# Other CLI commands

## 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](/writing-applications.md#running-applications))
2. Retrieve information ([See Retrieving Data](/retrieve-data.md#isabl-command-line-client))
3. and, Import and manage files into your workspace (See [Importing Data](/import-data.md#data-import))

```
$ 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.

```

{% hint style="warning" %}
Some of these commands are only available for the **admin** user, like:

* To manage files and data ([See Importing Data](/import-data.md)):`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`
  {% endhint %}

### 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:

{% code title="my\_commands/cli.py" %}

```python
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,
    )

```

{% endcode %}

Then you can add the commands to your CLI Settings ([Learn how to customize your cli](/isabl-settings.md#isabl-cli-settings)):

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

Now your custom commands will be available:

```bash
$ 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...
```


---

# Agent Instructions: Querying This Documentation

If you need additional information that is not directly available in this page, you can query the documentation dynamically by asking a question.

Perform an HTTP GET request on the current page URL with the `ask` query parameter:

```
GET https://docs.isabl.io/other-cli-commands.md?ask=<question>
```

The question should be specific, self-contained, and written in natural language.
The response will contain a direct answer to the question and relevant excerpts and sources from the documentation.

Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.