From 559e3d805836e9bd0234971e9c2e5c98e5adb6d5 Mon Sep 17 00:00:00 2001
From: Martin Tzvetanov Grigorov <mgrigorov@apache.org>
Date: Mon, 21 Oct 2024 10:04:15 +0300
Subject: [PATCH 1/2] centrifuge-core: add linux-aarch64 build

Signed-off-by: Martin Tzvetanov Grigorov <mgrigorov@apache.org>
---
 recipes/centrifuge-core/build.sh  |  5 ++++-
 recipes/centrifuge-core/meta.yaml | 12 +++++++++---
 2 files changed, 13 insertions(+), 4 deletions(-)

diff --git a/recipes/centrifuge-core/build.sh b/recipes/centrifuge-core/build.sh
index 78918ac22ed5a..0a82cdd89c045 100644
--- a/recipes/centrifuge-core/build.sh
+++ b/recipes/centrifuge-core/build.sh
@@ -1,4 +1,7 @@
 #!/bin/bash
+
+set -xe
+
 export LDFLAGS="-L$PREFIX/lib"
 export CPATH=${PREFIX}/include
 
@@ -7,6 +10,6 @@ mkdir -p $PREFIX/bin
 sed "/^GCC/d;/^CC =/d;/^CPP =/d;/^CXX =/d" < Makefile > Makefile.new
 mv Makefile.new Makefile
 cat Makefile
-make CC=$CC CXX=$CXX RELEASE_FLAGS="$CXXFLAGS"
+make -j"${CPU_COUNT}" CC=$CC CXX=$CXX RELEASE_FLAGS="$CXXFLAGS"
 make install prefix=$PREFIX
 
diff --git a/recipes/centrifuge-core/meta.yaml b/recipes/centrifuge-core/meta.yaml
index 3b6adc563f0be..b9347c7e85535 100644
--- a/recipes/centrifuge-core/meta.yaml
+++ b/recipes/centrifuge-core/meta.yaml
@@ -6,7 +6,7 @@ package:
   version: {{ version }}
 
 build:
-  number: 0
+  number: 1
   skip: true # [osx]
   run_exports:
     - {{ pin_subpackage("centrifuge-core", max_pin="x.x") }}
@@ -34,11 +34,17 @@ test:
     - centrifuge --help
 
 about:
-  home: https://github.com/DaehwanKimLab/centrifuge
-  license: GPL3
+  home: http://www.ccb.jhu.edu/software/centrifuge
+  license: GPL-3.0-only
+  license_file: LICENSE
+  license_family: GPL3
   summary: 'Classifier for metagenomic sequences. Does not include evaluation scripts'
+  dev_url: https://github.com/DaehwanKimLab/centrifuge
+  doc_url: https://genome.cshlp.org/content/26/12/1721
 
 extra:
+  additional-platforms:
+    - linux-aarch64
   identifiers:
     - biotools:Centrifuge
     - doi:10.1101/gr.210641.116

From de109eae272df8f0029ab63448beb9ef820fd8a0 Mon Sep 17 00:00:00 2001
From: Martin Tzvetanov Grigorov <mgrigorov@apache.org>
Date: Mon, 21 Oct 2024 10:45:25 +0300
Subject: [PATCH 2/2] Use specific compiler flags for ARM64

Signed-off-by: Martin Tzvetanov Grigorov <mgrigorov@apache.org>
---
 recipes/centrifuge-core/build.sh | 11 ++++++++++-
 1 file changed, 10 insertions(+), 1 deletion(-)

diff --git a/recipes/centrifuge-core/build.sh b/recipes/centrifuge-core/build.sh
index 0a82cdd89c045..e589cb971645c 100644
--- a/recipes/centrifuge-core/build.sh
+++ b/recipes/centrifuge-core/build.sh
@@ -7,9 +7,18 @@ export CPATH=${PREFIX}/include
 
 mkdir -p $PREFIX/bin
 
+case $(uname -m) in
+    aarch64 | arm64)
+        ARCH_FLAGS=(POPCNT_CAPABILITY=0 "RELEASE_FLAGS=${CXXFLAGS} -fsigned-char")
+        ;;
+    *)
+        ARCH_FLAGS=("RELEASE_FLAGS=${CXXFLAGS}")
+        ;;
+esac
+
 sed "/^GCC/d;/^CC =/d;/^CPP =/d;/^CXX =/d" < Makefile > Makefile.new
 mv Makefile.new Makefile
 cat Makefile
-make -j"${CPU_COUNT}" CC=$CC CXX=$CXX RELEASE_FLAGS="$CXXFLAGS"
+make -j"${CPU_COUNT}" CC=$CC CXX=$CXX "${ARCH_FLAGS[@]}"
 make install prefix=$PREFIX