
---- CMakeLists.txt.orig	2018-12-20 14:20:05 UTC
+--- CMakeLists.txt.orig	2020-07-22 22:36:50 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
+@@ -42,7 +42,7 @@ ExternalProject_Add(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)
++    BUILD_COMMAND gmake lib-static
+     INSTALL_COMMAND ""
+ )
  
- add_subdirectory(src)
Index: head/biology/kallisto/files/patch-ext_htslib_configure.ac
===================================================================
--- head/biology/kallisto/files/patch-ext_htslib_configure.ac	(nonexistent)
+++ head/biology/kallisto/files/patch-ext_htslib_configure.ac	(revision 544077)
@@ -0,0 +1,11 @@
+--- ext/htslib/configure.ac.orig	2019-11-04 16:28:52 UTC
++++ ext/htslib/configure.ac
+@@ -23,7 +23,7 @@
+ # DEALINGS IN THE SOFTWARE.
+ 
+ dnl Process this file with autoconf to produce a configure script
+-AC_INIT([HTSlib], m4_esyscmd_s([make print-version]),
++AC_INIT([HTSlib], [1.4.1],
+         [samtools-help@lists.sourceforge.net], [], [http://www.htslib.org/])
+ AC_PREREQ(2.63)  dnl This version introduced 4-argument AC_CHECK_HEADER
+ AC_CONFIG_SRCDIR(hts.c)

Property changes on: head/biology/kallisto/files/patch-ext_htslib_configure.ac
___________________________________________________________________
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