From 71ad8badc3d0e72efc884e5b03d18a6ee5476685 Mon Sep 17 00:00:00 2001
From: Alexis Lucattini <Alexis.Lucattini@umccr.org>
Date: Sun, 3 Nov 2024 17:04:29 +1100
Subject: [PATCH] CodeBuild doesn't support git-lfs

Download files from GitHub instead
---
 .../tasks/ora_decompression/Dockerfile        | 85 ++++++++++---------
 1 file changed, 47 insertions(+), 38 deletions(-)

diff --git a/lib/workload/components/ora-file-decompression-fq-pair-sfn/tasks/ora_decompression/Dockerfile b/lib/workload/components/ora-file-decompression-fq-pair-sfn/tasks/ora_decompression/Dockerfile
index bc31b827d..6446fc105 100644
--- a/lib/workload/components/ora-file-decompression-fq-pair-sfn/tasks/ora_decompression/Dockerfile
+++ b/lib/workload/components/ora-file-decompression-fq-pair-sfn/tasks/ora_decompression/Dockerfile
@@ -1,34 +1,35 @@
 FROM --platform=${TARGETPLATFORM} ubuntu:noble
 
 ARG ORAD_REF_DOWNLOAD_URL="https://s3.amazonaws.com/webdata.illumina.com/downloads/software/dragen-decompression/orad.2.7.0.linux.tar.gz"
+ARG ORAD_AARCH_64_DOWNLOAD_URL="https://media.githubusercontent.com/media/umccr/orcabus/refs/heads/main/lib/workload/components/ora-file-decompression-fq-pair-sfn/tasks/ora_decompression/binaries/orad.tar.gz"
 ARG ORA_MOUNT="/opt"
 ARG TARGETPLATFORM
 
 # Install ubuntu basics
 RUN \
-   if [ "${TARGETPLATFORM#linux/}" = "arm64" ]; then \
-    platform_url="aarch64";  \
-   else \
-    platform_url="x86_64"; \
-   fi && \
-   apt update -yq && \
-   apt upgrade -yq && \
-   apt install -yq \
-     wget \
-     jq \
-     tar \
-     gzip \
-     unzip \
-     python3.12 \
-     python3-pip && \
-   python3 -mpip install wrapica --break-system-packages && \
-   wget \
-    --quiet \
-    --output-document "awscliv2.zip" \
-    "https://awscli.amazonaws.com/awscli-exe-linux-${platform_url}.zip" && \
-   unzip -q "awscliv2.zip" && \
-   ./aws/install && \
-   rm "awscliv2.zip"
+    if [ "${TARGETPLATFORM#linux/}" = "arm64" ]; then \
+      platform_url="aarch64";  \
+    else \
+      platform_url="x86_64"; \
+    fi && \
+    apt update -yq && \
+    apt upgrade -yq && \
+    apt install -yq \
+      wget \
+      jq \
+      tar \
+      gzip \
+      unzip \
+      python3.12 \
+      python3-pip && \
+    python3 -mpip install wrapica --break-system-packages && \
+    wget \
+      --quiet \
+      --output-document "awscliv2.zip" \
+      "https://awscli.amazonaws.com/awscli-exe-linux-${platform_url}.zip" && \
+    unzip -q "awscliv2.zip" && \
+    ./aws/install && \
+    rm "awscliv2.zip"
 
 ## Install qemu-virtualization
 ## Commented out as we now have an orad arm64 binary version
@@ -56,27 +57,35 @@ RUN \
 # Install the ora reference data directly into the docker container
 # Remove the orad x86-64 binary since we use the arm64 binary provided instead
 RUN \
-   mkdir --parents --mode 744 "${ORA_MOUNT}" && \
-   wget --quiet \
-    --output-document /dev/stdout \
-    "${ORAD_REF_DOWNLOAD_URL}" | \
-   tar \
-      --directory "${ORA_MOUNT}" \
-      --extract \
-      --gunzip \
-      --strip-components=1 \
-      --file - && \
-   chmod 644 "${ORA_MOUNT}/oradata/" && \
-   chmod a+x "${ORA_MOUNT}/orad" && \
-   rm "${ORA_MOUNT}/orad"
+    mkdir --parents --mode 744 "${ORA_MOUNT}" && \
+    wget --quiet \
+     --output-document /dev/stdout \
+     "${ORAD_REF_DOWNLOAD_URL}" | \
+    tar \
+       --directory "${ORA_MOUNT}" \
+       --extract \
+       --gunzip \
+       --strip-components=1 \
+       --file - && \
+    chmod 644 "${ORA_MOUNT}/oradata/" && \
+    chmod a+x "${ORA_MOUNT}/orad" && \
+    rm "${ORA_MOUNT}/orad"
 
 # Set the ora reference to the path ORA_MOUNT/oradata
 ENV ORADATA_PATH="${ORA_MOUNT}/oradata/"
 
 # Add the orad binary to the docker container
 # And make it executable
-ADD binaries/orad.tar.gz /usr/local/bin/
-RUN chmod +x /usr/local/bin/orad
+RUN \
+    wget \
+      --output-document /dev/stdout \
+      "${ORAD_AARCH_64_DOWNLOAD_URL}" | \
+    tar \
+      --directory /usr/local/bin \
+      --extract \
+      --gzip \
+      --file - && \
+    chmod +x /usr/local/bin/orad
 
 # Copy the scripts to the docker container
 # Make the scripts executable