Date: Sun, 24 Feb 2019 20:32:20 +0000 (UTC) From: "Jason W. Bacon" <jwb@FreeBSD.org> To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r493810 - in head/biology/kallisto: . files Message-ID: <201902242032.x1OKWKQp024914@repo.freebsd.org>
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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@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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