Date: Wed, 19 Jan 2022 14:00:10 GMT From: "Jason W. Bacon" <jwb@FreeBSD.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org Subject: git: c9bd01bdf4c1 - main - biology/kallisto: Update to 0.48.0 Message-ID: <202201191400.20JE0A1B074583@gitrepo.freebsd.org>
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The branch main has been updated by jwb: URL: https://cgit.FreeBSD.org/ports/commit/?id=c9bd01bdf4c1dae17b53482e9dabe000d310cf50 commit c9bd01bdf4c1dae17b53482e9dabe000d310cf50 Author: Jason W. Bacon <jwb@FreeBSD.org> AuthorDate: 2022-01-19 13:57:36 +0000 Commit: Jason W. Bacon <jwb@FreeBSD.org> CommitDate: 2022-01-19 13:57:36 +0000 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 --- biology/kallisto/Makefile | 10 +++++--- biology/kallisto/distinfo | 6 ++--- biology/kallisto/files/kallisto-test.in | 29 +++++++++++++++++++-- biology/kallisto/files/patch-CMakeLists.txt | 30 ++++++++++++++++------ .../kallisto/files/patch-ext_htslib_configure.ac | 11 -------- biology/kallisto/files/patch-src_CMakeLists.txt | 26 +++++++++++++++++++ biology/kallisto/files/patch-src_kseq.h | 12 +++++++++ 7 files changed, 97 insertions(+), 27 deletions(-) diff --git a/biology/kallisto/Makefile b/biology/kallisto/Makefile index 996d22ee8720..3d4aecd0b9d3 100644 --- a/biology/kallisto/Makefile +++ b/biology/kallisto/Makefile @@ -1,6 +1,6 @@ PORTNAME= kallisto DISTVERSIONPREFIX= v -DISTVERSION= 0.46.1 +DISTVERSION= 0.48.0 PORTEPOCH= 1 CATEGORIES= biology @@ -12,7 +12,8 @@ LICENSE_FILE= ${WRKSRC}/license.txt BUILD_DEPENDS= autoconf>=0:devel/autoconf LIB_DEPENDS= libhdf5.so:science/hdf5 \ - libsz.so:science/szip + libsz.so:science/szip \ + libhts.so:biology/htslib USES= cmake:noninja compiler:c++11-lang gmake localbase:ldflags USE_GITHUB= yes @@ -29,10 +30,13 @@ EXAMPLES_PLIST_FILES= bin/kallisto-test # downstream tools. Remove this after Sleuth et al catch up. CMAKE_ARGS+= -DUSE_HDF5:BOOL=ON MAKE_JOBS_UNSAFE= yes -LDFLAGS+= -lz +LDFLAGS+= -lhts -lz OPTIONS_DEFINE= EXAMPLES +post-extract: + ${RM} -rf ${WRKSRC}/ext/htslib + post-install-EXAMPLES-on: ${INSTALL_SCRIPT} ${WRKDIR}/kallisto-test ${STAGEDIR}${PREFIX}/bin cd ${WRKSRC}/test && ${COPYTREE_SHARE} . ${STAGEDIR}${EXAMPLESDIR} diff --git a/biology/kallisto/distinfo b/biology/kallisto/distinfo index 98722ba0c842..1f2de73cccd4 100644 --- a/biology/kallisto/distinfo +++ b/biology/kallisto/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1595454023 -SHA256 (pachterlab-kallisto-v0.46.1_GH0.tar.gz) = 492ef081395e8858fcd9832aceb8b61c79358f00afb45e6709146c0fb51dd231 -SIZE (pachterlab-kallisto-v0.46.1_GH0.tar.gz) = 2254560 +TIMESTAMP = 1642516764 +SHA256 (pachterlab-kallisto-v0.48.0_GH0.tar.gz) = 1797ac4d1f0771e3f1f25dd7972bded735fcb43f853cf52184d3d9353a6269b0 +SIZE (pachterlab-kallisto-v0.48.0_GH0.tar.gz) = 2706838 diff --git a/biology/kallisto/files/kallisto-test.in b/biology/kallisto/files/kallisto-test.in old mode 100644 new mode 100755 index f713e9dc44c2..952063e4e66b --- a/biology/kallisto/files/kallisto-test.in +++ b/biology/kallisto/files/kallisto-test.in @@ -16,6 +16,20 @@ usage() } +########################################################################## +# Function description: +# Pause until user presses return +########################################################################## + +pause() +{ + local junk + + printf "Press return to continue..." + read junk +} + + ########################################################################## # Main ########################################################################## @@ -32,9 +46,20 @@ fi cp -iR %%EXAMPLESDIR%% "$dir" cd "$dir" -kallisto index -i transcripts.idx transcripts.fasta.gz -kallisto quant -i transcripts.idx -o output -b 100 reads_1.fastq.gz reads_2.fastq.gz +kallisto index --index=transcripts.idx transcripts.fasta.gz +pause + +kallisto quant --index=transcripts.idx --genomebam --chromosomes=chrom.txt \ + --gtf=transcripts.gtf.gz --output-dir=output \ + --boostrap-samples=100 reads_1.fastq.gz reads_2.fastq.gz +pause + ls -l output +pause + +# Test genomebam +samtools view output/pseudoalignments.bam | more + more output/abundance.tsv cat << EOM diff --git a/biology/kallisto/files/patch-CMakeLists.txt b/biology/kallisto/files/patch-CMakeLists.txt index b122ef10d345..fb498f8a945b 100644 --- a/biology/kallisto/files/patch-CMakeLists.txt +++ b/biology/kallisto/files/patch-CMakeLists.txt @@ -1,11 +1,25 @@ ---- CMakeLists.txt.orig 2020-07-22 22:36:50 UTC +--- CMakeLists.txt.orig 2019-11-04 16:28:52 UTC +++ CMakeLists.txt -@@ -42,7 +42,7 @@ ExternalProject_Add(htslib - BUILD_IN_SOURCE 1 - CONFIGURE_COMMAND autoheader && autoconf && ${PROJECT_SOURCE_DIR}/ext/htslib/configure - --prefix=${PREFIX} --disable-bz2 --disable-lzma --disable-libcurl +@@ -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 -+ BUILD_COMMAND gmake lib-static - INSTALL_COMMAND "" - ) +- INSTALL_COMMAND "" +-) +- +-include_directories(${htslib_PREFIX}/src/htslib) +- +- +- + # add_compile_options(-Wdeprecated-register) + add_subdirectory(src) diff --git a/biology/kallisto/files/patch-ext_htslib_configure.ac b/biology/kallisto/files/patch-ext_htslib_configure.ac deleted file mode 100644 index 0482cc554c45..000000000000 --- a/biology/kallisto/files/patch-ext_htslib_configure.ac +++ /dev/null @@ -1,11 +0,0 @@ ---- ext/htslib/configure.ac.orig 2019-11-04 16:28:52 UTC -+++ ext/htslib/configure.ac -@@ -23,7 +23,7 @@ - # DEALINGS IN THE SOFTWARE. - - dnl Process this file with autoconf to produce a configure script --AC_INIT([HTSlib], m4_esyscmd_s([make print-version]), -+AC_INIT([HTSlib], [1.4.1], - [samtools-help@lists.sourceforge.net], [], [http://www.htslib.org/]) - AC_PREREQ(2.63) dnl This version introduced 4-argument AC_CHECK_HEADER - AC_CONFIG_SRCDIR(hts.c) diff --git a/biology/kallisto/files/patch-src_CMakeLists.txt b/biology/kallisto/files/patch-src_CMakeLists.txt new file mode 100644 index 000000000000..fbeb9128522a --- /dev/null +++ b/biology/kallisto/files/patch-src_CMakeLists.txt @@ -0,0 +1,26 @@ +--- src/CMakeLists.txt.orig 2021-11-24 14:45:50 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 ${CMAKE_CURRENT_SOURCE_DIR}/../ext/htslib/libhts.a) ++target_link_libraries(kallisto kallisto_core pthread) + + if(LINK MATCHES static) + set(BUILD_SHARED_LIBS OFF) +@@ -56,4 +54,4 @@ else() + endif(LINK MATCHES static) + + +-install(TARGETS kallisto DESTINATION "${CMAKE_INSTALL_BINDIR}") +\ No newline at end of file ++install(TARGETS kallisto DESTINATION "${CMAKE_INSTALL_BINDIR}") diff --git a/biology/kallisto/files/patch-src_kseq.h b/biology/kallisto/files/patch-src_kseq.h new file mode 100644 index 000000000000..f7712a023fda --- /dev/null +++ b/biology/kallisto/files/patch-src_kseq.h @@ -0,0 +1,12 @@ +--- src/kseq.h.orig 2019-11-04 16:28:52 UTC ++++ src/kseq.h +@@ -32,6 +32,9 @@ + #include <string.h> + #include <stdlib.h> + ++// Prevent redefinition of kstring_t below ++#include <htslib/kstring.h> ++ + #define KS_SEP_SPACE 0 // isspace(): \t, \n, \v, \f, \r + #define KS_SEP_TAB 1 // isspace() && !' ' + #define KS_SEP_LINE 2 // line separator: "\n" (Unix) or "\r\n" (Windows)
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