svn commit: r493810 - in head/biology/kallisto: . files
Jason W. Bacon
jwb at FreeBSD.org
Sun Feb 24 20:32:22 UTC 2019
Author: jwb
Date: Sun Feb 24 20:32:19 2019
New Revision: 493810
URL: https://svnweb.freebsd.org/changeset/ports/493810
Log:
kallisto: Upgrade to 0.45.1, unbundle hstlib
Added:
head/biology/kallisto/files/patch-CMakeLists.txt (contents, props changed)
head/biology/kallisto/files/patch-src_CMakeLists.txt (contents, props changed)
Modified:
head/biology/kallisto/Makefile
head/biology/kallisto/distinfo (contents, props changed)
head/biology/kallisto/files/kallisto-test.in (contents, props changed)
Modified: head/biology/kallisto/Makefile
==============================================================================
--- head/biology/kallisto/Makefile Sun Feb 24 20:23:26 2019 (r493809)
+++ head/biology/kallisto/Makefile Sun Feb 24 20:32:19 2019 (r493810)
@@ -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 at 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
Modified: head/biology/kallisto/distinfo
==============================================================================
--- head/biology/kallisto/distinfo Sun Feb 24 20:23:26 2019 (r493809)
+++ head/biology/kallisto/distinfo Sun Feb 24 20:32:19 2019 (r493810)
@@ -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
Modified: head/biology/kallisto/files/kallisto-test.in
==============================================================================
--- head/biology/kallisto/files/kallisto-test.in Sun Feb 24 20:23:26 2019 (r493809)
+++ head/biology/kallisto/files/kallisto-test.in Sun Feb 24 20:32:19 2019 (r493810)
@@ -2,14 +2,11 @@
##########################################################################
# 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()
Added: head/biology/kallisto/files/patch-CMakeLists.txt
==============================================================================
--- /dev/null 00:00:00 1970 (empty, because file is newly added)
+++ head/biology/kallisto/files/patch-CMakeLists.txt Sun Feb 24 20:32:19 2019 (r493810)
@@ -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)
Added: head/biology/kallisto/files/patch-src_CMakeLists.txt
==============================================================================
--- /dev/null 00:00:00 1970 (empty, because file is newly added)
+++ head/biology/kallisto/files/patch-src_CMakeLists.txt Sun Feb 24 20:32:19 2019 (r493810)
@@ -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}")
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