# Advanced CLI

## Batch Runs in CLI

```
# Generate batch file by regex

$ dx generate_batch_inputs -iinput_fwd='(.*)_R1_001.fastq.gz' -iinput_rev='(.*)_R2_001.fastq.gz'

# Show the local file
$ cat dx_batch.0000.tsv

# Use the local batch file
$ dx run fastp --batch-tsv dx_batch.0000.tsv -iadapter_fa=/data/adapters.fa -iprefix='Sample1'
```

## Overview of DX Commands

There are about 100 `dx` commands, which you can find by executing **`dx help all`**:

* `add`: Add one or more items to a list
* `add developers`: Add developers for an app
* `add member`: Grant a user membership to an org
* `add stage`: Add a stage to a workflow
* `add users`: Add authorized users for an app
* `add_types`: Add types to a data object
* `api`: Call an API method
* `archive`: Requests for the specified set files or for the files in a single specified folder in one project to be archived on the platform
* `build`: Create a new applet/app, or a workflow
* `build_asset`: Build an asset bundle
* `cat`: Print file(s) to stdout
* `cd`: Change the current working directory
* `clearenv`: Clears all environment variables set by dx
* `close`: Close data object(s)
* `cp`: Copy objects and/or folders between different projects
* `describe`: Describe a remote object
* `download`: Download file(s)
* `env`: Print all environment variables in use
* `exit`: Exit out of the interactive shell
* `extract_dataset`: Retrieves the data or generates SQL to retrieve the data from a dataset or cohort for a set of entity.fields. Additionally, the dataset's dictionary can be extracted independently or in conjunction with data. Listing options enable enumeration of the entities and their respective fields in the dataset.
* `find analyses`: List analyses in the current project
* `find apps`: List available apps
* `find data`: List data objects in the current project
* `find executions`: List executions (jobs and analyses) in the current project
* `find globalworkflows`: List available global workflows
* `find jobs`: List jobs in the current project
* `find org members`: lists members in the org
* `find org projects`: lists projects billed to the org
* `find org apps`: lists apps billed to the org
* `find org apps`: List apps billed to the specified org
* `find org members`: List members in the specified org
* `find org projects`: List projects billed to the specified org
* `find orgs`: List orgs
* `find projects`: List projects
* `generate_batch_inputs`: Generate a batch plan (one or more TSV files) for batch execution
* `get`: Download records, apps, applets, workflows, files, and databases
* `get_details`: Get details of a data object (cf [details](https://documentation.dnanexus.com/developer/api/data-object-lifecycle/details-and-links))
* `head`: Print part of a file
* `help`: Display help messages and dx commands by category
* `install`: Install an app
* `invite`: Invite another user to a project or make it public
* `list database`: List entities associated with a specific database. For
* `list database files`: lists database files associated with a specific database.
* `list developers`: List developers for an app
* `list stages`: List the stages in a workflow
* `list users`: List authorized users for an app
* `login`: Log in (interactively or with an existing API token)
* `logout`: Log out and remove credentials
* `ls`: List folders and/or objects in a folder
* `make_download_url`: Create a file download link for sharing
* `mkdir`: Create a new folder
* `mv`: Move or rename objects and/or folders inside a project
* `new org`: Create new non-billable org
* `new project`: Create a new project
* `new record`: Create a new record
* `new user`: Create a new user account
* `new workflow`: Create a new workflow
* `publish`: Publish an app or a global workflow
* `pwd`: Print current working directory
* `remove developers`: Remove developers for an app
* `remove member`: Revoke the org membership of a user
* `remove stage`: Remove a stage from a workflow
* `remove users`: Remove authorized users for an app
* `remove_types`: Remove types from a data object
* `rename`: Rename a project or data object
* `rm`: Remove data objects and folders
* `rmdir`: Remove a folder
* `rmproject`: Delete a project
* `run`: Run an applet, app, or workflow
* `select`: List and select a project to switch to
* `set_details`: Set details on a data object
* `set_properties`: Set properties of a project, data object, or execution
* `set_visibility`: Set visibility on a data object
* `setenv`: Sets environment variables for the session
* `ssh`: Connect to a running job via SSH
* `ssh_config`: Configure SSH keys for your DNAnexus account
* `tag`: Tag a project, data object, or execution
* `terminate`: Terminate jobs or analyses
* `tree`: List folders and objects in a tree
* `unarchive`: Requests for the specified set files or for the files in a single specified folder in one project to be unarchived on the platform.
* `uninstall`: Uninstall an app
* `uninvite`: Revoke others' permissions on a project you administer
* `unset_properties`: Unset properties of a project, data object, or execution
* `untag`: Untag a project, data object, or execution
* `update member`: Update the membership of a user in an org
* `update org`: Update information about an org
* `update project`: Updates a specified project with the specified options
* `update stage`: Update the metadata for a stage in a workflow
* `update workflow`: Update the metadata for a workflow
* `upgrade`: Upgrade dx-toolkit (the DNAnexus SDK and this program)
* `upload`: Upload file(s) or directory
* `wait`: Wait for data object(s) to close or job(s) to finish
* `watch`: Watch logs of a job and its subjobs
* `whoami`: Print the username of the current user

## Review

You are now able to:

* Describe how to use metadata and the dx find data command on the CLI
* Create and use batch file processing using the CLI
* Describe the use cases that warrant the Cloud Workstation

## Resources

[Full Documentation](https://documentation.dnanexus.com/)

To create a support ticket if there are technical issues:

1. Go to the Help header (same section where Projects and Tools are) inside the platform
2. Select "Contact Support"
3. Fill in the Subject and Message to submit a support ticket.