diff options
Diffstat (limited to 'sci-biology/kallisto/files')
4 files changed, 260 insertions, 0 deletions
diff --git a/sci-biology/kallisto/files/kallisto-0.46.2-catch2.patch b/sci-biology/kallisto/files/kallisto-0.46.2-catch2.patch new file mode 100644 index 000000000000..7566966c1c68 --- /dev/null +++ b/sci-biology/kallisto/files/kallisto-0.46.2-catch2.patch @@ -0,0 +1,38 @@ +--- a/unit_tests/main.cpp ++++ b/unit_tests/main.cpp +@@ -1,2 +1,2 @@ + #define CATCH_CONFIG_MAIN +-#include "catch.hpp" ++#include <catch2/catch.hpp> +--- a/unit_tests/test_index.cpp ++++ b/unit_tests/test_index.cpp +@@ -1,4 +1,4 @@ +-#include "catch.hpp" ++#include <catch2/catch.hpp> + + #include "common.h" + #include "KmerIndex.h" +--- a/unit_tests/test_kmerhashtable.cpp ++++ b/unit_tests/test_kmerhashtable.cpp +@@ -1,4 +1,4 @@ +-#include "catch.hpp" ++#include <catch2/catch.hpp> + + #include <random> + #include <string> +--- a/unit_tests/test_multinomial.cpp ++++ b/unit_tests/test_multinomial.cpp +@@ -1,4 +1,4 @@ +-#include "catch.hpp" ++#include <catch2/catch.hpp> + + #include <iostream> + #include <vector> +--- a/unit_tests/test_weights.cpp ++++ b/unit_tests/test_weights.cpp +@@ -1,4 +1,4 @@ +-#include "catch.hpp" ++#include <catch2/catch.hpp> + + #include <vector> + diff --git a/sci-biology/kallisto/files/kallisto-0.46.2-cmake.patch b/sci-biology/kallisto/files/kallisto-0.46.2-cmake.patch new file mode 100644 index 000000000000..ba6114a9164f --- /dev/null +++ b/sci-biology/kallisto/files/kallisto-0.46.2-cmake.patch @@ -0,0 +1,149 @@ +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -11,9 +11,6 @@ + add_compile_definitions("USE_HDF5=ON") + endif(USE_HDF5) + +-set(EXT_PROJECTS_DIR ${PROJECT_SOURCE_DIR}/ext) +-set(CMAKE_CXX_FLAGS_PROFILE "-g") +- + # Set Release type for builds where CMAKE_BUILD_TYPE is unset + # This is usually a good default as this implictly enables + # +@@ -33,44 +30,12 @@ + set(CMAKE_CXX_EXTENSIONS OFF) + endif() + +-#add_compile_options(-Wall -Wno-unused-function) +- +-if(LINK MATCHES static) +- message("static build") +-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 +- INSTALL_COMMAND "" +-) +- +-include_directories(${htslib_PREFIX}/src/htslib) +- +- +- +-# add_compile_options(-Wdeprecated-register) +- + add_subdirectory(src) +-include_directories(${EXT_PROJECTS_DIR}) + + option(BUILD_TESTING "Build unit tests." OFF) + include(CTest) + + if (BUILD_TESTING) +- add_subdirectory(${EXT_PROJECTS_DIR}/catch) +- +- # Includes Catch in the project: +- include_directories(${CATCH_INCLUDE_DIR} ${COMMON_INCLUDES}) +- + add_subdirectory(unit_tests) + endif(BUILD_TESTING) + +--- a/src/CMakeLists.txt ++++ b/src/CMakeLists.txt +@@ -3,30 +3,17 @@ + + 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) +- +-if(LINK MATCHES static) +- set(BUILD_SHARED_LIBS OFF) +- set(HDF5_USE_STATIC_LIBRARIES 1) +- +- if (UNIX AND NOT APPLE) +- #set(CMAKE_EXE_LINKER_FLAGS "-static -static-libgcc -static-libstdc++") +- set(CMAKE_EXE_LINKER_FLAGS "-static -static-libstdc++") +- SET(CMAKE_FIND_LIBRARY_SUFFIXES ".a") +- set(CMAKE_EXE_LINKER_FLAGS "-static -static-libgcc -static-libstdc++") +- endif(UNIX AND NOT APPLE) +- +- SET_TARGET_PROPERTIES(kallisto kallisto_core PROPERTIES LINK_SEARCH_END_STATIC 1) +-endif(LINK MATCHES static) ++find_package( PkgConfig REQUIRED ) ++pkg_check_modules( HTSLIB REQUIRED htslib ) + ++find_package( Threads REQUIRED ) ++target_include_directories(kallisto PRIVATE ${HTSLIB_CFLAGS}) ++target_link_libraries(kallisto PRIVATE kallisto_core Threads::Threads ${HTSLIB_LDFLAGS}) + + if(USE_HDF5) + find_package( HDF5 REQUIRED ) +@@ -36,7 +23,7 @@ + + if ( ZLIB_FOUND ) + include_directories( ${ZLIB_INCLUDE_DIRS} ) +- target_link_libraries(kallisto kallisto_core ${ZLIB_LIBRARIES}) ++ target_link_libraries(kallisto PRIVATE kallisto_core ${ZLIB_LIBRARIES}) + else() + message(FATAL_ERROR "zlib not found. Required for to output files" ) + endif( ZLIB_FOUND ) +@@ -44,22 +31,17 @@ + if(USE_HDF5) + if(HDF5_FOUND) + include_directories( ${HDF5_INCLUDE_DIRS} ) +- target_link_libraries( kallisto_core ${HDF5_LIBRARIES} ) +- target_link_libraries( kallisto ${HDF5_LIBRARIES} ) ++ target_link_libraries( kallisto_core PRIVATE ${HDF5_LIBRARIES} ) ++ target_link_libraries( kallisto PRIVATE ${HDF5_LIBRARIES} ) + else() + message(FATAL_ERROR "HDF5 not found. Required to output files") + endif() + endif(USE_HDF5) + +-if(LINK MATCHES static) +- if (UNIX AND NOT APPLE) +- target_link_libraries(kallisto librt.a) +- endif() +-else() +- if (UNIX AND NOT APPLE) +- target_link_libraries(kallisto rt) +- endif() +-endif(LINK MATCHES static) +- ++target_compile_options( kallisto_core PRIVATE ${HTSLIB_CFLAGS} ) ++target_link_libraries( kallisto_core PRIVATE ${HTSLIB_LDFLAGS} ) + +-install(TARGETS kallisto DESTINATION "${CMAKE_INSTALL_BINDIR}") +\ No newline at end of file ++install(TARGETS kallisto DESTINATION "${CMAKE_INSTALL_BINDIR}") ++if ( BUILD_SHARED_LIBS ) ++ install(TARGETS kallisto_core DESTINATION "${CMAKE_INSTALL_LIBDIR}") ++endif() +--- a/unit_tests/CMakeLists.txt ++++ b/unit_tests/CMakeLists.txt +@@ -8,6 +8,10 @@ + add_executable(tests ${sources}) + add_test(unittest tests) + ++find_package( Catch2 REQUIRED ) ++include_directories( ${Catch2_INCLUDE_DIRS} ) ++target_link_libraries( tests ${Catch2_LIBRARIES} ) ++ + find_package( ZLIB REQUIRED ) + if ( ZLIB_FOUND ) + include_directories( ${ZLIB_INCLUDE_DIRS} ) diff --git a/sci-biology/kallisto/files/kallisto-0.46.2-gcc11.patch b/sci-biology/kallisto/files/kallisto-0.46.2-gcc11.patch new file mode 100644 index 000000000000..19594f067776 --- /dev/null +++ b/sci-biology/kallisto/files/kallisto-0.46.2-gcc11.patch @@ -0,0 +1,21 @@ +From 1d63e9d731bada64f6038818e27f06da63007d73 Mon Sep 17 00:00:00 2001 +From: Nilesh Patra <npatra974@gmail.com> +Date: Thu, 4 Mar 2021 23:38:30 +0530 +Subject: [PATCH] Fix GCC-11 Build Failure: include limits lib + +--- + src/MinCollector.h | 1 + + 1 file changed, 1 insertion(+) + +diff --git a/src/MinCollector.h b/src/MinCollector.h +index a905f1f..c4460fb 100644 +--- a/src/MinCollector.h ++++ b/src/MinCollector.h +@@ -7,6 +7,7 @@ + #include <sstream> + #include <vector> + #include <unordered_map> ++#include <limits> + + #include "KmerIndex.h" + #include "weights.h" diff --git a/sci-biology/kallisto/files/kallisto-0.46.2-htslib.patch b/sci-biology/kallisto/files/kallisto-0.46.2-htslib.patch new file mode 100644 index 000000000000..0e926136261c --- /dev/null +++ b/sci-biology/kallisto/files/kallisto-0.46.2-htslib.patch @@ -0,0 +1,52 @@ +--- a/src/KmerIndex.cpp ++++ b/src/KmerIndex.cpp +@@ -4,7 +4,7 @@ + #include <ctype.h> + #include <zlib.h> + #include <unordered_set> +-#include "kseq.h" ++#include <htslib/kseq.h> + + #ifndef KSEQ_INIT_READY + #define KSEQ_INIT_READY +--- a/src/ProcessReads.cpp ++++ b/src/ProcessReads.cpp +@@ -1,6 +1,6 @@ + /* + #include <zlib.h> +-#include "kseq.h" ++#include <htslib/kseq.h> + #include <string> + #include <vector> + #include <unordered_map> +@@ -20,7 +20,7 @@ + #include <iomanip> + + #include "ProcessReads.h" +-#include "kseq.h" ++#include <htslib/kseq.h> + #include "PseudoBam.h" + #include "Fusion.hpp" + #include "BUSData.h" +--- a/src/ProcessReads.h ++++ b/src/ProcessReads.h +@@ -2,7 +2,7 @@ + #define KALLISTO_PROCESSREADS_H + + #include <zlib.h> +-#include "kseq.h" ++#include <htslib/kseq.h> + #include <string> + #include <vector> + #include <unordered_map> +--- a/unit_tests/test_kmerhashtable.cpp ++++ b/unit_tests/test_kmerhashtable.cpp +@@ -13,7 +13,7 @@ + #include "KmerHashTable.h" + + #include <zlib.h> +-#include "kseq.h" ++#include <htslib/kseq.h> + + #ifndef KSEQ_INIT_READY + #define KSEQ_INIT_READY |