kallisto: Upgrade to 0.45.1, unbundle hstlib

5 files changed, 65 insertions, 16 deletions

diff --git a/biology/kallisto/Makefile b/biology/kallisto/Makefile
index c63d4ac8c7d5..a0596d986c4e 100644
--- a/biology/kallisto/Makefile
+++ b/biology/kallisto/Makefile
@@ -1,10 +1,9 @@
 # $FreeBSD$
 
-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
@@ -13,19 +12,21 @@ 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
diff --git a/biology/kallisto/distinfo b/biology/kallisto/distinfo
index a6cf773150b1..8426d8c5da9d 100644
--- a/biology/kallisto/distinfo
+++ b/biology/kallisto/distinfo
@@ -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
diff --git a/biology/kallisto/files/kallisto-test.in b/biology/kallisto/files/kallisto-test.in
index 7d989c08f4e2..f713e9dc44c2 100644
--- a/biology/kallisto/files/kallisto-test.in
+++ b/biology/kallisto/files/kallisto-test.in
@@ -2,14 +2,11 @@
 
 ##########################################################################
 #   Script description:
-#       
-#   Arguments:
-#       
-#   Returns:
+#       Run standard kallisto test data
 #       
 #   History:
 #   Date        Name        Modification
-#   2016-03-21  Charlie &   Begin
+#   2016-03-21  J Bacon     Begin
 ##########################################################################
 
 usage()
diff --git a/biology/kallisto/files/patch-CMakeLists.txt b/biology/kallisto/files/patch-CMakeLists.txt
new file mode 100644
index 000000000000..9fe2dc02f230
--- /dev/null
+++ b/biology/kallisto/files/patch-CMakeLists.txt
@@ -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)
diff --git a/biology/kallisto/files/patch-src_CMakeLists.txt b/biology/kallisto/files/patch-src_CMakeLists.txt
new file mode 100644
index 000000000000..d549027895ba
--- /dev/null
+++ b/biology/kallisto/files/patch-src_CMakeLists.txt
@@ -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}")