KubeIT - Command Line Interface (CLI)

Dedicated client for use with the KubeIT backend. This client allows users to preconfigure and use server sided schemes as templates for workflow creation.

Contents

• Description
• Installation
• Usage
• FAQ

Description

The KubeIT CLI is a dedicated interface method for the KubeIT Backend. It contains helper functions for communications with the backend and allows automated access to in- and output data via S3.

Installation

Download the lastest release for your desired operating system. All following examples reference the Linux binary kubeit, for other operating systems exchange ./kubeit with the specific program (e.g. ./kubeit.exe for windows)

Initial configuration:

Configure your backend connection with:

    ./kubeit configure

This will show a configuration dialogue that asks for your KubeIT URL and access token. The information is by default saved in ~/.kubeit/config.json. Other paths can be specified via the -c flag.

Usage

If more information is needed use the -h flag to access the help page with an overview for the chosen command.

Configure local scheme

To use KubeIT first a local scheme must be configured. Local schemes are variations of globally available backend schemes and can pre-configure backend-schemes with non-default parameters. Local schemes can be configured, via a dialogue, with:

    ./kubeit configure -s

In normal operation only required arguments will be shown. If you want to change defaulted backend parameters locally, use the -e flag to enable expert configuration mode. (e.g. ./kubeit configure -s -e)

Schedule local scheme to the cluster

The KubeIT CLI allows local schemes to be configured and executed in one step. A very basic example for this is:

    ./kubeit create workflow -s YOUR-LOCAL-SCHEME-NAME -i YOUR-INPUTFILE -o YOUR-OUTPUTFILE -w 

-s: specified your local scheme
-i: Your input-file on the local file system (The default-template accepts protein FASTA files (.faa))
-o: Automatically download results to the specified destination
-w: Watch the workflow execution and wait for either workflow completion or failure

Input upload in advance

Input files can either be automatically upload via -i or uploaded beforehand. This can be done with:

    ./kubeit create S3 -f YOUR-FILE

If uploaded beforehand KubeIT will print an associated time-limited download URL automatically. This URL can be used for future workflows.

Specify a parameter on scheduling

Sometime the needed parameters can differ. For this KubeIT can receive parameters in workflow creation. Parameters are specified with the -p flag followed by the parameter name and its desired value. Example: -p "input.inputdata=https://example.com/test"

Delete a workflow

Workflows can be deleted with:

    ./kubeit delete workflow -n WORKFLOW-NAME

Delete a collection of workflows

Multiple workflows can be deleted by specifying a project group.

    ./kubeit delete workflow -g PROJECT-GROUP-NAME

Get a workflow status

If a workflow is not scheduled with the -w flag, its status can be accessed once with:

    ./kubeit get workflow -n WORKFLOW-NAME

or for a complete project group:

    ./kubeit get workflow -g PROJECT-GROUP-NAME

Get more information about (a) local or remote scheme(s)

Get all available schemes:

    ./kubeit get scheme

get more information about a specific scheme:

    ./kubeit get scheme -n SCHEME-NAME

both commands can either be used for remote schemes, or for local schemes (with the -l flag)

Create new remote schemes

New remote schemes can be created with:

    ./kubeit create scheme -n SCHEME-NAME -f SCHEME-YAML-FILE

see here for a short guideline on how to create new schemes.

FAQ

How does KubeIT upload data to S3 ?

KubeIT uses pre-authenticated S3 links to upload data to S3. It automatically determines if a file have to be split up or can be uploaded as a whole.

How does the splitting work ?

Splitting is done using the Splitter WorkflowTemplate and the splitter interface. For mor information see here