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 <badshah...@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 badshah...@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 ++++++
