Index of dx commands

Search…
This page contains the help messages for each of the commands under dx, grouped by their primary category.
help
usage: dx help [-h] [command_or_category] [subcommand]
​
Displays the help message for the given command (and subcommand if given), or
displays the list of all commands in the given category.
​
CATEGORIES
​
  all		All commands
  session	Manage your login session
  fs		Navigate and organize your projects and files
  data		View, download, and upload data
  metadata	View and modify metadata for projects, data, and executions
  workflow	View and modify workflows
  exec		Manage and run apps, applets, and workflows
  org		Administer and operate on orgs
  other		Miscellaneous advanced utilities
​
EXAMPLE
​
  To find all commands related to running and monitoring a job and then display
  the help message for the command "run", run
​
  $ dx help exec
    <list of all execution-related dx commands>
  $ dx help run
    <help message for dx run>
​
positional arguments:
  command_or_category  Display the help message for the given command, or the
                       list of all available commands for the given category
  subcommand           Display the help message for the given subcommand of
                       the command
​
optional arguments:
  -h, --help           show this help message and exit
Overriding environment variables
usage: dx command ... [--apiserver-host APISERVER_HOST]
                      [--apiserver-port APISERVER_PORT]
                      [--apiserver-protocol APISERVER_PROTOCOL]
                      [--project-context-id PROJECT_CONTEXT_ID]
                      [--workspace-id WORKSPACE_ID]
                      [--security-context SECURITY_CONTEXT]
                      [--auth-token AUTH_TOKEN]
​
optional arguments:
  --apiserver-host APISERVER_HOST
                        API server host
  --apiserver-port APISERVER_PORT
                        API server port
  --apiserver-protocol APISERVER_PROTOCOL
                        API server protocol (http or https)
  --project-context-id PROJECT_CONTEXT_ID
                        Default project or project context ID
  --workspace-id WORKSPACE_ID
                        Workspace ID (for jobs only)
  --security-context SECURITY_CONTEXT
                        JSON string of security context
  --auth-token AUTH_TOKEN
                        Authentication token
Category: session
Manage your login session.
login
usage: dx login [-h] [--env-help] [--token TOKEN] [--noprojects] [--save]
                [--timeout TIMEOUT]
​
Log in interactively and acquire credentials. Use "--token" to log in with an
existing API token.
​
optional arguments:
  -h, --help         show this help message and exit
  --env-help         Display help message for overriding environment variables
  --token TOKEN      Authentication token to use
  --noprojects       Do not print available projects
  --save             Save token and other environment variables for future
                     sessions
  --timeout TIMEOUT  Timeout for this login token (in seconds, or use suffix
                     s, m, h, d, w, M, y)
logout
usage: dx logout [-h] [--env-help] [--host HOST] [--port PORT]
                 [--protocol PROTOCOL]
​
Log out and remove credentials
​
optional arguments:
  -h, --help           show this help message and exit
  --env-help           Display help message for overriding environment
                       variables
  --host HOST          Log out of the given auth server host (port must also
                       be given)
  --port PORT          Log out of the given auth server port (host must also
                       be given)
  --protocol PROTOCOL  Used in conjunction with host and port arguments, gives
                       the protocol to use when contacting auth server
exit
usage: dx exit [-h]
​
Exit out of the interactive shell
​
optional arguments:
  -h, --help  show this help message and exit
whoami
usage: dx whoami [-h] [--env-help] [--id]
​
Print the username of the current user, in the form "user-USERNAME"
​
optional arguments:
  -h, --help  show this help message and exit
  --env-help  Display help message for overriding environment variables
  --id        Print user ID instead of username
env
usage: dx env [-h] [--env-help] [--bash] [--dx-flags]
​
Prints all environment variables in use as they have been resolved from
environment variables and configuration files.  For more details, see
​
https://documentation.dnanexus.com/user/helpstrings-of-sdk-command-line-utilities#overriding-environment-variables
​
optional arguments:
  -h, --help  show this help message and exit
  --env-help  Display help message for overriding environment
              variables
  --bash      Prints a list of bash commands to export the environment
              variables
  --dx-flags  Prints the dx options to override the environment variables
clearenv
usage: dx clearenv [-h] [--reset]
​
Clears all environment variables set by dx. More specifically, it removes
local state stored in ~/.dnanexus_config/environment. Does not affect the
environment variables currently set in your shell.
​
optional arguments:
  -h, --help  show this help message and exit
  --reset     Reset dx environment variables to empty values. Use this to
              avoid interference between multiple dx sessions when using shell
              environment variables.
