Added ici-uploader as a multi-arch image

.gitattributes

@@ -1,2 +1,4 @@
 *.rpm filter=lfs diff=lfs merge=lfs -text
 *.bin filter=lfs diff=lfs merge=lfs -text
+repositories/ici-uploader/4.0.3/ici-uploader.amd64.tar.gz filter=lfs diff=lfs merge=lfs -text
+repositories/ici-uploader/4.0.3/ici-uploader.arm64.tar.gz filter=lfs diff=lfs merge=lfs -text

.github/workflows/scatter_build_and_push_to_ghcrio.yml

@@ -4,6 +4,8 @@ on:
   push:
     branches:
       - "main"
+  workflow_dispatch:
+
 
 concurrency: image_builds
 

repositories/ici-uploader/4.0.3/Dockerfile

@@ -0,0 +1,55 @@
+FROM alpine:3
+
+# ARGS
+# Target platform (linux/amd64, linux/arm64)
+ARG TARGETPLATFORM
+
+# For the ici-uploader
+ARG ICI_HOME="/usr/local/share/ici-uploader"
+# User args (we run from a non-root user)
+ARG USER="ici_user"
+ARG UID=1000
+ARG GID=1000
+ARG GROUP="ici_user"
+
+# ENV
+ENV ICI_HOME="${ICI_HOME}"
+
+# RUN
+# Install Java
+RUN apk update && \
+  apk add \
+    openjdk11 \
+    tar \
+    bash && \
+  mkdir -p "$(dirname "${ICI_HOME}")"
+
+# Add and extract tarball
+ADD "ici-uploader.${TARGETPLATFORM#linux/}.tar.gz" "${ICI_HOME%ici-uploader}"
+ADD "ici-uploader.sh" "/usr/local/bin/ici-uploader"
+
+# Change permissions
+RUN chmod a+r "${ICI_HOME}/" && \
+    chmod a+x "${ICI_HOME}/ici-uploader" && \
+    chmod a+x "/usr/local/bin/ici-uploader"
+
+# Add a non-root user
+RUN addgroup \
+    --system \
+    --gid "${GID}" \
+    "${GROUP}" && \
+    adduser \
+    --system \
+    --disabled-password \
+    --ingroup "${GROUP}" \
+    --uid "${UID}" \
+    "$USER"
+
+# Change ownership
+USER "$USER"
+
+# Add a softlink from the user home to the ici-uploader
+RUN mkdir -p "/home/${USER}/.illumina/" && \
+    ln -s "${ICI_HOME}" "/home/${USER}/.illumina/ici-uploader"
+
+CMD [ "ici-uploader" ]

repositories/ici-uploader/4.0.3/Readme.md

@@ -0,0 +1,64 @@
+# Alpine-rsync
+
+## Version 3.3.0
+
+## Package link
+[docker-who/alpine-rsync](https://github.com/umccr/docker-who/pkgs/container/alpine-rsync)
+
+## Platforms
+* linux/amd64
+* linux/arm64
+
+### Usage
+
+```bash
+docker pull ghcr.io/umccr/ici-uploader:4.0.3
+```
+
+### Description
+Run the ici-uploader commandline tool without needing to worry about daemons, or even installing this thing!!
+
+### Example
+```bash
+docker run --rm -it \
+  --workdir "$PWD" \
+  --volume "$PWD:$PWD" \
+  ici-uploader:4.0.3 \
+    ici-uploader help
+```
+
+Gives 
+
+```
+Usage: ici-uploader.jar [-hV] [--verbose] [--configFile=<configFile>] [COMMAND]
+ICI Command-line Interface (Uploader) for analysis, and file operations
+      --configFile, --config-file=<configFile>
+                  [Optional] Path to the uploader configuration file. Defaults to ~/.illumina/ici-uploader/uploader-config.json.
+  -h, --help      Show this help message and exit.
+  -V, --version   Print version information and exit.
+      --verbose   [Optional] Turn on INFO logging.
+Commands:
+  help                Displays help information about the specified command
+  configure           Configure ici-uploader tool
+  case-data           Set the metadata for the case via ici-uploader tool
+  analyses, analysis  Upload analyses into Illumina Connected Insights (ICI)
+  logs, ici-logs      Get ICI logs for Illumina Connected Insights (ICI)
+  files               List or download files
+```
+
+## Configuration File
+
+The only way to get this is to actually download the installer from the ICI site, this will provide you with the following keys
+
+```json
+[ {
+  "domain" : null,
+  "workgroup" : null,
+  "url" : null,
+  "apiKey" : null,
+  "project" : null,
+  "productKey" : null,
+  "isCloud" : null,
+  "isActive" : null
+} ]
+```

repositories/ici-uploader/4.0.3/ici-uploader.sh

@@ -0,0 +1,7 @@
+#!/usr/bin/env bash
+
+# Start the daemon
+"${ICI_HOME}/ici-uploader" start-daemon 1>/dev/null 2>&1
+
+# Run the ici-uploader command
+"${ICI_HOME}/ici-uploader" "${@:1}"