From 35593f1538cd5b4e46ce2ee6836c5ce3668c9124 Mon Sep 17 00:00:00 2001
From: mencian <joshua.zhuang@yahoo.com>
Date: Tue, 19 Nov 2024 15:21:30 -0600
Subject: [PATCH] Build strelka on osx

---
 recipes/strelka/boost.cmake.patch | 24 ++++++++++++++++
 recipes/strelka/build.sh          | 36 +++++++++++++++++------
 recipes/strelka/meta.yaml         | 48 ++++++++++++++++++++++---------
 3 files changed, 85 insertions(+), 23 deletions(-)
 create mode 100644 recipes/strelka/boost.cmake.patch

diff --git a/recipes/strelka/boost.cmake.patch b/recipes/strelka/boost.cmake.patch
new file mode 100644
index 0000000000000..035893b50a683
--- /dev/null
+++ b/recipes/strelka/boost.cmake.patch
@@ -0,0 +1,24 @@
+diff --git a/src/cmake/boost.cmake b/src/cmake/boost.cmake
+index 9b65798..9420db7 100644
+--- a/src/cmake/boost.cmake
++++ b/src/cmake/boost.cmake
+@@ -44,7 +44,9 @@ macro (initBoostParams)
+     # for test, so we need two lists now:
+     set (THIS_BOOST_BUILD_COMPONENTS date_time filesystem program_options
+                                      serialization system timer chrono test)
+-    set (Boost_USE_STATIC_LIBS ON)
++    set( Boost_USE_STATIC_LIBS OFF )
++    set( Boost_USE_MULTITHREADED TRUE )
++    set( Boost_DEBUG ON )
+     if (NOT WIN32)
+         # bjam on windows ignores this setting so skip for win32:
+         set (Boost_USE_MULTITHREADED OFF)
+@@ -108,6 +110,8 @@ endif ()
+ find_package(Boost ${THIS_BOOST_VERSION})
+ if (Boost_FOUND)
+     find_package(Boost ${THIS_BOOST_VERSION} COMPONENTS ${THIS_BOOST_COMPONENTS} QUIET)
++    include_directories(${Boost_INCLUDE_DIRS})
++    LINK_DIRECTORIES(${Boost_LIBRARY_DIRS})
+ endif ()
+ 
+ # CMAKE_PARALLEL is only used if boost is found, but moving the setting here (outside of the if below) supresses a cmake warning:
diff --git a/recipes/strelka/build.sh b/recipes/strelka/build.sh
index 63d653355e610..8d691d3108834 100644
--- a/recipes/strelka/build.sh
+++ b/recipes/strelka/build.sh
@@ -5,12 +5,30 @@ outdir=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM
 mkdir -p $outdir
 mkdir -p $PREFIX/bin
 
-cp -r bin lib libexec share $outdir
-sed -i.bak \
-    -e "s~scriptDir=.*~scriptDir='$outdir/bin'~" \
-    -e "s~workflowDir=.*~workflowDir='$outdir/lib/python'~" \
-    $outdir/bin/configure*.py
-sed -i.bak \
-    -e "s~scriptDir=.*~scriptDir='$outdir/bin'~" \
-    $outdir/bin/run*.bash
-ln -s $outdir/bin/config*.py $outdir/bin/run*.bash $PREFIX/bin
+export INCLUDES="-I${PREFIX}/include"
+export LIBPATH="-L${PREFIX}/lib"
+export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib"
+export CXXFLAGS="${CXXFLAGS} -O3 -I${PREFIX}/include"
+
+if [[ `uname` == "Darwin" ]]; then
+	export CONFIG_ARGS="-DCMAKE_FIND_FRAMEWORK=NEVER -DCMAKE_FIND_APPBUNDLE=NEVER"
+else
+	export CONFIG_ARGS=""
+fi
+
+cmake -S . -B build -DCMAKE_INSTALL_PREFIX="${outdir}" \
+	-DCMAKE_BUILD_TYPE=Release -DCMAKE_CXX_COMPILER="${CXX}" \
+	-DCMAKE_CXX_FLAGS="${CXXFLAGS}" -DCMAKE_C_COMPILER="${CC}" \
+	-DBOOST_ROOT="${PREFIX}" "${CONFIG_ARGS}"
+
+cmake --build build --target install -j "${CPU_COUNT}" -v
+
+#cp -r bin lib libexec share $outdir
+#sed -i.bak \
+#    -e "s~scriptDir=.*~scriptDir='$outdir/bin'~" \
+#    -e "s~workflowDir=.*~workflowDir='$outdir/lib/python'~" \
+#    $outdir/bin/configure*.py
+#sed -i.bak \
+#    -e "s~scriptDir=.*~scriptDir='$outdir/bin'~" \
+#    $outdir/bin/run*.bash
+ln -sf $outdir/bin/config*.py $outdir/bin/run*.bash $PREFIX/bin
diff --git a/recipes/strelka/meta.yaml b/recipes/strelka/meta.yaml
index 18ca2d5192d56..0583893f5a0d5 100644
--- a/recipes/strelka/meta.yaml
+++ b/recipes/strelka/meta.yaml
@@ -1,21 +1,34 @@
+{% set name = "strelka" %}
 {% set version = "2.9.10" %}
-{% set sha256 = "bde30e34e06548c876ff63658efd3d7e6a2e7b465909243ab7e2ed599f83312b" %}
+{% set sha256 = "45e78efec6e5272697f1d0a95851c7ae0d623dc8f93846e11fe37f15da9f1e30" %}
 
 package:
-  name: strelka
-  version: '{{ version }}'
+  name: {{ name }}
+  version: {{ version }}
 
 source:
-  url: https://github.com/Illumina/strelka/releases/download/v{{ version }}/strelka-{{ version }}.centos6_x86_64.tar.bz2
-  sha256: '{{ sha256 }}'
+  url: https://github.com/Illumina/strelka/releases/download/v{{ version }}/{{ name }}-{{ version }}.release_src.tar.bz2
+  sha256: {{ sha256 }}
+  patches:
+    - boost.cmake.patch
 
 build:
-  number: 1
-  skip: true # [osx]
+  number: 2
+  run_exports:
+    - {{ pin_subpackage('strelka', max_pin="x") }}
 
 requirements:
+  build:
+    - {{ compiler('cxx') }}
+    - cmake
+    - make
+  host:
+    - doxygen
+    - boost-cpp
+    - zlib
   run:
-    - python 2.7.*
+    - python <3
+    - boost-cpp
 
 test:
   commands:
@@ -23,13 +36,20 @@ test:
     - configureStrelkaSomaticWorkflow.py -h
 
 about:
-  home: https://github.com/Illumina/strelka
-  license: GPL-3.0
-  license_family: GPL
-  summary: Strelka calls somatic and germline small variants from mapped sequencing reads
+  home: "https://github.com/Illumina/strelka"
+  license: "GPL-3.0-or-later"
+  license_family: GPL3
+  license_file: "LICENSE.txt"
+  summary: "Strelka calls somatic and germline small variants from mapped sequencing reads."
+  dev_url: "https://github.com/Illumina/strelka"
+  doc_url: "https://github.com/Illumina/strelka/blob/v2.9.x/docs/userGuide/README.md"
 
 extra:
   identifiers:
     - biotools:strelka
-  skip-lints:
-    - should_be_noarch_generic
+    - usegalaxy-eu:strelka_germline
+    - usegalaxy-eu:strelka_somatic
+    - doi:10.1038/s41592-018-0051-x
+  additional-platforms:
+    - linux-aarch64
+    - osx-arm64