Merge pull request #45 from umccr/feature/add-ici-uploader-4-0-3

Added ici-uploader as a multi-arch image

repositories/ici-uploader/4.0.3/Dockerfile

@@ -0,0 +1,56 @@
+FROM alpine:3
+
+# ARGS
+# Target platform (linux/amd64, linux/arm64)
+ARG TARGETPLATFORM
+
+# For the ici-uploader
+ARG ICI_HOME="/usr/local/bin/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="${ICI_HOME}"
+
+# RUN
+# Install Java
+RUN apk update && \
+  apk add \
+    openjdk11 \
+    tar \
+    bash && \
+  mkdir -p "${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/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}"