From 505b9467db4bfe86778a095262eb52adda85c271 Mon Sep 17 00:00:00 2001
From: Martin Tzvetanov Grigorov <mgrigorov@apache.org>
Date: Fri, 23 Sep 2022 14:07:31 +0300
Subject: [PATCH 1/2] Add CI for Linux ARM64

Signed-off-by: Martin Tzvetanov Grigorov <mgrigorov@apache.org>
---
 .github/build.sh          | 59 +++++++++++++++++++++++++++++++++++++++
 .github/workflows/ci.yaml | 38 +++++++++++++++++++++++++
 2 files changed, 97 insertions(+)
 create mode 100755 .github/build.sh
 create mode 100644 .github/workflows/ci.yaml

diff --git a/.github/build.sh b/.github/build.sh
new file mode 100755
index 0000000..0588b8a
--- /dev/null
+++ b/.github/build.sh
@@ -0,0 +1,59 @@
+#!/usr/bin/env bash
+
+set -xe
+
+rm -rf bifrost bwa htslib samtools sickle
+
+BIN_FOLDER=$(mktemp -d)
+PATH=$BIN_FOLDER:$PATH
+NPROC=$(nproc)
+ARCH=$(echo $(uname -m) | tr '_' '-')
+
+# Bifrost
+git clone --recursive https://github.com/pmelsted/bifrost.git
+pushd bifrost
+mkdir build && cd build
+cmake ..
+make -j$NPROC
+sudo make install
+file /usr/local/bin/Bifrost | grep $ARCH
+popd
+
+# Bwa
+git clone --recursive https://github.com/lh3/bwa.git
+pushd bwa
+make -j$NPROC
+cp bwa $BIN_FOLDER/
+file $BIN_FOLDER/bwa | grep $ARCH
+popd
+
+# Samtools
+## Htslib
+git clone --recursive https://github.com/samtools/htslib.git
+pushd htslib
+autoreconf -i
+./configure
+make -j$NPROC
+popd
+
+## Samtools
+git clone --recursive https://github.com/samtools/samtools.git
+pushd samtools
+make -j$NPROC
+cp samtools $BIN_FOLDER/
+file $BIN_FOLDER/samtools | grep $ARCH
+popd
+
+# Sickle
+git clone --recursive https://github.com/najoshi/sickle.git
+pushd sickle
+make -j$NPROC
+cp sickle $BIN_FOLDER/
+file $BIN_FOLDER/sickle | grep $ARCH
+popd
+
+# PopIns2
+git config --global --add safe.directory .
+mkdir -p build
+make -j$NPROC
+file popins2 | grep $ARCH
\ No newline at end of file
diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
new file mode 100644
index 0000000..dff6715
--- /dev/null
+++ b/.github/workflows/ci.yaml
@@ -0,0 +1,38 @@
+name: CI
+
+on:
+  push:
+  pull_request:
+
+jobs:
+  build-x86_64:
+    runs-on: ubuntu-20.04
+
+    steps:
+    - name: Checkout
+      uses: actions/checkout@v3
+
+    - name: Build
+      run: .github/build.sh
+
+  build-aarch64:
+    runs-on: ubuntu-20.04
+
+    steps:
+    - name: Checkout
+      uses: actions/checkout@v3
+
+    - name: Build
+      uses: uraimo/run-on-arch-action@v2
+      with:
+        arch: aarch64
+        distro: ubuntu20.04
+        githubToken: ${{ github.token }}
+        dockerRunArgs: |
+          --volume "${PWD}:/PopIns2"
+        install: |
+          apt-get update -q -y
+          apt-get install -q -y build-essential autoconf git cmake file zlib1g-dev ncurses-dev sudo libbz2-dev liblzma-dev
+        run: |
+          pushd /PopIns2
+          .github/build.sh
\ No newline at end of file

From bca2d6e76468e7776bbc776c61154967f62a9fa8 Mon Sep 17 00:00:00 2001
From: Martin Grigorov <martin-g@users.noreply.github.com>
Date: Wed, 30 Nov 2022 14:15:02 +0200
Subject: [PATCH 2/2] Remove an optional deletion of pre-existing folders

---
 .github/build.sh | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/.github/build.sh b/.github/build.sh
index 0588b8a..dc05c05 100755
--- a/.github/build.sh
+++ b/.github/build.sh
@@ -2,8 +2,6 @@
 
 set -xe
 
-rm -rf bifrost bwa htslib samtools sickle
-
 BIN_FOLDER=$(mktemp -d)
 PATH=$BIN_FOLDER:$PATH
 NPROC=$(nproc)
@@ -56,4 +54,4 @@ popd
 git config --global --add safe.directory .
 mkdir -p build
 make -j$NPROC
-file popins2 | grep $ARCH
\ No newline at end of file
+file popins2 | grep $ARCH