Category: fs
Navigate and organize your projects and files
ls
usage: dx ls [-h] [--color {off,on,auto}] [--delimiter [DELIMITER]]
             [--env-help] [--brief | --verbose] [-a] [-l] [--obj] [--folders]
             [--full]
             [path]
​
List folders and/or objects in a folder
​
positional arguments:
  path                  Folder (possibly in another project) to list the
                        contents of, default is the current directory in the
                        current project. Syntax: projectID:/folder/path
​
optional arguments:
  -h, --help            show this help message and exit
  --color {off,on,auto}
                        Set when color is used (color=auto is used when stdout
                        is a TTY)
  --delimiter [DELIMITER], --delim [DELIMITER]
                        Always use exactly one of DELIMITER to separate fields
                        to be printed; if no delimiter is provided with this
                        flag, TAB will be used
  --env-help            Display help message for overriding environment
                        variables
  --brief               Display a brief version of the return value; for most
                        commands, prints a DNAnexus ID per line
  --verbose             If available, displays extra verbose output
  -a, --all             show hidden files
  -l, --long            Alias for "verbose"
  --obj                 show only objects
  --folders             show only folders
  --full                show full paths of folders
tree
usage: dx tree [-h] [--color {off,on,auto}] [--env-help] [-a] [-l] [path]
​
List folders and objects in a tree
​
positional arguments:
  path                  Folder (possibly in another project) to list the
                        contents of, default is the current directory in the
                        current project. Syntax: projectID:/folder/path
​
optional arguments:
  -h, --help            show this help message and exit
  --color {off,on,auto}
                        Set when color is used (color=auto is used when stdout
                        is a TTY)
  --env-help            Display help message for overriding environment
                        variables
  -a, --all             show hidden files
  -l, --long            use a long listing format
pwd
usage: dx pwd [-h] [--env-help]
​
Print current working directory
​
optional arguments:
  -h, --help  show this help message and exit
  --env-help  Display help message for overriding environment variables
select
usage: dx select [-h] [--env-help] [--name NAME]
                 [--level {VIEW,UPLOAD,CONTRIBUTE,ADMINISTER}] [--public]
                 [project]
​
Interactively list and select a project to switch to. By default, only lists
projects for which you have at least CONTRIBUTE permissions. Use --public to
see the list of public projects.
​
positional arguments:
  project               Name or ID of a project to switch to; if not provided
                        a list will be provided for you
​
optional arguments:
  -h, --help            show this help message and exit
  --env-help            Display help message for overriding environment
                        variables
  --name NAME           Name of the project (wildcard patterns supported)
  --level {VIEW,UPLOAD,CONTRIBUTE,ADMINISTER}
                        Minimum level of permissions expected
  --public              Include ONLY public projects (will automatically set
                        --level to VIEW)
cd
usage: dx cd [-h] [--env-help] [path]
​
Change the current working directory
​
positional arguments:
  path        Folder (possibly in another project) to which to change the
              current working directory, default is "/" in the current project
​
optional arguments:
  -h, --help  show this help message and exit
  --env-help  Display help message for overriding environment variables
cp
usage: dx cp [-h] [--env-help] [-a] source [source ...] destination
​
Copy objects and/or folders between different projects.  Folders will
automatically be copied recursively.  To specify which project to use as a
source or destination, prepend the path or ID of the object/folder with the
project ID or name and a colon.
​
EXAMPLES
​
  The first example copies a file in a project called "FirstProj" to the
  current directory of the current project.  The second example copies the
  object named "reads.fq.gz" in the current directory to the folder
  /folder/path in the project with ID "project-B0VK6F6gpqG6z7JGkbqQ000Q",
  and finally renaming it to "newname.fq.gz".
​
  $ dx cp FirstProj:file-B0XBQFygpqGK8ZPjbk0Q000q .
  $ dx cp reads.fq.gz project-B0VK6F6gpqG6z7JGkbqQ000Q:/folder/path/newname.fq.gz
​
positional arguments:
  source       Objects and/or folder names to copy
  destination  Folder into which to copy the sources or new pathname (if only
               one source is provided).  Must be in a different
               project/container than all source paths.
​
optional arguments:
  -h, --help   show this help message and exit
  --env-help   Display help message for overriding environment
               variables
  -a, --all    Apply to all results with the same name without
               prompting
mv
usage: dx mv [-h] [--env-help] [-a] source [source ...] destination
​
Move or rename data objects and/or folders inside a single project.  To copy
data between different projects, use 'dx cp' instead.
​
positional arguments:
  source       Objects and/or folder names to move
  destination  Folder into which to move the sources or new pathname (if only
               one source is provided).  Must be in the same project/container
               as all source paths.
​
optional arguments:
  -h, --help   show this help message and exit
  --env-help   Display help message for overriding environment
               variables
  -a, --all    Apply to all results with the same name without
               prompting
mkdir
usage: dx mkdir [-h] [--env-help] [-p] path [path ...]
​
Create a new folder
​
positional arguments:
  path           Paths to folders to create
​
optional arguments:
  -h, --help     show this help message and exit
  --env-help     Display help message for overriding environment variables
  -p, --parents  no error if existing, create parent directories as needed
rmdir
usage: dx rmdir [-h] [--env-help] path [path ...]
​
Remove a folder
​
positional arguments:
  path        Paths to folders to remove
​
optional arguments:
  -h, --help  show this help message and exit
  --env-help  Display help message for overriding environment variables
rm
usage: dx rm [-h] [--env-help] [-a] [-r] [-f] path [path ...]
​
Remove data objects and folders.
​
positional arguments:
  path             Paths to remove
​
optional arguments:
  -h, --help       show this help message and exit
  --env-help       Display help message for overriding environment variables
  -a, --all        Apply to all results with the same name without prompting
  -r, --recursive  Recurse into a directory
  -f, --force      Force removal of files
rmproject
usage: dx rmproject [-h] [--env-help] [-y] [-q] project [project ...]
​
Delete projects and all their associated data
​
positional arguments:
  project      Projects to remove
​
optional arguments:
  -h, --help   show this help message and exit
  --env-help   Display help message for overriding environment variables
  -y, --yes    Do not ask for confirmation
  -q, --quiet  Do not print purely informational messages
archive
usage: dx archive [-h] [-a] [-q] [--all-copies] [-y] [--no-recurse]
                  path [path ...]
​
Requests for the specified set files or for the files in a single specified folder in ONE project to be archived on the platform.
