Hello community, here is the log from the commit of package bowtie2 for openSUSE:Factory checked in at 2020-05-29 21:23:47 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Comparing /work/SRC/openSUSE:Factory/bowtie2 (Old) and /work/SRC/openSUSE:Factory/.bowtie2.new.3606 (New) ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Package is "bowtie2" Fri May 29 21:23:47 2020 rev:3 rq:809909 version:2.4.1 Changes: -------- --- /work/SRC/openSUSE:Factory/bowtie2/bowtie2.changes 2020-05-13 22:56:52.451101718 +0200 +++ /work/SRC/openSUSE:Factory/.bowtie2.new.3606/bowtie2.changes 2020-05-29 21:37:40.674703602 +0200 @@ -1,0 +2,42 @@ +Tue May 26 21:58:10 UTC 2020 - Atri Bhattacharya <badshah400@gmail.com> + +- Update to version 2.4.1: + * Fixed an issue that would cause the bowtie2 wrapper script to + incorrectly process certain arguments. +- Changes from version 2.4.0: + * Fixed an issue in BAM pattern source where one thread would + prematurely close the read file pointer resulting in other + threads crashing because of "Bad file descriptor" errors. + * Fixed an issue that would cause bowtie2 to crash with + `--no-1mm-upfront` specified. + * Modified bowtie2-build script to better handle of flags and + positional parameters. + * Migrated all python scripts to python3. + * Added support for wildcards in input files to bowtie2 wrapper + script e.g. `bowtie2 -x index -q *.fq` as opposed to `bowtie2 + -x index -q 1.fq,2.fq,3.fq...`. + * Fixed an issue causing bowtie2 to incorrectly process read + names see [gh#BenLangmead/bowtie2#265]. + * Added support for allowing presets to be overridden by more + specific options e.g `bowtie2 -x index --local + --very-fast-local --L22 -q reads.fq` will cause bowtie2 to use + a seed length of 22 instead of a seed length of 25 that's + configured for `--very-fast-local` preset. + * Modified SAM output for `-k`/`-a` so that supplementary + alignments get assigned a MAPQ of 255. + * Fixed an issue that would cause bowtie2-build to not generate + reverse index files. + * Added preliminary support for ppc64le architectures with the + help of SIMDE project see [gh#BenLangmead/bowtie2#271] for + details. + * Fixed an issue causing bowtie2 to incorrectly calculate the + MAPQ when `--mp` was specified in combination with + `--ignore-quals`. +- Add bowtie2-cmake-install-targets.patch to fix cmake scripts, + specfically adding install targets and fixing tests (still does + not work) [gh#BenLangmead/bowtie2#292]. +- Use cmake for building (BuildRequires: cmake); adapt + appropriately for aarch64. +- Use pkgconfig based BuildRequires for zlib. + +------------------------------------------------------------------- Old: ---- bowtie2-2.3.5.1.tar.gz New: ---- bowtie2-2.4.1.tar.gz bowtie2-cmake-install-targets.patch ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Other differences: ------------------ ++++++ bowtie2.spec ++++++ --- /var/tmp/diff_new_pack.Y353yQ/_old 2020-05-29 21:37:41.258705341 +0200 +++ /var/tmp/diff_new_pack.Y353yQ/_new 2020-05-29 21:37:41.262705352 +0200 @@ -20,7 +20,7 @@ %define _lto_cflags %{nil} %endif Name: bowtie2 -Version: 2.3.5.1 +Version: 2.4.1 Release: 0 Summary: Fast and memory-efficient short read aligner License: GPL-3.0-only @@ -28,9 +28,13 @@ URL: http://bowtie-bio.sourceforge.net/bowtie2/index.shtml Source0: https://github.com/BenLangmead/bowtie2/archive/v%{version}.tar.gz#/%{name}-%{version}.tar.gz Source1: simde-0.0~git20190101.422ed9c.tar.xz +# PATCH-FIX-UPSTREAM bowtie2-cmake-install-targets.patch gh#BenLangmead/bowtie2#292 badshah400@gmail.com -- Add install targets to cmake scripts and fix tests; patch taken from upstream git +Patch0: bowtie2-cmake-install-targets.patch +BuildRequires: cmake BuildRequires: gcc-c++ +BuildRequires: pkgconfig BuildRequires: tbb-devel -BuildRequires: zlib-devel +BuildRequires: pkgconfig(zlib) ExclusiveArch: x86_64 s390x ppc64le ppc64 aarch64 %description @@ -45,19 +49,28 @@ %prep %setup -q %setup -q -b 1 +%patch0 -p1 pushd third_party rmdir simde ln -s ../../simde-*/ simde popd +# Workaround to find simde/x86/*.h on aarch64 +ln -s ../simde-*/simde simde %build %ifarch aarch64 -export POPCNT_CAPABILITY=0 +sed -i -e 's/-msse2//' CMakeLists.txt +sed -i -e 's/-m64//' CMakeLists.txt %endif -make %{?