centrifuge: add linux-aarch64 build

recipes/centrifuge/build.sh

@@ -1,10 +1,23 @@
 #!/bin/bash
+
+set -xe
+
 export LDFLAGS="-L$PREFIX/lib"
 export CPATH=${PREFIX}/include
 
 mkdir -p $PREFIX/bin
 
-make CXX=$CXX RELEASE_FLAGS="$CXXFLAGS"
+case $(uname -m) in
+    aarch64)
+        CXXFLAGS="${CXXFLAGS} -fsigned-char"
+        ARCH_OPTS="SSE_FLAG= POPCNT_CAPABILITY=0"
+        ;;
+    *)
+        ARCH_OPTS=""
+        ;;
+esac
+
+make -j ${CPU_COUNT} CXX=$CXX RELEASE_FLAGS="$CXXFLAGS" ${ARCH_OPTS}
 make install prefix=$PREFIX
 
 cp evaluation/{centrifuge_evaluate.py,centrifuge_simulate_reads.py} $PREFIX/bin

recipes/centrifuge/centrifuge-linux-aarch64.patch

@@ -0,0 +1,51 @@
+diff --git i/Makefile w/Makefile
+index 10e42f5..42cb38d 100644
+--- i/Makefile
++++ w/Makefile
+@@ -142,24 +142,25 @@ GIT_VERSION = $(VERSION)
+
+ # Convert BITS=?? to a -m flag
+ BITS=32
++BITS_FLAG =
+ ifeq (x86_64,$(shell uname -m))
+ BITS=64
++BITS_FLAG = -m64
++else ifeq (aarch64,$(shell uname -m))
++BITS=64
+ endif
+ # msys will always be 32 bit so look at the cpu arch instead.
+ ifneq (,$(findstring AMD64,$(PROCESSOR_ARCHITEW6432)))
+ 	ifeq (1,$(MINGW))
+ 		BITS=64
++		BITS_FLAG = -m64
+ 	endif
+ endif
+-BITS_FLAG =
+
+ ifeq (32,$(BITS))
+ 	BITS_FLAG = -m32
+ endif
+
+-ifeq (64,$(BITS))
+-	BITS_FLAG = -m64
+-endif
+ SSE_FLAG=-msse2
+
+ DEBUG_FLAGS    = -O0 -g3 $(BIToS_FLAG) $(SSE_FLAG) -std=c++11
+diff --git i/third_party/cpuid.h w/third_party/cpuid.h
+index 6a9688f..7c935c9 100644
+--- i/third_party/cpuid.h
++++ w/third_party/cpuid.h
+@@ -21,6 +21,7 @@
+  * <http://www.gnu.org/licenses/>.
+  */
+
++#ifndef __ARM_NEON
+ /* %ecx */
+ #define bit_SSE3	(1 << 0)
+ #define bit_PCLMUL	(1 << 1)
+@@ -185,3 +186,4 @@ __get_cpuid (unsigned int __level,
+   __cpuid (__level, *__eax, *__ebx, *__ecx, *__edx);
+   return 1;
+ }
++#endif // not __ARM_NEON

recipes/centrifuge/meta.yaml

@@ -6,14 +6,16 @@ package:
   version: {{ version }}
 
 build:
-  number: 1
+  number: 2
   skip: true # [osx]
   run_exports:
     - {{ pin_subpackage("centrifuge", max_pin="x.x") }}
 
 source:
   url: https://github.com/DaehwanKimLab/centrifuge/archive/refs/tags/v{{ version }}.tar.gz
   sha256: 638cc6701688bfdf81173d65fa95332139e11b215b2d25c030f8ae873c34e5cc
+  patches:
+    - centrifuge-linux-aarch64.patch # [linux and aarch64]
 
 requirements:
   build:
@@ -26,19 +28,22 @@ requirements:
     - perl
     - wget
     - tar
-    - python <3
+    - python
 
 test:
   commands:
     - centrifuge --help
 
 about:
   home: https://github.com/DaehwanKimLab/centrifuge
-  license: GPL3
+  license: GPL-3.0-only
   license_file: LICENSE
+  license_family: GPL3
   summary: 'Classifier for metagenomic sequences. Supports classifier scripts'
 
 extra:
+  additional-platforms:
+    - linux-aarch64
   identifiers:
     - biotools:Centrifuge
     - doi:10.1101/gr.210641.116