For each file, if this is the last copy of a file to have archival requested, it will trigger the full archival of the object. 
Otherwise, the file will be marked in an archival state denoting that archival has been requested.
​
The input paths should be either 1 folder path or up to 1000 files, and all path(s) need to be in the same project. 
To specify which project to use, prepend the path or ID of the file/folder with the project ID or name and a colon. 
​
EXAMPLES:
​
    # archive 3 files in project "FirstProj" with project ID project-B0VK6F6gpqG6z7JGkbqQ000Q
    $ dx archive FirstProj:file-B0XBQFygpqGK8ZPjbk0Q000Q FirstProj:/path/to/file1 project-B0VK6F6gpqG6z7JGkbqQ000Q:/file2
    
    # archive 2 files in current project. Specifying file ids saves time by avoiding file name resolution.
    $ dx select FirstProj
    $ dx archive file-A00000ygpqGK8ZPjbk0Q000Q file-B00000ygpqGK8ZPjbk0Q000Q
​
    # archive all files recursively in project-B0VK6F6gpqG6z7JGkbqQ000Q
    $ dx archive project-B0VK6F6gpqG6z7JGkbqQ000Q:/
  
​
positional arguments:
  path          May refer to a single folder or specify up to 1000
                files inside a project.
​
optional arguments:
  -h, --help    show this help message and exit
  -a, --all     Apply to all results with the same name without
                prompting
  -q, --quiet   Do not print extra info messages
  --all-copies  If true, archive all the copies of files in projects
                with the same billTo org.
                See https://documentation.dnanexus.com/developer/api/d
                ata-containers/projects#api-method-project-xxxx-archiv
                e for details.
  -y, --yes     Do not ask for confirmation.
  --no-recurse  When `path` refers to a single folder, this flag
                causes only files in the specified folder and not its
                subfolders to be archived. This flag has no impact
                when `path` input refers to a collection of files.
​
Output:
  If -q option is not specified, prints "Tagged <count> file(s) for archival"
unarchive
usage: dx unarchive [-h] [-a] [--rate {Expedited,Standard,Bulk}] [-q] [-y] [--no-recurse] path [path ...]
​
Requests for a specified set files or for the files in a single specified folder in ONE project to be unarchived on the platform.
The requested copy will eventually be transitioned over to the live state while all other copies will move over to the archival state.
​
The input paths should be either 1 folder path or up to 1000 files, and all path(s) need to be in the same project. 
To specify which project to use, prepend the path or ID of the file/folder with the project ID or name and a colon.
​
EXAMPLES:
​
    # unarchive 3 files in project "FirstProj" with project ID project-B0VK6F6gpqG6z7JGkbqQ000Q 
    $ dx unarchive FirstProj:file-B0XBQFygpqGK8ZPjbk0Q000Q FirstProj:/path/to/file1 project-B0VK6F6gpqG6z7JGkbqQ000Q:/file2
 
    # unarchive 2 files in current project. Specifying file ids saves time by avoiding file name resolution.
    $ dx select FirstProj
    $ dx unarchive file-A00000ygpqGK8ZPjbk0Q000Q file-B00000ygpqGK8ZPjbk0Q000Q
​
    # unarchive all files recursively in project-B0VK6F6gpqG6z7JGkbqQ000Q
    $ dx unarchive project-B0VK6F6gpqG6z7JGkbqQ000Q:/
  
​
positional arguments:
  path                  May refer to a single folder or specify up to 1000 files inside a project.
​
optional arguments:
  -h, --help            show this help message and exit
  -a, --all             Apply to all results with the same name without prompting
  --rate {Expedited,Standard,Bulk}
                        The speed at which all files in this request are unarchived.
                          - Azure regions: {Expedited, Standard}
                          - AWS regions: {Expedited, Standard, Bulk}
  -q, --quiet           Do not print extra info messages
  -y, --yes             Do not ask for confirmation.
  --no-recurse          When `path` refers to a single folder, this flag causes only files in the
                        specified folder and not its subfolders to be unarchived. This flag has no
                        impact when `path` input refers to a collection of files.
​
Output:
  If -q option is not specified, prints "Tagged <> file(s) for unarchival, totalling <> GB, costing <> "
list database files
usage: dx list database files [-h] [--env-help] [--folder FOLDER] [--recurse]
                              [--csv] [--timeout TIMEOUT]
                              database
​
List files associated with a specific database
​
positional arguments:
  database           Data object ID or path of the database.
​
optional arguments:
  -h, --help         show this help message and exit
  --env-help         Display help message for overriding environment variables
  --folder FOLDER    Name of folder (directory) in which to start searching
                     for database files. This will typically match the name of
                     the table whose files are of interest. The default value
                     is "/" which will start the search at the root folder of
                     the database.
  --recurse          Look for files recursively down the directory structure.
                     Otherwise, by default, only look on one level.
  --csv              Write output as comma delimited fields, suitable as CSV
                     format.
  --timeout TIMEOUT  Number of seconds to wait before aborting the request. If
                     omitted, default timeout is 120 seconds.
Category: data
View, download, and upload data
describe
usage: dx describe [-h] [--json] [--color {off,on,auto}]
                   [--delimiter [DELIMITER]] [--env-help] [--details]
                   [--verbose] [--name] [--multi]
                   path
​
Describe a DNAnexus entity.  Use this command to describe data objects by name
or ID, jobs, apps, users, organizations, etc.  If using the "--json" flag, it
will thrown an error if more than one match is found (but if you would like a
JSON array of the describe hashes of all matches, then provide the "--multi"
flag).  Otherwise, it will always display all results it finds.
