Merge pull request #46 from umccr/feature/add-ici-uploader-4-0-3

Add readme test directory error

repositories/ici-uploader/4.0.3/Dockerfile

@@ -5,8 +5,7 @@ FROM alpine:3
 ARG TARGETPLATFORM
 
 # For the ici-uploader
-ARG ICI_HOME="/usr/local/bin/share/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
@@ -30,7 +29,7 @@ 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 "${ICI_HOME}/" && \
+RUN ls "${ICI_HOME}" && chmod a+r "${ICI_HOME}/" && \
     chmod a+x "${ICI_HOME}/ici-uploader" && \
     chmod a+x "/usr/local/bin/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
+} ]
+```