# dx-toolkit Commands

Below is a list of commands, with their usage overview, that are part of the dx-toolkit. You can view more details about each command, including the different options, by typing in the help command on the far right column for each command. The format for the help command is dx \_\_\_ -h .

| Command                   | Usage                                                                                                                                                                                                                                                                                                                                                            | Help Command                    |
| ------------------------- | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ------------------------------- |
| add                       | Add one or more items to a list                                                                                                                                                                                                                                                                                                                                  | dx add -h                       |
| add developers            | Add developers for an app. Need to be a developer of an app to run it                                                                                                                                                                                                                                                                                            | dx add developers -h            |
| add member                | Grant a user membership to an org                                                                                                                                                                                                                                                                                                                                | dx add member -h                |
| add stage                 | Add a stage to a workflow                                                                                                                                                                                                                                                                                                                                        | dx add stage -h                 |
| add users                 | Add authorized users for an app. Need to be a developer of an app to run                                                                                                                                                                                                                                                                                         | dx add users -h                 |
| add\_types                | Add types to a data object                                                                                                                                                                                                                                                                                                                                       | dx add\_types -h                |
| api                       | Call an API method                                                                                                                                                                                                                                                                                                                                               | dx api -h                       |
| archive                   | <p>Requests for the specified set files or for the files in a</p><p>single specified folder in one project</p><p>to be archived on the platform</p>                                                                                                                                                                                                              | dx archive -h                   |
| build                     | Create a new applet/app, or a workflow                                                                                                                                                                                                                                                                                                                           | dx build -h                     |
| build\_asset              | Build an asset bundle                                                                                                                                                                                                                                                                                                                                            | dx build\_asset -h              |
| cat                       | Print file(s) to stdout                                                                                                                                                                                                                                                                                                                                          | dx cat -h                       |
| cd                        | Change the current working directory                                                                                                                                                                                                                                                                                                                             | dx cd -h                        |
| clearenv                  | Clears all environment variables set by dx                                                                                                                                                                                                                                                                                                                       | dx clearenv -h                  |
| close                     | Close data object(s)                                                                                                                                                                                                                                                                                                                                             | dx close -h                     |
| cp                        | Copy objects and/or folders between different projects                                                                                                                                                                                                                                                                                                           | dx cp -h                        |
| create\_cohort            | <p>Generates a new Cohort object on the platform from an</p><p>existing Dataset or Cohort object and</p><p>using list of IDs.</p>                                                                                                                                                                                                                                | dx create\_cohort -h            |
| describe                  | Describe a remote object                                                                                                                                                                                                                                                                                                                                         | dx describe -h                  |
| download                  | Download file(s)                                                                                                                                                                                                                                                                                                                                                 | dx download -h                  |
| env                       | Print all environment variables in use                                                                                                                                                                                                                                                                                                                           | dx env -h                       |
| exit                      | Exit out of the interactive shell                                                                                                                                                                                                                                                                                                                                | dx exit -h                      |
| extract\_assay            | <p>Retrieve the selected data or generate SQL to retrieve the</p><p>data from a genetic variant or somatic</p><p>assay in a dataset or cohort based on</p><p>provided rules.</p>                                                                                                                                                                                 | dx extract\_assay -h            |
| extract\_assay expression | <p>Retrieve the selected data or generate SQL to retrieve the</p><p>data from a genetic variant or somatic</p><p>assay in a dataset or cohort based on</p><p>provided rules.</p>                                                                                                                                                                                 | dx extract\_assay expression -h |
| extract\_assay germline   | <p>Retrieve the selected data or generate SQL to retrieve the</p><p>data from a genetic variant or somatic</p><p>assay in a dataset or cohort based on</p><p>provided rules.</p>                                                                                                                                                                                 | dx extract\_assay germline -h   |
| extract\_assay somatic    | <p>Retrieve the selected data or generate SQL to retrieve the</p><p>data from a genetic variant or somatic</p><p>assay in a dataset or cohort based on</p><p>provided rules.</p>                                                                                                                                                                                 | dx extract\_assay somatic -h    |
| extract\_dataset          | <p>Retrieves the data or generates SQL to retrieve the data</p><p>from a dataset or cohort for a set of</p><p>entity.fields. Additionally, the</p><p>dataset's dictionary can be extracted</p><p>independently or in conjunction with</p><p>data. Listing options enable</p><p>enumeration of the entities and their</p><p>respective fields in the dataset.</p> | dx extract\_dataset -h          |
| find                      | Search functionality over various DNAnexus entities                                                                                                                                                                                                                                                                                                              | dx find -h                      |
| find analyses             | List analyses in the current project                                                                                                                                                                                                                                                                                                                             | dx find analyses -h             |
| find apps                 | List available apps                                                                                                                                                                                                                                                                                                                                              | dx find apps -h                 |
| find data                 | List data objects in the current project                                                                                                                                                                                                                                                                                                                         | dx find data -h                 |
| find executions           | List executions (jobs and analyses) in the current project                                                                                                                                                                                                                                                                                                       | dx find executions -h           |
| find globalworkflows      | List available global workflows                                                                                                                                                                                                                                                                                                                                  | dx find globalworkflows -h      |
| find jobs                 | List jobs in the current project                                                                                                                                                                                                                                                                                                                                 | dx find jobs -h                 |