​
NOTES:
​
- The project found in the path is used as a HINT when you are using an object
ID; you may still get a result if you have access to a copy of the object in
some other project, but if it exists in the specified project, its description
will be returned.
​
- When describing apps or applets, options marked as advanced inputs will be
hidden unless --verbose is provided
​
positional arguments:
  path                  Object ID or path to an object (possibly in another
                        project) to describe.
​
optional arguments:
  -h, --help            show this help message and exit
  --json                Display return value in JSON
  --color {off,on,auto}
                        Set when color is used (color=auto is used when stdout
                        is a TTY)
  --delimiter [DELIMITER], --delim [DELIMITER]
                        Always use exactly one of DELIMITER to separate fields
                        to be printed; if no delimiter is provided with this
                        flag, TAB will be used
  --env-help            Display help message for overriding environment
                        variables
  --details             Include details of data objects
  --verbose             Include all possible metadata
  --name                Only print the matching names, one per line
  --multi               If the flag --json is also provided, then returns a
                        JSON array of describe hashes of all matching results
upload
usage: dx upload [-h] [--visibility {hidden,visible}] [--property KEY=VALUE]
                 [--type TYPE] [--tag TAG] [--details DETAILS] [-p]
                 [--brief | --verbose] [--env-help] [--path [PATH]] [-r]
                 [--wait] [--no-progress] [--buffer-size WRITE_BUFFER_SIZE]
                 [--singlethread]
                 filename [filename ...]
​
Upload local file(s) or directory. If "-" is provided, stdin will be used
instead. By default, the filename will be used as its new name. If
--path/--destination is provided with a path ending in a slash, the filename
will be used, and the folder path will be used as a destination. If it does
not end in a slash, then it will be used as the final name.
​
positional arguments:
  filename              Local file or directory to upload ("-" indicates stdin
                        input); provide multiple times to upload multiple
                        files or directories
​
optional arguments:
  -h, --help            show this help message and exit
  --brief               Display a brief version of the return value; for most
                        commands, prints a DNAnexus ID per line
  --verbose             If available, displays extra verbose output
  --env-help            Display help message for overriding environment
                        variables
  --path [PATH], --destination [PATH]
                        DNAnexus path to upload file(s) to (default uses
                        current project and folder if not provided)
  -r, --recursive       Upload directories recursively
  --wait                Wait until the file has finished closing
  --no-progress         Do not show a progress bar
  --buffer-size WRITE_BUFFER_SIZE
                        Set the write buffer size (in bytes)
  --singlethread        Enable singlethreaded uploading
​
metadata arguments:
  --visibility {hidden,visible}
                        Whether the object is hidden or not
  --property KEY=VALUE  Key-value pair to add as a property; repeat as
                        necessary, e.g. "--property key1=val1 --property
                        key2=val2"
  --type TYPE           Type of the data object; repeat as necessary, e.g. "--
                        type type1 --type type2"
  --tag TAG             Tag of the data object; repeat as necessary, e.g. "--
                        tag tag1 --tag tag2"
  --details DETAILS     JSON to store as details
  -p, --parents         Create any parent folders necessary
download
usage: dx download [-h] [--env-help] [-o OUTPUT] [-f] [-r] [-a]
                   [--no-progress] [--lightweight] [--unicode]
                   path [path ...]
​
Download the contents of a file object or multiple objects. Use "-o -" to
direct the output to stdout.
​
positional arguments:
  path                  Data object ID or name, or folder to download
​
optional arguments:
  -h, --help            show this help message and exit
  --env-help            Display help message for overriding environment
                        variables
  -o OUTPUT, --output OUTPUT
                        Local filename or directory to be used ("-" indicates
                        stdout output); if not supplied or a directory is
                        given, the object's name on the platform will be used,
                        along with any applicable extensions
  -f, --overwrite       Resume an interupted download if the local and remote
                        file signatures match. If the signatures do not match
                        the local file will be overwritten.
  -r, --recursive       Download folders recursively
  -a, --all             If multiple objects match the input, download all of
                        them
  --no-progress         Do not show a progress bar
  --lightweight         Skip some validation steps to make fewer API calls
  --unicode             Display the characters as text/unicode when writing to
                        stdout
make_download_url
usage: dx make_download_url [-h] [--duration DURATION] [--filename FILENAME]
                            path
​
Creates a pre-authenticated link that can be used to download a file without
logging in.
​
positional arguments:
  path                 Data object ID or name to access
​
optional arguments:
  -h, --help           show this help message and exit
  --duration DURATION  Time for which the URL will remain valid (in seconds,
                       or use suffix s, m, h, d, w, M, y). Default: 1 day
  --filename FILENAME  Name that the server will instruct the client to save
                       the file as (default is the filename)
cat
usage: dx cat [-h] [--env-help] [--unicode] path [path ...]
​
positional arguments:
  path        File ID or name(s) to print to stdout
​
optional arguments:
  -h, --help  show this help message and exit
  --env-help  Display help message for overriding environment variables
  --unicode   Display the characters as text/unicode when writing to stdout
head
usage: dx head [-h] [--color {off,on,auto}] [--env-help] [-n N] path
​
Print the first part of a file. By default, prints the first 10 lines.
