Add Minimac4 (#52011)

recipes/minimac4/build.sh

@@ -0,0 +1,49 @@
+#!/bin/bash
+set -euo pipefail
+
+echo "Building Minimac4 version ${PKG_VERSION}"
+
+# Set CXXFLAGS to include the correct path to lzma.h and LDFLAGS to include the path to liblzma
+export CXXFLAGS="-I${PREFIX}/include -I${PREFIX}/lib"
+export LDFLAGS="-L${PREFIX}/lib -llzma"
+CMAKE_MAKE_PROGRAM="$(which make)"
+CMAKE_C_COMPILER="${CC}"
+CMAKE_CXX_COMPILER="${CXX}"
+
+export CMAKE_MAKE_PROGRAM
+export CMAKE_C_COMPILER
+export CMAKE_CXX_COMPILER
+
+# Set up dependencies and directories
+if [ ! -f ./requirements.txt ]; then
+    echo "Error: requirements.txt not found"
+    exit 1
+fi
+cget ignore xz || exit 1
+cget install -f ./requirements.txt || exit 1
+
+cmake --version
+mkdir -p build || exit 1
+cd build || exit 1
+
+cmake \
+    -DBUILD_TESTS=1 \
+    -DCMAKE_TOOLCHAIN_FILE=../cget/cget/cget.cmake \
+    -DCMAKE_CXX_FLAGS="${CXXFLAGS}" \
+    -DCMAKE_EXE_LINKER_FLAGS="${LDFLAGS}" \
+    -DCMAKE_MAKE_PROGRAM=${CMAKE_MAKE_PROGRAM} \
+    -DCMAKE_C_COMPILER=${CMAKE_C_COMPILER} \
+    -DCMAKE_CXX_COMPILER=${CMAKE_CXX_COMPILER} \
+    -DCMAKE_BUILD_TYPE=Release \
+    -DCMAKE_INSTALL_PREFIX=${PREFIX} \
+    -DCMAKE_BUILD_WITH_INSTALL_RPATH=ON \
+    -DCPACK_GENERATOR="STGZ" \
+    -DCPACK_PACKAGE_CONTACT="[email protected]" \
+    ..
+
+make || exit 1
+make install || exit 1
+make CTEST_OUTPUT_ON_FAILURE=1 test || exit 1
+echo "Minimac4 installation completed successfully"
+
+cd .. || exit 1

recipes/minimac4/meta.yaml

@@ -0,0 +1,41 @@
+{% set version = "4.1.6" %}
+
+package:
+  name: minimac4
+  version: {{ version }}
+
+build:
+  number: 0
+  run_exports:
+    - {{ pin_subpackage('minimac4', max_pin='x.x.x') }}
+
+source:
+  url: https://github.com/statgen/Minimac4/archive/refs/tags/v{{ version }}.tar.gz
+  sha256: 0bce8d6edbf5d5d944b19c4e36403d0bc1d18f2d6003d88e01086488c3eb9333
+
+requirements:
+  build:
+    - make
+    - cmake >=3.24
+    - {{ compiler('c') }}
+    - {{ compiler('cxx') }}
+    - cget
+  host:
+    - bcftools >=1.20
+    - zlib
+    - savvy ==2.1.0
+    - xz
+  run:
+    - cget
+
+test:
+  commands:
+    - minimac4 --help
+    - minimac4 --version
+
+about:
+  home: https://github.com/statgen/Minimac4
+  license: GPL-3.0-or-later
+  license_file: LICENSE
+  summary: "Computationally efficient genotype imputation"
+  description: "Minimac4 is a lower memory and more computationally efficient implementation of the genotype imputation algorithms in minimac/mininac2/minimac3."