head 1.6; access; symbols pkgsrc-2026Q1:1.6.0.14 pkgsrc-2026Q1-base:1.6 pkgsrc-2025Q4:1.6.0.12 pkgsrc-2025Q4-base:1.6 pkgsrc-2025Q3:1.6.0.10 pkgsrc-2025Q3-base:1.6 pkgsrc-2025Q2:1.6.0.8 pkgsrc-2025Q2-base:1.6 pkgsrc-2025Q1:1.6.0.6 pkgsrc-2025Q1-base:1.6 pkgsrc-2024Q4:1.6.0.4 pkgsrc-2024Q4-base:1.6 pkgsrc-2024Q3:1.6.0.2 pkgsrc-2024Q3-base:1.6 pkgsrc-2024Q2:1.4.0.6 pkgsrc-2024Q2-base:1.4 pkgsrc-2024Q1:1.4.0.4 pkgsrc-2024Q1-base:1.4 pkgsrc-2023Q4:1.4.0.2 pkgsrc-2023Q4-base:1.4 pkgsrc-2023Q3:1.3.0.14 pkgsrc-2023Q3-base:1.3 pkgsrc-2023Q2:1.3.0.12 pkgsrc-2023Q2-base:1.3 pkgsrc-2023Q1:1.3.0.10 pkgsrc-2023Q1-base:1.3 pkgsrc-2022Q4:1.3.0.8 pkgsrc-2022Q4-base:1.3 pkgsrc-2022Q3:1.3.0.6 pkgsrc-2022Q3-base:1.3 pkgsrc-2022Q2:1.3.0.4 pkgsrc-2022Q2-base:1.3 pkgsrc-2022Q1:1.3.0.2 pkgsrc-2022Q1-base:1.3 pkgsrc-2020Q2:1.1.0.14 pkgsrc-2020Q2-base:1.1 pkgsrc-2020Q1:1.1.0.10 pkgsrc-2020Q1-base:1.1 pkgsrc-2019Q4:1.1.0.12 pkgsrc-2019Q4-base:1.1 pkgsrc-2019Q3:1.1.0.8 pkgsrc-2019Q3-base:1.1 pkgsrc-2019Q2:1.1.0.6 pkgsrc-2019Q2-base:1.1 pkgsrc-2019Q1:1.1.0.4 pkgsrc-2019Q1-base:1.1 pkgsrc-2018Q4:1.1.0.2 pkgsrc-2018Q4-base:1.1; locks; strict; comment @# @; 1.6 date 2024.09.20.00.03.15; author bacon; state Exp; branches; next 1.5; commitid vGzFMkGm3GMJAtqF; 1.5 date 2024.07.27.12.22.54; author bacon; state Exp; branches; next 1.4; commitid OLdxWtcRDO02stjF; 1.4 date 2023.11.04.14.35.07; author bacon; state Exp; branches; next 1.3; commitid 1gIhLVph3euAJiLE; 1.3 date 2022.02.27.01.57.27; author bacon; state Exp; branches; next 1.2; commitid 8xLjjdzaBviZicuD; 1.2 date 2020.07.30.07.59.19; author wiz; state dead; branches; next 1.1; commitid 5HZgDwlox2FyR4iC; 1.1 date 2018.12.21.19.00.56; author bacon; state Exp; branches; next ; commitid fPsZiwOysvbpoH4B; desc @@ 1.6 log @biology/kallisto: Update to 0.51.1 Enhancements to ir-kallisto and pseudoalignments Changes: https://github.com/pachterlab/kallisto/releases Reported by: portscout @ text @$NetBSD$ # Use external htslib --- CMakeLists.txt.orig 2024-07-20 19:07:27.000000000 +0000 +++ CMakeLists.txt @@@@ -23,16 +23,12 @@@@ add_compile_definitions("MAX_KMER_SIZE=$ option(USE_HDF5 "Compile with HDF5 support" OFF) #OFF by default -option(USE_BAM "Compile with HTSLIB support" OFF) # OFF by default +option(USE_BAM "Compile with HTSLIB support" ON) if(USE_HDF5) add_compile_definitions("USE_HDF5=ON") endif(USE_HDF5) -if(NOT USE_BAM) - add_compile_definitions("NO_HTSLIB=ON") -endif() - set(EXT_PROJECTS_DIR ${PROJECT_SOURCE_DIR}/ext) set(CMAKE_CXX_FLAGS_PROFILE "-g") @@@@ -73,42 +69,16 @@@@ ENDIF(LINK MATCHES static) include(ExternalProject) -if (USE_BAM) -ExternalProject_Add(htslib - PREFIX ${PROJECT_SOURCE_DIR}/ext/htslib - SOURCE_DIR ${PROJECT_SOURCE_DIR}/ext/htslib - BUILD_IN_SOURCE 1 - CONFIGURE_COMMAND autoreconf -i && autoheader && autoconf && ${PROJECT_SOURCE_DIR}/ext/htslib/configure - --prefix=${PREFIX} --disable-bz2 --disable-lzma --disable-libcurl - BUILD_COMMAND make lib-static - INSTALL_COMMAND "" -) -endif(USE_BAM) ExternalProject_Add(bifrost