Other CLI commands

☄️Isabl comes with a bunch of built-in commands to run from the terminal.

Getting Super Powers

The python package of isabl-cli comes with a lot of useful functions that allows you to achieve mainly 3 type of needs:

1. Create and Execute analyses (See Running Applications)

2. Retrieve information (See Retrieving Data)

3. and, Import and manage files into your workspace (See Importing Data)

$ isabl --help

Usage: isabl [OPTIONS] COMMAND [ARGS]...

  Run Isabl command line tools.

Options:
  --version  Show the version and exit.
  --help     Show this message and exit.

Commands:
  apps-grch37                GRCh37 applications.
  apps-grcm38                GRCm38 applications.
  get-bams                   Get storage directories, use `pattern` to
                             match...
  get-bed                    Get a BED file for a given Sequencing...
  get-count                  Get count of database instances.
  get-data                   Get file paths for experiments raw data.
  get-metadata               Retrieve metadata for multiple instances.
  get-outdirs                Get analyses outdirs, use `pattern` to match...
  get-paths                  Get storage directories, use `pattern` to
                             match...
  get-reference              Retrieve reference data from assemblies...
  get-results                Get analyses results.
  import-bedfiles            Register targets and baits BED files in a...
  import-data                Find and import experiments data from many...
  import-reference-data      Register reference data for assemblies...
  import-reference-genome    Register an assembly reference genome.
  login                      Login with isabl credentials.
  merge-individual-analyses  Merge analyses by individual.
  merge-project-analyses     Merge analyses by project.
  patch-results              Update the results field of many analyses.
  process-finished           Process and update finished analyses.
  rerun-signals              Rerun failed signals.
  run-failed-analyses        Command to run failed analyses in batch.
  run-signals                Run any arbitrary signal on analyses or...
  run-web-signals            Run signals triggered from the frontend.

Some of these commands are only available for the admin user, like:

• To manage files and data (See Importing Data):import-data, import-bedfiles, import-reference-data, import-reference-genome

• To change permissions of finished analyses: process-finished

• To update the linked results of completed analyses: patch-results

Create your custom CLI Commands

You can customize your available commands, by extending the isabl-cli. The following are examples of cases where you want to create commands that execute more than one app at the same time, or create a method for a common metadata query:

my_commands/cli.py

import datetime
import click
from isabl_cli import options
from isabl_cli import commands
from my_apps import apps


@click.command()
@options.PAIRS
@options.PAIRS_FROM_FILE
@options.SKIP
@options.COMMIT
@options.FORCE
@options.RESTART
@options.QUIET
def triple_caller(commit, force, quiet, restart, skip, pairs, pairs_from_file):
    """
    Command to run THE 3-CALLER pipeline.
    """
    for pipe in [
        apps.CallerOneGRCh37,
        apps.CallerTwoGRCh37,
        apps.CallerThreeGRCh37,
    ]:
        pipe().run(
            tuples=pairs + pairs_from_file,
            commit=commit,
            force=force,
            restart=restart,
            verbose=not quiet,
            run_args=dict(skip=skip),
        )
        

@click.command()
@click.pass_context
def get_succeded_kids_analyses(ctx):
    """
    Command to print information from all Succeded Analyses executed on
    Pediatric Children (age <= 18) of MSK Kids.
    """
    current_year = datetime.datetime.now().year
    filters = dict(
        status="SUCCEEDED",
        targets__center__name="MSK Kids",
        targets__sample__individual__birth_year__gte=(current_year - 18),
    )
    fields = [
        "targets__sample__individual__system_id",
        "pk",
        "status",
        "application__name",
        "application__version",
    ]
    ctx.invoke(
        commands.get_metadata,
        identifiers=None,
        endpoint="analyses",
        field=[i.split("__") for i in fields],
        filters=filters,
        no_headers=False,
        json_=False,
        use_fx=False,
    )

Then you can add the commands to your CLI Settings (Learn how to customize your cli):

CUSTOM_COMMANDS = [
    my_commands.cli.triple_caller,
    my_commands.cli.get_succeded_kids_analyses
]

Now your custom commands will be available:

$ isabl --help

Usage: isabl [OPTIONS] COMMAND [ARGS]...

  Run Isabl command line tools.

Options:
  --version  Show the version and exit.
  --help     Show this message and exit.

Commands:
  
  ...
  
  triple_caller                Command to run THE 3-CALLER pipeline.
  get-succeded-kids-analyses   Command to print metadata of all Succeded...