| find org                  | <p>List entities within a specific org. "dx find org</p><p>members" lists members in the</p><p>specified org "dx find org</p><p>projects" lists projects billed to the</p><p>specified org "dx find org</p><p>apps" lists apps billed to the</p><p>specified org Please execute "dx find</p><p>org -h" for more information.</p>                                 | dx find org -h                  |
| find org apps             | List apps billed to the specified org                                                                                                                                                                                                                                                                                                                            | dx find org apps -h             |
| find org members          | List members in the specified org                                                                                                                                                                                                                                                                                                                                | dx find org members -h          |
| find org projects         | List projects billed to the specified org                                                                                                                                                                                                                                                                                                                        | dx find org projects -h         |
| find orgs                 | List orgs                                                                                                                                                                                                                                                                                                                                                        | dx find orgs -h                 |
| find projects             | List projects                                                                                                                                                                                                                                                                                                                                                    | dx find projects -h             |
| generate\_batch\_inputs   | <p>Generate a batch plan (one or more TSV files) for batch</p><p>execution</p>                                                                                                                                                                                                                                                                                   | dx generate\_batch\_inputs -h   |
| get                       | <p>Download records, apps, applets, workflows, files, and</p><p>databases.</p>                                                                                                                                                                                                                                                                                   | dx get -h                       |
| get\_details              | Get details of a data object                                                                                                                                                                                                                                                                                                                                     | dx get\_details -h              |
| head                      | Print part of a file                                                                                                                                                                                                                                                                                                                                             | dx head -h                      |
| help                      | Display help messages and dx commands by category                                                                                                                                                                                                                                                                                                                | dx help -h                      |
| install                   | Install an app                                                                                                                                                                                                                                                                                                                                                   | dx install -h                   |
| invite                    | Invite another user to a project or make it public                                                                                                                                                                                                                                                                                                               | dx invite -h                    |
| list                      | Print the members of a list                                                                                                                                                                                                                                                                                                                                      | dx list -h                      |
| list database             | <p>List entities associated with a specific database. For</p><p>example, "dx list database</p><p>files" lists database files associated</p><p>with a specific database.</p><p>Please execute "dx list database -h"</p><p>for more information.</p>                                                                                                               | dx list database -h             |
| list database files       | List files associated with a specific database                                                                                                                                                                                                                                                                                                                   | dx list database files -h       |
| list developers           | List developers for an app                                                                                                                                                                                                                                                                                                                                       | dx list developers -h           |
| list stages               | List the stages in a workflow                                                                                                                                                                                                                                                                                                                                    | dx list stages -h               |
| list users                | List authorized users for an app                                                                                                                                                                                                                                                                                                                                 | dx list users -h                |
| login                     | Log in (interactively or with an existing API token)                                                                                                                                                                                                                                                                                                             | dx login -h                     |
| logout                    | Log out and remove credentials                                                                                                                                                                                                                                                                                                                                   | dx logout -h                    |
| ls                        | List folders and/or objects in a folder                                                                                                                                                                                                                                                                                                                          | dx ls -h                        |
| make\_download\_url       | Create a file download link for sharing                                                                                                                                                                                                                                                                                                                          | dx make\_download\_url -h       |
| mkdir                     | Create a new folder                                                                                                                                                                                                                                                                                                                                              | dx mkdir -h                     |
| mv                        | Move or rename objects and/or folders inside a project                                                                                                                                                                                                                                                                                                           | dx mv -h                        |
| new                       | Create a new project or data object                                                                                                                                                                                                                                                                                                                              | dx new -h                       |
| new org                   | Create new non-billable org                                                                                                                                                                                                                                                                                                                                      | dx new org -h                   |
| new project               | Create a new project                                                                                                                                                                                                                                                                                                                                             | dx new project -h               |
| new record                | Create a new record                                                                                                                                                                                                                                                                                                                                              | dx new record -h                |
| new user                  | Create a new user account                                                                                                                                                                                                                                                                                                                                        | dx new user -h                  |
| new workflow              | Create a new workflow                                                                                                                                                                                                                                                                                                                                            | dx new workflow -h              |
| publish                   | Publish an app or a global workflow                                                                                                                                                                                                                                                                                                                              | dx publish -h                   |
| pwd                       | Print current working directory                                                                                                                                                                                                                                                                                                                                  | dx pwd -h                       |
| remove                    | Remove one or more items to a list                                                                                                                                                                                                                                                                                                                               | dx remove -h                    |
| remove developers         | Remove developers for an app                                                                                                                                                                                                                                                                                                                                     | dx remove developers -h         |
