NECAT: add arm64 builds (#52873)

* NECAT: add aarch64/arm64 builds

* add patch

recipes/necat/build.sh

@@ -1,28 +1,36 @@
 #!/bin/bash
 set -ex
 
+mkdir -p ${PREFIX}/bin
+
 export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib"
-export CFLAGS="${CFLAGS} -O3 -I${PREFIX}/include"
+export CFLAGS="${CFLAGS} -O3 -Wno-incompatible-function-pointer-types -Wno-implicit-function-declaration -L${PREFIX}/lib"
 export CXXFLAGS="${CXXFLAGS} -O3 -I${PREFIX}/include"
 
-BIN_ROOT="Linux-amd64/bin"
 case $(uname -m) in
-    arm64|aarch64) BIN_ROOT="Linux-aarch64/bin" ;;
+    aarch64) BIN_ROOT="Linux-aarch64/bin" ;;
+    arm64) BIN_ROOT="Darwin-arm64/bin" ;;
+    x86_64) BIN_ROOT="Linux-amd64/bin" ;;
 esac
 
+if [[ "$(uname)" == "Darwin" && "$(uname -m)" == "x86_64" ]]; then
+	BIN_ROOT="Darwin-amd64/bin"
+fi
+
 # build
 make -C src CFLAGS+="${CFLAGS}" LDFLAGS+="${LDFLAGS}" CXXFLAGS+="${CXXFLAGS}" -j"${CPU_COUNT}"
 
 # create and populate binary file
-mkdir -p $PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM/bin/
-cp -rf $BIN_ROOT/*  $PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM/bin/
+mkdir -p $PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM/bin
+cp -rf $BIN_ROOT/Plgd $PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM/bin && rm -rf $BIN_ROOT/Plgd
+rm -rf $BIN_ROOT/trim_bases_accurate*
+install -v -m 0755 $BIN_ROOT/* "${PREFIX}/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM/bin"
 
 # create calling script
-mkdir -p ${PREFIX}/bin/
 cat <<EOF > $PREFIX/bin/necat
 #!/bin/bash
 
 PATH=\$PATH:$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM/bin/ necat.pl "\$@"
 EOF
 
-chmod 755 ${PREFIX}/bin/necat
+chmod 0755 ${PREFIX}/bin/necat

recipes/necat/meta.yaml

@@ -51,10 +51,10 @@ source:
     - src_fsa_rd_extract.mk.patch
     - src_fsa_rd_stat.mk.patch
     - src_fsa_rd_tools.mk.patch
+    - simple_align.patch  # [linux]
 
 build:
-  skip: True  # [osx]
-  number: 5
+  number: 6
   run_exports:
     - {{ pin_subpackage("necat", max_pin="x.x") }}
 
@@ -83,6 +83,7 @@ about:
 extra:
   additional-platforms:
     - linux-aarch64
+    - osx-arm64
   identifiers:
     - doi:10.1038/s41467-020-20236-7
     - biotools:necat

recipes/necat/simple_align.patch

@@ -0,0 +1,12 @@
+diff --git a/src/fsa/simple_align.hpp b/src/fsa/simple_align.hpp
+index 7344707..33949ce 100644
+--- a/src/fsa/simple_align.hpp
++++ b/src/fsa/simple_align.hpp
+@@ -1,6 +1,7 @@
+ #ifndef FSA_ALIGN_SIMPLE_ALIGN_HPP
+ #define FSA_ALIGN_SIMPLE_ALIGN_HPP
+
++#include <stdint.h>
+ #include <array>
+ #include <string>
+ #include <unordered_map>