​
positional arguments:
  path                  File ID or name to access
​
optional arguments:
  -h, --help            show this help message and exit
  --color {off,on,auto}
                        Set when color is used (color=auto is used when stdout
                        is a TTY)
  --env-help            Display help message for overriding environment
                        variables
  -n N, --lines N       Print the first N lines (default 10)
new
usage: dx new [-h] class ...
​
Use this command with one of the available subcommands (classes) to create a
new project or data object from scratch. Not all data types are supported. See
'dx upload' for files and 'dx build' for applets.
​
positional arguments:
  class
    user      Create a new user account
    org       Create new non-billable org
    project   Create a new project
    record    Create a new record
    workflow  Create a new workflow
​
optional arguments:
  -h, --help  show this help message and exit
new project
usage: dx new project [-h] [--brief | --verbose] [--env-help]
                      [--region REGION] [-s] [--bill-to BILL_TO] [--phi]
                      [--database-ui-view-only]
                      [name]
​
Create a new project
​
positional arguments:
  name                  Name of the new project
​
optional arguments:
  -h, --help            show this help message and exit
  --brief               Display a brief version of the return value; for most
                        commands, prints a DNAnexus ID per line
  --verbose             If available, displays extra verbose output
  --env-help            Display help message for overriding environment
                        variables
  --region REGION       Region affinity of the new project
  -s, --select          Select the new project as current after creating
  --bill-to BILL_TO     ID of the user or org to which the project will be
                        billed. The default value is the billTo of the
                        requesting user.
  --phi                 Add PHI protection to project
  --database-ui-view-only
                        If set to true, viewers of the project will not be
                        able to access database data directly
new record
usage: dx new record [-h] [--visibility {hidden,visible}]
                     [--property KEY=VALUE] [--type TYPE] [--tag TAG]
                     [--details DETAILS] [-p] [--brief | --verbose]
                     [--env-help] [--init INIT] [--close]
                     [path]
​
Create a new record
​
positional arguments:
  path                  DNAnexus path for the new data object (default uses
                        current project and folder if not provided)
​
optional arguments:
  -h, --help            show this help message and exit
  --brief               Display a brief version of the return value; for most
                        commands, prints a DNAnexus ID per line
  --verbose             If available, displays extra verbose output
  --env-help            Display help message for overriding environment
                        variables
  --init INIT           Path to record from which to initialize all metadata
  --close               Close the record immediately after creating it
​
metadata arguments:
  --visibility {hidden,visible}
                        Whether the object is hidden or not
  --property KEY=VALUE  Key-value pair to add as a property; repeat as
                        necessary,
                         e.g. "--property key1=val1 --property key2=val2"
  --type TYPE           Type of the data object; repeat as necessary,
                         e.g. "--type type1 --type type2"
  --tag TAG             Tag of the data object; repeat as necessary,
                         e.g. "--tag tag1 --tag tag2"
  --details DETAILS     JSON to store as details
  -p, --parents         Create any parent folders necessary
new workflow
usage: dx new workflow [-h] [--visibility {hidden,visible}]
                       [--property KEY=VALUE] [--type TYPE] [--tag TAG]
                       [--details DETAILS] [-p] [--brief | --verbose]
                       [--env-help] [--title TITLE] [--summary SUMMARY]
                       [--description DESCRIPTION]
                       [--output-folder OUTPUT_FOLDER] [--init INIT]
                       [path]
​
Create a new workflow
​
positional arguments:
  path                  DNAnexus path for the new data object (default uses
                        current project and folder if not provided)
​
optional arguments:
  -h, --help            show this help message and exit
  --brief               Display a brief version of the return value; for most
                        commands, prints a DNAnexus ID per line
  --verbose             If available, displays extra verbose output
  --env-help            Display help message for overriding environment
                        variables
  --title TITLE         Workflow title
  --summary SUMMARY     Workflow summary
  --description DESCRIPTION
                        Workflow description
  --output-folder OUTPUT_FOLDER
                        Default output folder for the workflow
  --init INIT           Path to workflow or an analysis ID from which to
                        initialize all metadata
​
metadata arguments:
  --visibility {hidden,visible}
                        Whether the object is hidden or not
  --property KEY=VALUE  Key-value pair to add as a property; repeat as
                        necessary,
                         e.g. "--property key1=val1 --property key2=val2"
  --type TYPE           Type of the data object; repeat as necessary,
                         e.g. "--type type1 --type type2"
  --tag TAG             Tag of the data object; repeat as necessary,
                         e.g. "--tag tag1 --tag tag2"
  --details DETAILS     JSON to store as details
  -p, --parents         Create any parent folders necessary
close
usage: dx close [-h] [--env-help] [-a] [--wait] path [path ...]
​
Close a remote data object or set of objects.
​
positional arguments:
  path        Path to a data object to close
​
optional arguments:
  -h, --help  show this help message and exit
  --env-help  Display help message for overriding environment variables
  -a, --all   Apply to all results with the same name without prompting
  --wait      Wait for the object(s) to close
wait
usage: dx wait [-h] [--env-help] [--from-file] path [path ...]
​
Polls the state of specified data object(s) or job(s) until they are all in
the desired state. Waits until the "closed" state for a data object, and for
any terminal state for a job ("terminated", "failed", or "done"). Exits with a
non-zero code if a job reaches a terminal state that is not "done". Can also
provide a local file containing a list of data object(s) or job(s), one per
line; the file will be read if "--from-file" argument is added.
