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biology/kallisto: Update to 0.48.0
Fixes segfault with --genomebam in 0.46.2 Unbundle htslib A few new features and performance improvements Changes: https://github.com/pachterlab/kallisto/tags
This commit is contained in:
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f9a2f32279
commit
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@ -1,6 +1,6 @@
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PORTNAME= kallisto
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DISTVERSIONPREFIX= v
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DISTVERSION= 0.46.1
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DISTVERSION= 0.48.0
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PORTEPOCH= 1
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CATEGORIES= biology
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@ -12,7 +12,8 @@ LICENSE_FILE= ${WRKSRC}/license.txt
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BUILD_DEPENDS= autoconf>=0:devel/autoconf
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LIB_DEPENDS= libhdf5.so:science/hdf5 \
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libsz.so:science/szip
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libsz.so:science/szip \
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libhts.so:biology/htslib
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USES= cmake:noninja compiler:c++11-lang gmake localbase:ldflags
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USE_GITHUB= yes
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@ -29,10 +30,13 @@ EXAMPLES_PLIST_FILES= bin/kallisto-test
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# downstream tools. Remove this after Sleuth et al catch up.
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CMAKE_ARGS+= -DUSE_HDF5:BOOL=ON
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MAKE_JOBS_UNSAFE= yes
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LDFLAGS+= -lz
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LDFLAGS+= -lhts -lz
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OPTIONS_DEFINE= EXAMPLES
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post-extract:
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${RM} -rf ${WRKSRC}/ext/htslib
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post-install-EXAMPLES-on:
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${INSTALL_SCRIPT} ${WRKDIR}/kallisto-test ${STAGEDIR}${PREFIX}/bin
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cd ${WRKSRC}/test && ${COPYTREE_SHARE} . ${STAGEDIR}${EXAMPLESDIR}
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@ -1,3 +1,3 @@
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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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TIMESTAMP = 1642516764
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SHA256 (pachterlab-kallisto-v0.48.0_GH0.tar.gz) = 1797ac4d1f0771e3f1f25dd7972bded735fcb43f853cf52184d3d9353a6269b0
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SIZE (pachterlab-kallisto-v0.48.0_GH0.tar.gz) = 2706838
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29
biology/kallisto/files/kallisto-test.in
Normal file → Executable file
29
biology/kallisto/files/kallisto-test.in
Normal file → Executable file
@ -16,6 +16,20 @@ usage()
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}
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##########################################################################
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# Function description:
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# Pause until user presses return
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##########################################################################
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pause()
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{
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local junk
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printf "Press return to continue..."
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read junk
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}
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##########################################################################
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# Main
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##########################################################################
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@ -32,9 +46,20 @@ fi
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cp -iR %%EXAMPLESDIR%% "$dir"
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cd "$dir"
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kallisto index -i transcripts.idx transcripts.fasta.gz
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kallisto quant -i transcripts.idx -o output -b 100 reads_1.fastq.gz reads_2.fastq.gz
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kallisto index --index=transcripts.idx transcripts.fasta.gz
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pause
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kallisto quant --index=transcripts.idx --genomebam --chromosomes=chrom.txt \
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--gtf=transcripts.gtf.gz --output-dir=output \
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--boostrap-samples=100 reads_1.fastq.gz reads_2.fastq.gz
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pause
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ls -l output
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pause
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# Test genomebam
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samtools view output/pseudoalignments.bam | more
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more output/abundance.tsv
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cat << EOM
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@ -1,11 +1,25 @@
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--- CMakeLists.txt.orig 2020-07-22 22:36:50 UTC
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--- CMakeLists.txt.orig 2019-11-04 16:28:52 UTC
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+++ CMakeLists.txt
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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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+ BUILD_COMMAND gmake lib-static
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INSTALL_COMMAND ""
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)
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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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- 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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add_subdirectory(src)
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@ -1,11 +0,0 @@
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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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26
biology/kallisto/files/patch-src_CMakeLists.txt
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26
biology/kallisto/files/patch-src_CMakeLists.txt
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@ -0,0 +1,26 @@
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--- src/CMakeLists.txt.orig 2021-11-24 14:45:50 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 ${CMAKE_CURRENT_SOURCE_DIR}/../ext/htslib/libhts.a)
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+target_link_libraries(kallisto kallisto_core pthread)
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if(LINK MATCHES static)
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set(BUILD_SHARED_LIBS OFF)
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@@ -56,4 +54,4 @@ else()
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endif(LINK MATCHES static)
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-install(TARGETS kallisto DESTINATION "${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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12
biology/kallisto/files/patch-src_kseq.h
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12
biology/kallisto/files/patch-src_kseq.h
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@ -0,0 +1,12 @@
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--- src/kseq.h.orig 2019-11-04 16:28:52 UTC
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+++ src/kseq.h
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@@ -32,6 +32,9 @@
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#include <string.h>
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#include <stdlib.h>
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+// Prevent redefinition of kstring_t below
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+#include <htslib/kstring.h>
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+
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#define KS_SEP_SPACE 0 // isspace(): \t, \n, \v, \f, \r
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#define KS_SEP_TAB 1 // isspace() && !' '
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#define KS_SEP_LINE 2 // line separator: "\n" (Unix) or "\r\n" (Windows)
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