# 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. 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