​
positional arguments:
  path         Path to a data object, job ID, or file with IDs to wait for
​
optional arguments:
  -h, --help   show this help message and exit
  --env-help   Display help message for overriding environment variables
  --from-file  Read the list of objects to wait for from the file provided in
               path
get
usage: dx get [-h] [--env-help] [-o OUTPUT] [--filename FILENAME]
              [--allow-all-files] [--recurse] [--no-ext] [--omit-resources]
              [-f]
              path
​
Download the contents of some types of data (records, apps, applets,
workflows, files, and databases). Downloading an app, applet or a workflow
will attempt to reconstruct a source directory that can be used to rebuild it
with "dx build". Use "-o -" to direct the output to stdout.
​
positional arguments:
  path                  Data object ID or name to access
​
optional arguments:
  -h, --help            show this help message and exit
  --env-help            Display help message for overriding environment
                        variables
  -o OUTPUT, --output OUTPUT
                        local file path where the data is to be saved ("-"
                        indicates stdout output for objects of class file and
                        record). If not supplied, the object's name on the
                        platform will be used, along with any applicable
                        extensions. For app(let) and workflow objects, if
                        OUTPUT does not exist, the object's source directory
                        will be created there; if OUTPUT is an existing
                        directory, a new directory with the object's name will
                        be created inside it.
  --filename FILENAME   When downloading from a database, name of the file or
                        folder to be downloaded. If omitted, all files in the
                        database will be downloaded, so use caution and
                        include the --allow-all-files argument.
  --allow-all-files     When downloading from a database, this allows all
                        files in a database to be downloaded when --filename
                        argument is omitted.
  --recurse             When downloading from a database, look for files
                        recursively down the directory structure. Otherwise,
                        by default, only look on one level.
  --no-ext              If -o is not provided, do not add an extension to the
                        filename
  --omit-resources      When downloading an app(let), omit fetching the
                        resources associated with the app(let).
  -f, --overwrite       Overwrite the local file if necessary
find data
usage: dx find data [-h] [--brief | --verbose] [--json]
                    [--color {off,on,auto}] [--delimiter [DELIMITER]]
                    [--env-help] [--property KEY[=VALUE]] [--tag TAG]
                    [--class {record,file,applet,workflow,database}]
                    [--state {open,closing,closed,any}]
                    [--visibility {hidden,visible,either}] [--name NAME]
                    [--type TYPE] [--link LINK] [--all-projects]
                    [--path PROJECT:FOLDER] [--norecurse]
                    [--created-after CREATED_AFTER]
                    [--created-before CREATED_BEFORE] [--mod-after MOD_AFTER]
                    [--mod-before MOD_BEFORE] [--region REGION]
​
Finds data objects subject to the given search parameters. By default,
restricts the search to the current project if set. To search over all
projects (excluding public projects), use --all-projects (overrides --path and
--norecurse).
​
optional arguments:
  -h, --help            show this help message and exit
  --brief               Display a brief version of the return value; for most
                        commands, prints a DNAnexus ID per line
  --verbose             If available, displays extra verbose output
  --json                Display return value in JSON
  --color {off,on,auto}
                        Set when color is used (color=auto is used when stdout
                        is a TTY)
  --delimiter [DELIMITER], --delim [DELIMITER]
                        Always use exactly one of DELIMITER to separate fields
                        to be printed; if no delimiter is provided with this
                        flag, TAB will be used
  --env-help            Display help message for overriding environment
                        variables
  --property KEY[=VALUE]
                        Key-value pair of a property or simply a property key;
                        if only a key is provided, matches a result that has
                        the key with any value; repeat as necessary, e.g. "--
                        property key1=val1 --property key2"
  --tag TAG             Tag to match; repeat as necessary, e.g. "--tag tag1
                        --tag tag2" will require both tags
  --class {record,file,applet,workflow,database}
                        Data object class
  --state {open,closing,closed,any}
                        State of the object
  --visibility {hidden,visible,either}
                        Whether the object is hidden or not
  --name NAME           Name of the object
  --type TYPE           Type of the data object
  --link LINK           Object ID that the data object links to
  --all-projects, --allprojects
                        Extend search to all projects (excluding public
                        projects)
  --path PROJECT:FOLDER
                        Project and/or folder in which to restrict the results
  --norecurse           Do not recurse into subfolders
  --created-after CREATED_AFTER
                        Date (e.g. 2012-01-01) or integer timestamp after
                        which the object was created (negative number means ms
                        in the past, or use suffix s, m, h, d, w, M, y)
                        Negative input example "--created-after=-2d"
  --created-before CREATED_BEFORE
                        Date (e.g. 2012-01-01) or integer timestamp before
                        which the object was created (negative number means ms
                        in the past, or use suffix s, m, h, d, w, M, y)
                        Negative input example "--created-before=-2d"
  --mod-after MOD_AFTER
                        Date (e.g. 2012-01-01) or integer timestamp after
                        which the object was last modified (negative number
                        means ms in the past, or use suffix s, m, h, d, w, M,
                        y) Negative input example "--mod-after=-2d"
  --mod-before MOD_BEFORE
                        Date (e.g. 2012-01-01) or integer timestamp before
                        which the object was last modified (negative number
                        means ms in the past, or use suffix s, m, h, d, w, M,
                        y) Negative input example "--mod-before=-2d"
  --region REGION       Restrict the search to the provided region
find projects
usage: dx find projects [-h] [--brief | --verbose] [--json]
                        [--delimiter [DELIMITER]] [--env-help]
                        [--property KEY[=VALUE]] [--tag TAG]
                        [--phi {true,false}] [--name NAME]
                        [--level {VIEW,UPLOAD,CONTRIBUTE,ADMINISTER}]
                        [--public] [--created-after CREATED_AFTER]
                        [--created-before CREATED_BEFORE] [--region REGION]
​
Finds projects subject to the given search parameters. Use the --public flag
to list all public projects.
