git: 771236eb8e1a - main - biology/kallisto: Update to 0.51.0,1

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From: Jason W. Bacon <jwb_at_FreeBSD.org>
Date: Sat, 27 Jul 2024 12:04:00 UTC
The branch main has been updated by jwb:

URL: https://cgit.FreeBSD.org/ports/commit/?id=771236eb8e1a66e7a33689e30179ef5fe858ec78

commit 771236eb8e1a66e7a33689e30179ef5fe858ec78
Author:     Jason W. Bacon <jwb@FreeBSD.org>
AuthorDate: 2024-07-27 12:02:57 +0000
Commit:     Jason W. Bacon <jwb@FreeBSD.org>
CommitDate: 2024-07-27 12:02:57 +0000

    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
---
 biology/kallisto/Makefile                          |  3 +-
 biology/kallisto/distinfo                          |  6 ++--
 biology/kallisto/files/patch-CMakeLists.txt        | 38 ++++++++--------------
 .../patch-ext_bifrost_src_strict__fstream.hpp      |  2 +-
 biology/kallisto/files/patch-src_CMakeLists.txt    | 16 +++++----
 5 files changed, 29 insertions(+), 36 deletions(-)

diff --git a/biology/kallisto/Makefile b/biology/kallisto/Makefile
index 158ff03a9137..51753b55b794 100644
--- a/biology/kallisto/Makefile
+++ b/biology/kallisto/Makefile
@@ -1,7 +1,6 @@
 PORTNAME=		kallisto
 DISTVERSIONPREFIX=	v
-DISTVERSION=		0.50.1
-PORTREVISION=		1
+DISTVERSION=		0.51.0
 PORTEPOCH=		1
 CATEGORIES=		biology
 
diff --git a/biology/kallisto/distinfo b/biology/kallisto/distinfo
index f01c0d8e6e1c..7b28d6d6f1ee 100644
--- a/biology/kallisto/distinfo
+++ b/biology/kallisto/distinfo
@@ -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
diff --git a/biology/kallisto/files/patch-CMakeLists.txt b/biology/kallisto/files/patch-CMakeLists.txt
index 0eff9653f86c..7d56e7d9b1a1 100644
--- a/biology/kallisto/files/patch-CMakeLists.txt
+++ b/biology/kallisto/files/patch-CMakeLists.txt
@@ -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)
diff --git a/biology/kallisto/files/patch-ext_bifrost_src_strict__fstream.hpp b/biology/kallisto/files/patch-ext_bifrost_src_strict__fstream.hpp
index 1a4191325e7c..7d61dfda93f0 100644
--- a/biology/kallisto/files/patch-ext_bifrost_src_strict__fstream.hpp
+++ b/biology/kallisto/files/patch-ext_bifrost_src_strict__fstream.hpp
@@ -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 {
diff --git a/biology/kallisto/files/patch-src_CMakeLists.txt b/biology/kallisto/files/patch-src_CMakeLists.txt
index 87cd4b49b02d..099ca40ac667 100644
--- a/biology/kallisto/files/patch-src_CMakeLists.txt
+++ b/biology/kallisto/files/patch-src_CMakeLists.txt
@@ -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)