bayestyper: add arm64/aarch64 builds (#52076)

* bayestyper: add arm64/aarch64 builds

* remove from blacklist

* Update build.sh

* Update bayestyper.patch

build-fail-blacklist

@@ -220,7 +220,6 @@ recipes/unitig-counter
 recipes/probcons
 recipes/spydrpick
 recipes/bctools
-recipes/bayestyper
 recipes/group_humann2_uniref_abundances_to_go
 recipes/isonclust2
 recipes/sibelia

recipes/bayestyper/0001-CMakeLists.patch

@@ -0,0 +1,45 @@
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index 6bc8406..3a9a766 100755
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -42,9 +42,39 @@ else(${BUILD_STATIC} EQUAL 0)
+ endif(${BUILD_STATIC} EQUAL 0)
+
+
+-FIND_PACKAGE(Boost COMPONENTS iostreams program_options system filesystem serialization REQUIRED)
++# When user specifies boost paths to use, we need to disable searching from the
++# environment and from using cmake's internal boost variables.
++if (BOOST_ROOT OR BOOST_INCLUDEDIR OR BOOST_LIBRARYDIR OR DEFINED ENV{BOOST_ROOT} OR DEFINED ENV{BOOST_INCLUDEDIR} OR DEFINED ENV{BOOST_LIBRARYDIR})
++  # Don't search for system include dirs for boost
++  set(Boost_NO_SYSTEM_PATHS ON)
++  # Disable excessive warning messages when using multiple boost versions
++  set(Boost_NO_WARN_NEW_VERSION ON)
++endif()
++
++# Use the OLD way of looking for Boost
++# The NEW way only respects BOOST_ROOT, not these more-specific variables.
++if (BOOST_INCLUDEDIR OR BOOST_LIBRARYDIR OR DEFINED ENV{BOOST_INCLUDEDIR} OR DEFINED ENV{BOOST_LIBRARYDIR})
++  # Ignore cmake boost variables
++  set(Boost_NO_BOOST_CMAKE ON)
++endif()
++
++set( Boost_USE_STATIC_LIBS OFF )   
++set( Boost_USE_MULTITHREADED TRUE )
++set( Boost_DEBUG ON )
++
++find_package(Boost 1.71.0 COMPONENTS iostreams program_options system filesystem serialization REQUIRED)
+ message(STATUS ${Boost_LIBRARIES})
+
++if(Boost_FOUND)
++        include_directories(${Boost_INCLUDE_DIRS})
++        LINK_DIRECTORIES(${Boost_LIBRARY_DIRS})
++endif()
++
++MESSAGE("Boost configuration results:")
++MESSAGE("  Boost_INCLUDE_DIRS: ${Boost_INCLUDE_DIR}")
++MESSAGE("  Boost_LIBRARY_DIRS: ${Boost_LIBRARY_DIRS}")
++MESSAGE("  Boost_LIBRARIES: ${Boost_LIBRARIES}")
++
+ add_subdirectory(${CMAKE_SOURCE_DIR}/external/kmc_api)
+ add_subdirectory(${CMAKE_SOURCE_DIR}/src/vcf++)
+ add_subdirectory(${CMAKE_SOURCE_DIR}/src/kmerBloom)

recipes/bayestyper/bayestyper.patch

@@ -0,0 +1,28 @@
+diff --git i/include/vcf++/VcfFile.hpp w/include/vcf++/VcfFile.hpp
+index 4a2f69e..aaf49be 100644
+--- i/include/vcf++/VcfFile.hpp
++++ w/include/vcf++/VcfFile.hpp
+@@ -35,8 +35,8 @@ THE SOFTWARE.
+ #include <string>
+ #include <unordered_set>
+
+-#include "boost/iostreams/filtering_stream.hpp"
+-#include "boost/iostreams/filter/gzip.hpp"
++#include <boost/iostreams/filtering_stream.hpp>
++#include <boost/iostreams/filter/gzip.hpp>
+
+ #include "Variant.hpp"
+ #include "VcfMetaData.hpp"
+diff --git i/src/vcf++/CMakeLists.txt w/src/vcf++/CMakeLists.txt
+index c8a6142..beddd90 100755
+--- i/src/vcf++/CMakeLists.txt
++++ w/src/vcf++/CMakeLists.txt
+@@ -3,6 +3,8 @@ project(vcf++)
+ SET(LIBRARY_OUTPUT_PATH ${CMAKE_SOURCE_DIR}/lib)
+
+ include_directories(${CMAKE_SOURCE_DIR}/include/vcf++ ${Boost_INCLUDE_DIRS})
++message(STATUS "====== DEBUG Boost_INCLUDE_DIRS: " ${Boost_INCLUDE_DIRS})
++message(STATUS "====== DEBUG Boost_LIB_DIRS: " ${Boost_LIB_DIRS})
+ link_directories(${Boost_LIB_DIRS})
+
+ add_library(${PROJECT_NAME} VcfFile.cpp Variant.cpp Allele.cpp VcfMetaData.cpp AttributeSet.cpp Sample.cpp Utils.cpp Attribute.cpp JoiningString.cpp Stats.cpp AttributeFilter.cpp SampleAlleleAttributeFilter.cpp FastaReader.cpp FastaRecord.cpp Auxiliaries.cpp Trio.cpp Contig.cpp Regions.cpp)

