WuXi Nextcode commandline utilities
NextCODE Command Line Interface
Introduction... What is the CLI all about and what can it do.
- Python 3.7
To install the package you have to run the following command:
$ pip3 install nextcode-cli -U
To verify that the installation was successful you can run the following command:
$ nextcode version nextcode-cli/x.y.z (yyyy.mm.dd)
Start by pulling the sourcecode from git (usually from develop to be on the bleeding edge).
There are two ways to set up the CLI. We recommend trying to install it into your system python in
develop mode by simply running the following command in the nextcode-cli folder (depending on your system setup you might need
$ pip3 install -e .
If you get any errors you can set up a local virtualenv in the nextcode-cli path:
$ source ./setup.sh $ pip3 install -e .
Using this method means that you will always need to do
source ./setup.sh to enter the virtualenv before using the tool, so we would recommend getting the first method to work unless you intend on make edits to the code yourself.
Set up a service profile
Create a service profile
For any work to happen a service profile must be defined. One example is the one here below, which is Platform Dev test specific. For QA purposes this is of course test environment dependent!:
The command is:
$ nextcode profile add <profile-name>
Follow the prompts to enter a server name and then log in through the browser window that opens up.
You can also set up the profile without a prompt like this:
$ nextcode profile add <profile-name> --domain=mydomain.wuxinextcode.com --api-key=<key>
Running the CLI for the first time
Once your installation has succeeded you can run the following command anywhere in your system:
Once you finish the authentication process you should be able to view workflow jobs:
nextcode workflow jobs
To start familiarizing yourself with the sdk you can use the --help option on all commands to see detailed information about their use.
$ nextcode --help Usage: nextcode [OPTIONS] COMMAND [ARGS]... A utility for interfacing with WuXi Nextcode services. This tool allows you to communicate with the pipelines service, CSA, workflow service and GOR Query API. For all usage you will need to authenticate against the specific service profile you are using. Please look at the subcommands below for details. Options: -v, --verbose [warning|error|info] Output logs for debugging -p, --profile TEXT Use a specific profile for this command --help Show this message and exit. Commands: csa_authenticate Authenticate against CSA (for import). import Import a TSV manifest into CSA. keycloak Manage keycloak users Requires the keycloak admin... login Authenticate against keycloak. pipelines Root subcommand for pipelines functionality profile Configure server profile to use. query Root subcommand for query api functionality token Print out an access token for the current profile version Show the Nextcode CLI version. workflow Root subcommand for workflow functionality $ nextcode workflow --help Usage: nextcode workflow [OPTIONS] COMMAND [ARGS]... Root subcommand for workflow functionality Options: --help Show this message and exit. Commands: job View or manage individual jobs. jobs List jobs pipelines List pipelines projects List projects run Start a new nextflow job. smoketest Run a smoketest of the workflow service status Show the status of the workflow service
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