_smp_mflags} RELEASE_FLAGS="%{optflags}" +%cmake \ +%ifarch aarch64 + -DNO_POPCNT_CAPABILITY=1 \ +%endif + +%cmake_build %install -%make_install prefix=%{_prefix} +%cmake_install # CONVERT env HASHBANGS TO USE DIRECT EXECUTABLE perlbin=`which perl` ++++++ bowtie2-2.3.5.1.tar.gz -> bowtie2-2.4.1.tar.gz ++++++ /work/SRC/openSUSE:Factory/bowtie2/bowtie2-2.3.5.1.tar.gz /work/SRC/openSUSE:Factory/.bowtie2.new.3606/bowtie2-2.4.1.tar.gz differ: char 12, line 1 ++++++ bowtie2-cmake-install-targets.patch ++++++ ff --git a/CMakeLists.txt b/CMakeLists.txt index 09870962..d2703545 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -23,6 +23,8 @@ set(NO_SPINLOCK ${NO_SPINLOCK}) set(USE_SRA ${USE_SRA}) set(WITH_THREAD_PROFILING ${WITH_THREAD_PROFILING}) set(NO_POPCNT_CAPABILITY ${NO_POPCNT_CAPABILITY}) +set(CMAKE_INSTALL_RPATH "${CMAKE_INSTALL_PREFIX}/lib") +set(CMAKE_BUILD_WITH_INSTALL_RPATH FALSE) set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -m64 -g3 -Wall -msse2") set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -O0") set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -O3 -funroll-loops") @@ -30,7 +32,6 @@ set(INSTALL_DIR "${CMAKE_INSTALL_PREFIX}/bin" CACHE PATH "Installation directory set(CMAKE_EXPORT_COMPILE_COMMANDS on) - if (MINGW) option(BOWTIE_MM "Memory mapped files not supported on Windows" OFF) option(BOWTIE_SHARED_MEM "Shared memory not supported on Windows" OFF) @@ -50,6 +51,12 @@ set(BOWTIE2_BIN_LIST bowtie2-inspect-l ) +set(BOWTIE2_WRAPPER_SCRIPTS + bowtie2 + bowtie2-build + bowtie2-inspect + ) + set(SHARED_CPPS ccnt_lut.cpp ref_read.cpp @@ -204,9 +211,8 @@ if (NO_TBB) set(SHARED_CPPS ${SHARED_CPPS} tinythread.cpp) else() find_library(TBB_LIB_PATH tbb) - if (TBB_LIB_PATH) - find_path(TBB_INCLUDE_PATH tbb) + find_path(TBB_INCLUDE_PATH tbb/tbb.h) link_libraries(${TBB_LIB_PATH}) find_library(TBBMALLOC_PROXY_LIB_PATH tbbmalloc_proxy) if (NOT TBBMALLOC_PROXY_LIB_PATH) @@ -244,6 +250,7 @@ else() set(TBB_SOURCE_DIR ${SOURCE_DIR}) set(TBB_RELEASE_DIR ${TBB_SOURCE_DIR}/build/${TBB_VER}_release) include_directories(${TBB_SOURCE_DIR}/include) + find_path(TBB_INCLUDE_PATH PATHS ${TBB_SOURCE_DIR}/include NAMES tbb/tbb.h) link_directories(${TBB_RELEASE_DIR}) add_library(tbb SHARED IMPORTED) @@ -286,6 +293,29 @@ add_executable(bowtie2-inspect-l ${INSPECT_CPPS} ${SHARED_CPPS}) set_target_properties(bowtie2-align-l bowtie2-build-l bowtie2-inspect-l PROPERTIES COMPILE_FLAGS "-DBOWTIE2_64BIT_INDEX") set_target_properties(bowtie2-inspect-s bowtie2-inspect-l PROPERTIES COMPILE_FLAGS "-DBOWTIE_INSPECT_MAIN") -set_target_properties(${BOWTIE2_BIN_LIST} PROPERTIES DEBUG_POSTFIX -debug) +# set_target_properties(${BOWTIE2_BIN_LIST} PROPERTIES DEBUG_POSTFIX -debug) + +install(TARGETS ${BOWTIE2_BIN_LIST} DESTINATION bin) +install(FILES ${BOWTIE2_WRAPPER_SCRIPTS} + PERMISSIONS OWNER_READ OWNER_WRITE OWNER_EXECUTE GROUP_READ GROUP_EXECUTE WORLD_READ WORLD_EXECUTE + DESTINATION bin) +if (LIBTBB) + install(FILES ${LIBTBB} DESTINATION lib) + install(DIRECTORY ${TBB_INCLUDE_PATH} DESTINATION include) +endif() +if (LIBTBBMALLOC) + install(FILES ${LIBTBBMALLOC} DESTINATION lib) +endif() +if (LIBTBBMALLOC_PROXY) + install(FILES ${LIBTBBMALLOC_PROXY} DESTINATION lib) +endif() -add_test(NAME simple-align COMMAND ${PROJECT_SOURCE_DIR}/bowtie2 -x example/index/lambda_virus example/reads/longreads.fq) +add_test(NAME simple-align + WORKING_DIRECTORY ${PROJECT_SOURCE_DIR} + COMMAND bowtie2 -x example/index/lambda_virus example/reads/longreads.fq -u 10) +add_test(NAME simple-build + WORKING_DIRECTORY ${PROJECT_SOURCE_DIR} + COMMAND bowtie2-build-s -c GGGCGGCGACCTCGCGGGTTTTCGCTA out) +add_test(NAME simple-inspect + WORKING_DIRECTORY ${PROJECT_SOURCE_DIR} + COMMAND bowtie2-inspect-s out && rm out*) ++++++ simde-0.0~git20190101.422ed9c.obscpio ++++++