recipes/bayestyper/build.sh

@@ -1,10 +1,28 @@
 #!/bin/bash
 
-mkdir build && cd build
-cmake ..
-make
-
 mkdir -p ${PREFIX}/bin
 
-cp ../bin/bayesTyper ${PREFIX}/bin
-cp ../bin/bayesTyperTools ${PREFIX}/bin
+export INCLUDES="-I${PREFIX}/include"
+export CPLUS_INCLUDE_PATH="${PREFIX}/include"
+export LIBPATH="-L${PREFIX}/lib"
+export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib"
+export CXXFLAGS="${CXXFLAGS} -O3 -std=c++14 -I${PREFIX}/include"
+
+if [[ `uname` == "Darwin" ]]; then
+	export CONFIG_ARGS="-DCMAKE_FIND_FRAMEWORK=NEVER -DCMAKE_FIND_APPBUNDLE=NEVER"
+	export CXXFLAGS="${CXXFLAGS} -Wno-dev -Wno-deprecated-declarations -Wno-unused-command-line-argument"
+else
+	export CONFIG_ARGS=""
+fi
+
+cmake -S . -B build -DCMAKE_BUILD_TYPE=Release \
+	-DCMAKE_INSTALL_PREFIX="${PREFIX}" \
+	-DCMAKE_CXX_COMPILER="${CXX}" \
+	-DCMAKE_CXX_FLAGS="${CXXFLAGS}" \
+	-DBOOST_ROOT="${PREFIX}" \
+	"${CONFIG_ARGS}"
+cmake --build build -j "${CPU_COUNT}"
+
+chmod 0755 bin/*
+mv bin/bayesTyper ${PREFIX}/bin
+mv bin/bayesTyperTools ${PREFIX}/bin

recipes/bayestyper/kmer_defs.patch

@@ -0,0 +1,18 @@
+diff --git a/external/kmc_api/kmer_defs.h b/external/kmc_api/kmer_defs.h
+index 8328822..89ae5e0 100644
+--- a/external/kmc_api/kmer_defs.h
++++ b/external/kmc_api/kmer_defs.h
+@@ -33,7 +33,12 @@
+
+
+ 	#include <stdio.h>
+-	#include <ext/algorithm>
++    #if defined(__clang__)
++        #include <algorithm>
++    #elif defined(__GNUC__)
++        #include <ext/algorithm>
++        using __gnu_cxx::copy_n;
++    #endif
+ 	#include <iostream>
+ 	using namespace std;
+

recipes/bayestyper/meta.yaml

@@ -1,16 +1,23 @@
+{% set name = "bayestyper" %}
 {% set version = "1.5" %}
 
 package:
-  name: bayestyper
+  name: {{ name }}
   version: {{ version }}
 
-build:
-  number: 1
-  skip: True # [osx]
-
 source:
   url: https://github.com/bioinformatics-centre/BayesTyper/archive/v{{ version }}.tar.gz
   sha256: 917cd1b1ca7b5cfb6b8327138515ca1ad70878f0c4e8df393fddcbe42f281e14
+  patches:
+    - 0001-CMakeLists.patch
+    - bayestyper.patch
+    - kmer_defs.patch  # [osx]
+    - stdafx.patch  # [osx]
+
+build:
+  number: 2
+  run_exports:
+    - {{ pin_subpackage('bayestyper', max_pin="x") }}
 
 requirements:
   build:
@@ -21,15 +28,23 @@ requirements:
     - zlib
     - boost-cpp
   run:
-    - zlib
     - boost-cpp
 
 about:
-  home: https://github.com/bioinformatics-centre/BayesTyper
+  home: "https://github.com/bioinformatics-centre/BayesTyper"
   license: MIT
-  summary: A method for variant graph genotyping based on exact alignment of k-mers
+  license_family: MIT
+  summary: "A method for variant graph genotyping based on exact alignment of k-mers."
+  dev_url: "https://github.com/bioinformatics-centre/BayesTyper"
+  doc_url: "https://github.com/bioinformatics-centre/BayesTyper/blob/v{{ version }}/README.md"
 
 test:
   commands:
-    - bayesTyper | grep BayesTyper
-    - bayesTyperTools | grep BayesTyperTools
+    - bayesTyper | grep "BayesTyper"
+    - bayesTyperTools | grep "BayesTyperTools"
+  identifiers:
+    - biotools:bayestyper
+    - doi:10.1038/s41588-018-0145-5
+  additional-platforms:
+    - linux-aarch64
+    - osx-arm64

recipes/bayestyper/stdafx.patch

@@ -0,0 +1,10 @@
+diff --git a/external/kmc_api/stdafx.h b/external/kmc_api/stdafx.h
+index 5b8d29d..3610d6c 100644
+--- a/external/kmc_api/stdafx.h
++++ b/external/kmc_api/stdafx.h
+@@ -1,4 +1,4 @@
+ #include <stdio.h>
+-#include <ext/algorithm>
++#include <algorithm>
+ #include <iostream>
+ using namespace std;