Rebuild gemma recipe (#64281)

Author: mencian

recipes/gemma/build.sh

@@ -1,11 +1,27 @@
 #!/bin/bash
 set -eu
 
-export C_INCLUDE_PATH=${PREFIX}/include
-export CPP_INCLUDE_PATH=${PREFIX}/include
-export LIBRARY_PATH=${PREFIX}/lib
+export CPPFLAGS="${CPPFLAGS} -I${PREFIX}/include"
+export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib"
+export CXXFLAGS="${CXXFLAGS} -O3 -DHAVE_INLINE -pthread -Wall -std=c++14"
 
-make release
+mkdir -p "${PREFIX}/bin"
 
-mkdir -p ${PREFIX}/bin
-cp bin/gemma ${PREFIX}/bin/gemma
+case $(uname -m) in
+    aarch64)
+	export CXXFLAGS="${CXXFLAGS} -march=armv8-a"
+	;;
+    arm64)
+	export CXXFLAGS="${CXXFLAGS} -march=armv8.4-a"
+	;;
+    x86_64)
+	export CXXFLAGS="${CXXFLAGS} -march=x86-64-v3"
+	;;
+esac
+
+sed -i.bak "s|-lgsl -lz|-L${PREFIX}/lib -lgsl -lz|" Makefile
+rm -f *.bak
+
+make GCC_FLAGS="${CXXFLAGS}" release
+
+install -v -m 0755 bin/gemma "${PREFIX}/bin"

recipes/gemma/meta.yaml

@@ -1,4 +1,5 @@
-{% set version='0.98.5' %}
+{% set version = "0.98.5" %}
+
 package:
   name: gemma
   version: {{ version }}
@@ -9,16 +10,17 @@ source:
   sha256: 3ed336deee29e370f96ec8f1a240f7b62550e57dcd1694245ce7ec8f42241677
 
 build:
-  number: 0
+  number: 1
   run_exports:
     - {{ pin_subpackage('gemma', max_pin="x.x") }}
 
 requirements:
   build:
     - make
     - {{ compiler('cxx') }}
+    - pkg-config
   host:
-    - gsl =2
+    - gsl
     - openblas
     - eigen
     - zlib
@@ -30,7 +32,23 @@ test:
     - gemma
 
 about:
-  home: https://github.com/genetics-statistics/GEMMA
-  license: GPLv3
+  home: "https://github.com/genetics-statistics/GEMMA"
+  license: "GPL-3.0-or-later"
+  license_family: GPL3
   license_file: LICENSE
-  summary: Linear mixed models (LMMs) for genome-wide association (GWA)
+  summary: "Linear mixed models (LMMs) for genome-wide association (GWA)."
+  dev_url: "https://github.com/genetics-statistics/GEMMA"
+  doc_url: "https://github.com/genetics-statistics/GEMMA/blob/v{{ version }}/README.md"
+
+extra:
+  additional-platforms:
+    - linux-aarch64
+    # src/debug.cpp:108:24: error: no member named '__control' in 'fenv_t'
+    # src/debug.cpp:112:10: error: no member named '__mxcsr' in 'fenv_t'
+    #- osx-arm64
+  identifiers:
+    - usegalaxy-eu:gemma
+    - biotools:gemma_algorithm
+    - doi:10.1038/ng.2310
+  skip-lints:
+    - compiler_needs_stdlib_c