diff --git a/repositories/ici-uploader/4.0.3/Dockerfile b/repositories/ici-uploader/4.0.3/Dockerfile index f8d3dae..e10214f 100644 --- a/repositories/ici-uploader/4.0.3/Dockerfile +++ b/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" diff --git a/repositories/ici-uploader/4.0.3/Readme.md b/repositories/ici-uploader/4.0.3/Readme.md new file mode 100644 index 0000000..d4bca43 --- /dev/null +++ b/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=] [COMMAND] +ICI Command-line Interface (Uploader) for analysis, and file operations + --configFile, --config-file= + [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 +} ] +``` \ No newline at end of file