biology/kallisto: Revert to 0.46.1
0.46.2 has long-standing regressions that are not being addressed, including a seg fault when using --genomebam. Also revert to bundled htslib in preparation for biology/htslib upgrade to 1.10. Kallisto source contains modified bits of htslib 1.4.1 that are incompatible with htslib > 1.9.
This commit is contained in:
Jason W. Bacon
parent
52b815fde4
commit
c3b030a079
Notes:
svn2git
2021-03-31 03:12:20 +00:00
svn path=/head/; revision=544077
@ -2,8 +2,8 @@
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PORTNAME= kallisto
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DISTVERSIONPREFIX= v
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DISTVERSION= 0.46.2
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PORTREVISION= 1
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DISTVERSION= 0.46.1
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PORTEPOCH= 1
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CATEGORIES= biology
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MAINTAINER= jwb@FreeBSD.org
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@ -12,11 +12,11 @@ COMMENT= Quantify abundances of transcripts from RNA-Seq data
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LICENSE= BSD2CLAUSE
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LICENSE_FILE= ${WRKSRC}/license.txt
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BUILD_DEPENDS= autoconf>=0:devel/autoconf
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LIB_DEPENDS= libhdf5.so:science/hdf5 \
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libsz.so:science/szip \
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libhts.so:biology/htslib
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libsz.so:science/szip
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USES= cmake:noninja compiler:c++11-lang localbase:ldflags
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USES= cmake:noninja compiler:c++11-lang gmake localbase:ldflags
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USE_GITHUB= yes
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GH_ACCOUNT= pachterlab
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@ -26,10 +26,11 @@ PORTEXAMPLES= *
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PLIST_FILES= bin/kallisto
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EXAMPLES_PLIST_FILES= bin/kallisto-test
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# hdf5 is being phased out and is no longer build in by default, but is still
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# required for Sleuth and other downstream tools. Remove this after Sleuth
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# et all catch up.
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CMAKE_ARGS+= -DUSE_HDF5:BOOL=ON
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# hdf5 is being phased out and is no longer built in by default, but is still
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# required for Sleuth (requires kallisto bootstrap estimates) and other
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# downstream tools. Remove this after Sleuth et all catch up.
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CMAKE_ARGS+= -DUSE_HDF5:BOOL=ON
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MAKE_JOBS_UNSAFE= yes
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OPTIONS_DEFINE= EXAMPLES
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@ -1,3 +1,3 @@
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TIMESTAMP = 1581611719
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SHA256 (pachterlab-kallisto-v0.46.2_GH0.tar.gz) = 10bab0c2929d8c345750e02735b305bbbfa89e8a48f42c4b9af44f3d44ff4c82
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SIZE (pachterlab-kallisto-v0.46.2_GH0.tar.gz) = 2693857
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TIMESTAMP = 1595454023
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SHA256 (pachterlab-kallisto-v0.46.1_GH0.tar.gz) = 492ef081395e8858fcd9832aceb8b61c79358f00afb45e6709146c0fb51dd231
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SIZE (pachterlab-kallisto-v0.46.1_GH0.tar.gz) = 2254560
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@ -1,25 +1,11 @@
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--- CMakeLists.txt.orig 2018-12-20 14:20:05 UTC
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--- CMakeLists.txt.orig 2020-07-22 22:36:50 UTC
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+++ CMakeLists.txt
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@@ -34,22 +34,6 @@ ELSE(LINK MATCHES shared)
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message("shared build")
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ENDIF(LINK MATCHES static)
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-
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-include(ExternalProject)
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-ExternalProject_Add(htslib
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- PREFIX ${PROJECT_SOURCE_DIR}/ext/htslib
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- SOURCE_DIR ${PROJECT_SOURCE_DIR}/ext/htslib
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- BUILD_IN_SOURCE 1
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- CONFIGURE_COMMAND autoheader && autoconf && ${PROJECT_SOURCE_DIR}/ext/htslib/configure
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- --prefix=${PREFIX} --disable-bz2 --disable-lzma --disable-libcurl
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@@ -42,7 +42,7 @@ ExternalProject_Add(htslib
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BUILD_IN_SOURCE 1
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CONFIGURE_COMMAND autoheader && autoconf && ${PROJECT_SOURCE_DIR}/ext/htslib/configure
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--prefix=${PREFIX} --disable-bz2 --disable-lzma --disable-libcurl
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- BUILD_COMMAND make lib-static
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- INSTALL_COMMAND ""
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-)
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-
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-include_directories(${htslib_PREFIX}/src/htslib)
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-
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-
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-
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# add_compile_options(-Wdeprecated-register)
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+ BUILD_COMMAND gmake lib-static
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INSTALL_COMMAND ""
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)
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add_subdirectory(src)
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11
biology/kallisto/files/patch-ext_htslib_configure.ac
Normal file
11
biology/kallisto/files/patch-ext_htslib_configure.ac
Normal file
@ -0,0 +1,11 @@
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--- ext/htslib/configure.ac.orig 2019-11-04 16:28:52 UTC
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+++ ext/htslib/configure.ac
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@@ -23,7 +23,7 @@
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# DEALINGS IN THE SOFTWARE.
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dnl Process this file with autoconf to produce a configure script
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-AC_INIT([HTSlib], m4_esyscmd_s([make print-version]),
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+AC_INIT([HTSlib], [1.4.1],
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[samtools-help@lists.sourceforge.net], [], [http://www.htslib.org/])
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AC_PREREQ(2.63) dnl This version introduced 4-argument AC_CHECK_HEADER
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AC_CONFIG_SRCDIR(hts.c)
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@ -1,26 +0,0 @@
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--- src/CMakeLists.txt.orig 2018-10-17 23:58:22 UTC
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+++ src/CMakeLists.txt
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@@ -3,15 +3,13 @@ file(GLOB headers *.h *.hpp)
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list(REMOVE_ITEM sources main.cpp)
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-include_directories(../ext/htslib)
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-
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add_library(kallisto_core ${sources} ${headers})
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target_include_directories(kallisto_core PUBLIC ${CMAKE_CURRENT_SOURCE_DIR})
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add_executable(kallisto main.cpp)
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find_package( Threads REQUIRED )
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-target_link_libraries(kallisto kallisto_core pthread ${CMAKE_CURRENT_SOURCE_DIR}/../ext/htslib/libhts.a)
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+target_link_libraries(kallisto kallisto_core pthread hts)
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if(LINK MATCHES static)
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set(BUILD_SHARED_LIBS OFF)
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@@ -56,4 +54,4 @@ else()
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endif(LINK MATCHES static)
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-install(TARGETS kallisto DESTINATION "${CMAKE_INSTALL_BINDIR}")
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\ No newline at end of file
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+install(TARGETS kallisto DESTINATION "${CMAKE_INSTALL_BINDIR}")
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