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biology/kallisto: Update to 0.51.0,1

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Add support for long reads to kallisto bus and kallisto quant-tcc
Changes: https://github.com/pachterlab/kallisto/releases

Reported by:    portscout
This commit is contained in:
Jason W. Bacon 2024-07-27 07:02:57 -05:00
parent 7ca85acd52
commit 771236eb8e
5 changed files with 29 additions and 36 deletions
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3
biology/kallisto/Makefile
View File

@ -1,7 +1,6 @@
PORTNAME= kallisto
DISTVERSIONPREFIX= v
DISTVERSION= 0.50.1
PORTREVISION= 1
DISTVERSION= 0.51.0
PORTEPOCH= 1
CATEGORIES= biology

6
biology/kallisto/distinfo
View File

@ -1,3 +1,3 @@
TIMESTAMP = 1698923323
SHA256 (pachterlab-kallisto-v0.50.1_GH0.tar.gz) = 030752bab3b0e33cd3f23f6d8feddd74194e5513532ffbf23519e84db2a86d34
SIZE (pachterlab-kallisto-v0.50.1_GH0.tar.gz) = 5947303
TIMESTAMP = 1722080687
SHA256 (pachterlab-kallisto-v0.51.0_GH0.tar.gz) = efeb0191c1a6a0d6de69111fb66f4bda51ff31fb40c513280f072bd44556f80d
SIZE (pachterlab-kallisto-v0.51.0_GH0.tar.gz) = 5952096

38
biology/kallisto/files/patch-CMakeLists.txt
View File

@ -1,20 +1,19 @@
--- CMakeLists.txt.orig 2023-06-27 10:45:00 UTC
--- CMakeLists.txt.orig 2024-07-20 19:07:27 UTC
+++ CMakeLists.txt
@@ -33,10 +33,11 @@ if(${CMAKE_VERSION} VERSION_LESS 3.1)
@@ -50,10 +50,11 @@ else()
# remove this block once CMake >=3.1 has fixated in the ecosystem
add_compile_options(-std=c++11)
else()
+ # Use c++11 to silence warnings
include(CheckCXXCompilerFlag)
- check_cxx_compiler_flag(-std=c++17 COMPILER_SUPPORTS_CXX17)
+ check_cxx_compiler_flag(-std=c++11 COMPILER_SUPPORTS_CXX17)
check_cxx_compiler_flag(-std=c++17 COMPILER_SUPPORTS_CXX17)
if(COMPILER_SUPPORTS_CXX17)
- set(CMAKE_CXX_STANDARD 17)
+ set(CMAKE_CXX_STANDARD 11)
else()
set(CMAKE_CXX_STANDARD 11)
endif()
@@ -44,9 +45,7 @@ else()
@@ -61,9 +62,7 @@ endif()
set(CMAKE_CXX_EXTENSIONS OFF)
endif()
@ -25,7 +24,7 @@
if(LINK MATCHES static)
message("static build")
@@ -56,42 +55,16 @@ ENDIF(LINK MATCHES static)
@@ -73,24 +72,13 @@ include(ExternalProject)
include(ExternalProject)
@ -45,27 +44,18 @@
PREFIX ${PROJECT_SOURCE_DIR}/ext/bifrost
SOURCE_DIR ${PROJECT_SOURCE_DIR}/ext/bifrost
BUILD_IN_SOURCE 1
CONFIGURE_COMMAND mkdir -p build && cd build && cmake .. -DCMAKE_INSTALL_PREFIX=${PREFIX} -DCMAKE_CXX_FLAGS=${PROJECT_BIFROST_CMAKE_CXX_FLAGS}
CONFIGURE_COMMAND mkdir -p build && cd build && cmake .. -DMAX_KMER_SIZE=${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}
@@ -101,7 +89,7 @@ if (ZLIBNG)
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)
+ BUILD_COMMAND cd zlib-ng && gmake
INSTALL_COMMAND ""
)
endif(ZLIBNG)

2
biology/kallisto/files/patch-ext_bifrost_src_strict__fstream.hpp
View File

@ -1,4 +1,4 @@
--- ext/bifrost/src/strict_fstream.hpp.orig 2023-07-06 14:11:32 UTC
--- ext/bifrost/src/strict_fstream.hpp.orig 2024-07-23 11:27:57 UTC
+++ ext/bifrost/src/strict_fstream.hpp
@@ -64,7 +64,7 @@ static std::string strerror()
} else {

16
biology/kallisto/files/patch-src_CMakeLists.txt
View File

@ -1,6 +1,6 @@
--- src/CMakeLists.txt.orig 2023-06-27 10:45:00 UTC
--- src/CMakeLists.txt.orig 2024-07-20 19:07:27 UTC
+++ src/CMakeLists.txt
@@ -3,12 +3,6 @@ file(GLOB headers *.h *.hpp)
@@ -3,16 +3,10 @@ list(REMOVE_ITEM sources main.cpp)
list(REMOVE_ITEM sources main.cpp)
@ -8,17 +8,21 @@
-include_directories(../ext/htslib)
-endif(USE_BAM)
-
if(NOT MAX_KMER_SIZE)
set(MAX_KMER_SIZE "32")
endif()
-add_compile_options(-Wno-subobject-linkage) # Suppress bifrost warning
-
add_library(kallisto_core ${sources} ${headers})
target_include_directories(kallisto_core PUBLIC ${CMAKE_CURRENT_SOURCE_DIR})
@@ -17,7 +11,7 @@ add_executable(kallisto main.cpp)
@@ -21,7 +15,7 @@ if (USE_BAM)
find_package( Threads REQUIRED )
ExternalProject_Get_Property(bifrost install_dir)
if (USE_BAM)
-target_link_libraries(kallisto kallisto_core pthread ${CMAKE_CURRENT_SOURCE_DIR}/../ext/htslib/libhts.a ${install_dir}/build/src/libbifrost.a)
+target_link_libraries(kallisto kallisto_core pthread hts ${install_dir}/build/src/libbifrost.a)
-target_link_libraries(kallisto kallisto_core pthread ${CMAKE_CURRENT_SOURCE_DIR}/../ext/htslib/libhts.a ${install_dir}/build/src/libbifrost.a -DMAX_KMER_SIZE=${MAX_KMER_SIZE})
+target_link_libraries(kallisto kallisto_core pthread ${install_dir}/build/src/libbifrost.a -DMAX_KMER_SIZE=${MAX_KMER_SIZE})
else()
target_link_libraries(kallisto kallisto_core pthread ${install_dir}/build/src/libbifrost.a)
target_link_libraries(kallisto kallisto_core pthread ${install_dir}/build/src/libbifrost.a -DMAX_KMER_SIZE=${MAX_KMER_SIZE})
endif(USE_BAM)