| remove member             | Revoke the org membership of a user                                                                                                                                                                                                                                                                                                                              | dx remove member -h             |
| remove stage              | Remove a stage from a workflow                                                                                                                                                                                                                                                                                                                                   | dx remove stage -h              |
| remove users              | Remove authorized users for an app                                                                                                                                                                                                                                                                                                                               | dx remove users -h              |
| remove\_types             | Remove types from a data object                                                                                                                                                                                                                                                                                                                                  | dx remove\_types -h             |
| rename                    | Rename a project or data object                                                                                                                                                                                                                                                                                                                                  | dx rename -h                    |
| rm                        | Remove data objects and folders                                                                                                                                                                                                                                                                                                                                  | dx rm -h                        |
| rmdir                     | Remove a folder                                                                                                                                                                                                                                                                                                                                                  | dx rmdir -h                     |
| rmproject                 | Delete a project                                                                                                                                                                                                                                                                                                                                                 | dx rmproject -h                 |
| run                       | Run an applet, app, or workflow                                                                                                                                                                                                                                                                                                                                  | dx run -h                       |
| select                    | List and select a project to switch to                                                                                                                                                                                                                                                                                                                           | dx select -h                    |
| set\_details              | Set details on a data object                                                                                                                                                                                                                                                                                                                                     | dx set\_details -h              |
| set\_properties           | Set properties of a project, data object, or execution                                                                                                                                                                                                                                                                                                           | dx set\_properties -h           |
| set\_visibility           | Set visibility on a data object                                                                                                                                                                                                                                                                                                                                  | dx set\_visibility -h           |
| setenv                    | Sets environment variables for the session                                                                                                                                                                                                                                                                                                                       | dx setenv -h                    |
| ssh                       | Connect to a running job via SSH                                                                                                                                                                                                                                                                                                                                 | dx ssh -h                       |
| ssh\_config               | Configure SSH keys for your DNAnexus account                                                                                                                                                                                                                                                                                                                     | dx ssh\_config -h               |
| tag                       | Tag a project, data object, or execution                                                                                                                                                                                                                                                                                                                         | dx tag -h                       |
| terminate                 | Terminate jobs or analyses                                                                                                                                                                                                                                                                                                                                       | dx terminate -h                 |
| tree                      | List folders and objects in a tree                                                                                                                                                                                                                                                                                                                               | dx tree -h                      |
| unarchive                 | <p>Requests for the specified set files or for the files in a</p><p>single specified folder in one project</p><p>to be unarchived on the platform.</p>                                                                                                                                                                                                           | dx unarchive -h                 |
| uninstall                 | Uninstall an app                                                                                                                                                                                                                                                                                                                                                 | dx uninstall -h                 |
| uninvite                  | Revoke others' permissions on a project you administer                                                                                                                                                                                                                                                                                                           | dx uninvite -h                  |
| unset\_properties         | Unset properties of a project, data object, or execution                                                                                                                                                                                                                                                                                                         | dx unset\_properties -h         |
| untag                     | Untag a project, data object, or execution                                                                                                                                                                                                                                                                                                                       | dx untag -h                     |
| update                    | Update certain types of metadata                                                                                                                                                                                                                                                                                                                                 | dx update -h                    |
| update member             | Update the membership of a user in an org                                                                                                                                                                                                                                                                                                                        | dx update member -h             |
| update org                | Update information about an org                                                                                                                                                                                                                                                                                                                                  | dx update org -h                |
| update project            | Updates a specified project with the specified options                                                                                                                                                                                                                                                                                                           | dx update project -h            |
| update stage              | Update the metadata for a stage in a workflow                                                                                                                                                                                                                                                                                                                    | dx update stage -h              |
| update workflow           | Update the metadata for a workflow                                                                                                                                                                                                                                                                                                                               | dx update workflow -h           |
| upload                    | Upload file(s) or directory                                                                                                                                                                                                                                                                                                                                      | dx upload -h                    |
| wait                      | Wait for data object(s) to close or job(s) to finish                                                                                                                                                                                                                                                                                                             | dx wait -h                      |
| watch                     | Watch logs of a job and its subjobs                                                                                                                                                                                                                                                                                                                              | dx watch -h                     |
| whoami                    | Print the username of the current user                                                                                                                                                                                                                                                                                                                           | dx whoami -h                    |