​
optional arguments:
  -h, --help            show this help message and exit
  --brief               Display a brief version of the return value; for most
                        commands, prints a DNAnexus ID per line
  --verbose             If available, displays extra verbose output
  --json                Display return value in JSON
  --delimiter [DELIMITER], --delim [DELIMITER]
                        Always use exactly one of DELIMITER to separate fields
                        to be printed; if no delimiter is provided with this
                        flag, TAB will be used
  --env-help            Display help message for overriding environment
                        variables
  --property KEY[=VALUE]
                        Key-value pair of a property or simply a property key;
                        if only a key is provided, matches a result that has
                        the key with any value; repeat as necessary, e.g. "--
                        property key1=val1 --property key2"
  --tag TAG             Tag to match; repeat as necessary, e.g. "--tag tag1
                        --tag tag2" will require both tags
  --phi {true,false}    If set to true, only projects that contain PHI data
                        will be retrieved. If set to false, only projects that
                        do not contain PHI data will be retrieved.
  --name NAME           Name of the project
  --level {VIEW,UPLOAD,CONTRIBUTE,ADMINISTER}
                        Minimum level of permissions expected
  --public              Include ONLY public projects (will automatically set
                        --level to VIEW)
  --created-after CREATED_AFTER
                        Date (e.g. 2012-01-01) or integer timestamp after
                        which the project was created (negative number means
                        ms in the past, or use suffix s, m, h, d, w, M, y)
                        Negative input example "--created-after=-2d"
  --created-before CREATED_BEFORE
                        Date (e.g. 2012-01-01) or integer timestamp after
                        which the project was created (negative number means
                        ms in the past, or use suffix s, m, h, d, w, M, y)
                        Negative input example "--created-before=-2d"
  --region REGION       Restrict the search to the provided region
update project
usage: dx update project [-h] [--brief | --verbose] [--env-help] [--name NAME]
                         [--summary SUMMARY] [--description DESCRIPTION]
                         [--protected {true,false}]
                         [--restricted {true,false}]
                         [--download-restricted {true,false}]
                         [--containsPHI {true}]
                         [--database-ui-view-only {true,false}]
                         [--bill-to BILL_TO]
                         [--allowed-executables ALLOWED_EXECUTABLES 
                                [ALLOWED_EXECUTABLES ...]
                         | --unset-allowed-executables]
                         project_id
​
positional arguments:
  project_id            Project ID or project name
​
optional arguments:
  -h, --help            show this help message and exit
  --brief               Display a brief version of the return value; for most
                        commands, prints a DNAnexus ID per line
  --verbose             If available, displays extra verbose output
  --env-help            Display help message for overriding environment
                        variables
  --name NAME           New project name
  --summary SUMMARY     Project summary
  --description DESCRIPTION
                        Project description
  --protected {true,false}
                        Whether the project should be PROTECTED
  --restricted {true,false}
                        Whether the project should be RESTRICTED
  --download-restricted {true,false}
                        Whether the project should be DOWNLOAD RESTRICTED
  --containsPHI {true}  Flag to tell if project contains PHI
  --database-ui-view-only {true,false}
                        Whether the viewers on the project can access the
                        database data directly
  --bill-to BILL_TO     Update the user or org ID of the billing account
  --allowed-executables ALLOWED_EXECUTABLES [ALLOWED_EXECUTABLES ...]
                        Executable ID(s) this project is allowed to run. This
                        operation overrides any existing list of executables.
  --unset-allowed-executables
                        Removes any restriction to run executables as set by
                        --allowed-executables
extract_dataset
usage: dx extract_dataset [-h] [-ddd] [--fields FIELDS [FIELDS ...]] [--sql]
                          [--delim [DELIM]] [-o OUTPUT]
                          path
                          
(Preview Feature) 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. Note: A separate version of pandas may be required to install when using this functionality.
​
positional arguments:
  path                  v3.0 Dataset or Cohort object ID (project-id:record-id
                        where "record-id" indicates the record ID in the
                        currently selected project) or name
optional arguments:
  -h, --help            show this help message and exit
  -ddd, --dump-dataset-dictionary
                        If provided, the three dictionary files,
                        <record_name>.data_dictionary.csv,
                        <record_name>.entity_dictionary.csv, and
                        <record_name>.codings.csv will be generated. Files
                        will be comma delimited and written to the local
                        working directory, unless otherwise specified using
                        --delimiter and --output arguments. If any of the
                        three dictionary files does not contain data (i.e. the
                        dictionary is empty), then that particular file will
                        not be created.
  --fields FIELDS [FIELDS ...]
                        A comma-separated string where each value is the
                        phenotypic entity name and field name, separated by a
                        dot.  For example: "<entity_name>.<field_name>,<entity
                        _name>.<field_name>". If multiple entities are
                        provided, field values will be automatically inner
                        joined. If only the --fields argument is provided,
                        data will be retrieved and returned. If both --fields
                        and --sql arguments are provided, a SQL statement to
                        retrieve the specified field data will be
                        automatically generated and returned.