PREFIX ${PROJECT_SOURCE_DIR}/ext/bifrost SOURCE_DIR ${PROJECT_SOURCE_DIR}/ext/bifrost BUILD_IN_SOURCE 1 CONFIGURE_COMMAND mkdir -p build && cd build && cmake .. -DMAX_KMER_SIZE=${MAX_KMER_SIZE} -DCMAKE_INSTALL_PREFIX=${PREFIX} -DCMAKE_CXX_FLAGS=${PROJECT_BIFROST_CMAKE_CXX_FLAGS} ${DO_ENABLE_AVX2} ${DO_ENABLE_COMPILATION_ARCH} - BUILD_COMMAND cd build && make + BUILD_COMMAND cd build && gmake INSTALL_COMMAND "" ) -if (ZLIBNG) - message("zlib-ng enabled.") - ExternalProject_Add(zlib-ng - PREFIX ${PROJECT_SOURCE_DIR}/ext/zlib-ng - SOURCE_DIR ${PROJECT_SOURCE_DIR}/ext/zlib-ng - BUILD_IN_SOURCE 1 - CONFIGURE_COMMAND mkdir -p zlib-ng && cd zlib-ng && cmake .. -DZLIB_COMPAT=ON -DZLIB_ENABLE_TESTS=OFF -DCMAKE_INSTALL_PREFIX=${PREFIX} - BUILD_COMMAND cd zlib-ng && make - INSTALL_COMMAND "" - ) -endif(ZLIBNG) - -if (USE_BAM) -include_directories(${htslib_PREFIX}/src/htslib) -endif(USE_BAM) include_directories(${EXT_PROJECTS_DIR}/bifrost/build/src) ExternalProject_Get_Property(bifrost install_dir) @ 1.5 log @biology/kallisto: Update to 0.51.0,1 Add support for long reads to kallisto bus and kallisto quant-tcc Changes: https://github.com/pachterlab/kallisto/releases Reported by: portscout @ text @@ 1.4 log @biology/kallisto: Update to 0.50.1 Update kallisto index version to 13 A few other new features Changes: https://github.com/pachterlab/kallisto/releases @ text @d3 1 a3 1 # Unbundle htslib and zlib, use gmake d5 1 a5 1 --- CMakeLists.txt.orig 2023-06-27 10:45:00.000000000 +0000 d7 19 a25 1 @@@@ -56,42 +56,16 @@@@ ENDIF(LINK MATCHES static) d45 1 a45 1 CONFIGURE_COMMAND mkdir -p build && cd build && cmake .. -DCMAKE_INSTALL_PREFIX=${PREFIX} -DCMAKE_CXX_FLAGS=${PROJECT_BIFROST_CMAKE_CXX_FLAGS} @ 1.3 log @biology/kallisto: Update to 0.48.0 Long awaited bug fix release Also unbundled htslib Changes: https://github.com/pachterlab/kallisto/tags @ text @d3 1 a3 1 # Unbundle htslib d5 1 a5 1 --- CMakeLists.txt.orig 2022-02-26 16:36:13.527572702 +0000 d7 1 a7 1 @@@@ -43,15 +43,6 @@@@ ENDIF(LINK MATCHES static) d11 1 d16 1 a16 1 - CONFIGURE_COMMAND autoheader && autoconf && ${PROJECT_SOURCE_DIR}/ext/htslib/configure d21 1 d23 9 a31 1 include_directories(${htslib_PREFIX}/src/htslib) d33 18 @ 1.2 log @kallisto: remove patches that were removed from distinfo during update @ text @d1 1 a1 1 $NetBSD: patch-CMakeLists.txt,v 1.1 2018/12/21 19:00:56 bacon Exp $ d5 1 a5 1 --- CMakeLists.txt.orig 2018-12-19 17:13:04.000000000 +0000 d7 1 a7 2 @@@@ -35,21 +35,6 @@@@ ELSE(LINK MATCHES shared) ENDIF(LINK MATCHES static) d10 1 a10 1 -include(ExternalProject) a19 6 - -include_directories(${htslib_PREFIX}/src/htslib) - - - # add_compile_options(-Wdeprecated-register) d21 2 a22 1 add_subdirectory(src) @ 1.1 log @biology/kallisto: import kallisto-0.45.0 Kallisto is a program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. It is based on the novel idea of pseudoalignment for rapidly determining the compatibility of reads with targets, without the need for alignment. @ text @d1 1 a1 1 $NetBSD$ @