Install Pipeline

Copy Pipeline

Start the brave service with the following command:

brave  \
    --mysql-url root:123456@localhost:63306/brave \
    --port 5008 \
    --base-dir /opt/brave/workspace \
    --use-https

In the startup log, you can see the currently used 'PIPELINE_DIR' directory, which is the directory that the pipeline needs to be installed

Using PIPELINE_DIR: /opt/brave/workspace/pipeline

To install the pipeline, simply copy the written pipeline directory to this folder. Since brave supports multiple pipelines, it needs to be isolated using namespaces as folders.The name of the command space can be viewed in the namespace.json file.

Take the metagenomic pipeline pipeline-metagenomics as an example:

• namespace: 7530139e-8985-423f-9fb6-32650828ca40
• git url：https://github.com/pybrave/pipeline-metagenomics.git
• PIPELINE_DIR: /opt/brave/workspace/pipeline

The installation command is:

git clone \
    https://github.com/pybrave/pipeline-metagenomics.git \
    /opt/brave/workspace/pipeline/7530139e-8985-423f-9fb6-32650828ca40

OR

git clone \
    git@github.com:pybrave/pipeline-metagenomics.git \
    /opt/brave/workspace/pipeline/7530139e-8985-423f-9fb6-32650828ca40

The pipeline directory structure is as follows:

.
├── container.json
├── namespace.json
├── nextflow.config
├── pipeline
├── pipeline_component.json
├── pipeline_component_relation.json
├── README.md
├── script
└── software

Installation of pipelines to the database

• open brave-ui
• click Install namespace -> Install