  --sql                 If provided, a SQL statement (string) will be returned
                        to query the set of entity.fields, instead of
                        returning stored values from the set of entity.fields
  --delim [DELIM], --delimiter [DELIM]
                        Always use exactly one of DELIMITER to separate fields
                        to be printed; if no delimiter is provided with this
                        flag, COMMA will be used
  -o OUTPUT, --output OUTPUT
                        Local filename or directory to be used ("-" indicates
                        stdout output). If not supplied, output will create a
                        file with a default name in the current folder
​
Category: metadata
View and modify metadata for projects and data objects.
See also dx describe and dx close.
set_details
usage: dx set_details [-h] [--env-help] [-a] [-f DETAILS_FILE] path [details]
​
Set the JSON details of a data object.
​
positional arguments:
  path                  ID or path to data object to modify
  details               JSON to store as details
​
optional arguments:
  -h, --help            show this help message and exit
  --env-help            Display help message for overriding environment
                        variables
  -a, --all             Apply to all results with the same name without
                        prompting
  -f DETAILS_FILE, --details-file DETAILS_FILE
                        Path to local file containing JSON to store as details
get_details
usage: dx get_details [-h] [--env-help] path
​
Get the JSON details of a data object.
​
positional arguments:
  path        ID or path to data object to get details for
​
optional arguments:
  -h, --help  show this help message and exit
  --env-help  Display help message for overriding environment variables
set_visibility
usage: dx set_visibility [-h] [--env-help] [-a] path {hidden,visible}
​
Set visibility on a data object.
​
positional arguments:
  path              ID or path to data object to modify
  {hidden,visible}  Visibility that the object should have
​
optional arguments:
  -h, --help        show this help message and exit
  --env-help        Display help message for overriding environment variables
  -a, --all         Apply to all results with the same name without prompting
add_types
usage: dx add_types [-h] [--env-help] [-a] path type [type ...]
​
Add types to a data object. See
https://documentation.dnanexus.com/developer/api/data-object-lifecycle/types
for a list of DNAnexus types.
​
positional arguments:
  path        ID or path to data object to modify
  type        Types to add
​
optional arguments:
  -h, --help  show this help message and exit
  --env-help  Display help message for overriding environment variables
  -a, --all   Apply to all results with the same name without prompting
remove_types
usage: dx remove_types [-h] [--env-help] [-a] path type [type ...]
​
Remove types from a data object. See
https://documentation.dnanexus.com/developer/api/data-object-lifecycle/types
for a list of DNAnexus types.
​
positional arguments:
  path        ID or path to data object to modify
  type        Types to remove
​
optional arguments:
  -h, --help  show this help message and exit
  --env-help  Display help message for overriding environment variables
  -a, --all   Apply to all results with the same name without prompting
tag
usage: dx tag [-h] [--env-help] [-a] path tag [tag ...]
​
Tag a project, data object, or execution. Note that a project context must be
either set or specified for data object IDs or paths.
​
positional arguments:
  path        ID or path to project, data object, or execution to modify
  tag         Tags to add
​
optional arguments:
  -h, --help  show this help message and exit
  --env-help  Display help message for overriding environment variables
  -a, --all   Apply to all results with the same name without prompting
untag
usage: dx untag [-h] [--env-help] [-a] path tag [tag ...]
​
Untag a project, data object, or execution. Note that a project context must
be either set or specified for data object IDs or paths.
​
positional arguments:
  path        ID or path to project, data object, or execution to modify
  tag         Tags to remove
​
optional arguments:
  -h, --help  show this help message and exit
  --env-help  Display help message for overriding environment variables
  -a, --all   Apply to all results with the same name without prompting
rename
usage: dx rename [-h] [--env-help] [-a] path name
​
Rename a project or data object. To rename folders, use 'dx mv' instead. Note
that a project context must be either set or specified to rename a data
object. To specify a project or a project context, append a colon character
":" after the project ID or name.
​
positional arguments:
  path        Path to project or data object to rename
  name        New name
​
optional arguments:
  -h, --help  show this help message and exit
  --env-help  Display help message for overriding environment variables
  -a, --all   Apply to all results with the same name without prompting
set_properties
usage: dx set_properties [-h] [--env-help] [-a]
                         path propertyname=value [propertyname=value ...]
​
Set properties of a project, data object, or execution. Note that a project
context must be either set or specified for data object IDs or paths.
​
positional arguments:
  path                ID or path to project, data object, or execution to
                      modify
  propertyname=value  Key-value pairs of property names and their new values
​
optional arguments:
  -h, --help          show this help message and exit
  --env-help          Display help message for overriding environment
                      variables
  -a, --all           Apply to all results with the same name without
                      prompting
unset_properties
usage: dx unset_properties [-h] [--env-help] [-a]
                           path propertyname [propertyname ...]
​
Unset properties of a project, data object, or execution. Note that a project
context must be either set or specified for data object IDs or paths.
​
positional arguments:
  path          ID or path to project, data object, or execution to modify
  propertyname  Property names to unset
​
optional arguments:
  -h, --help    show this help message and exit
  --env-help    Display help message for overriding environment variables
  -a, --all     Apply to all results with the same name without prompting
Category: exec
Manage and run your apps, applets, and workflows.
build
usage: dx build [-h] [--env-help] [--brief | --verbose] [--ensure-upload]
                [--force-symlinks] [--app] [--workflow] [--globalworkflow]
                [-d DESTINATION] [--dry-run] [--publish] [--from _FROM]
                [--remote] [--no-watch] [-f] [-a] [-v VERSION]
                [-b USER_OR_ORG] [--no-check-syntax]
                [--no-version-autonumbering] [--no-update]
                [--no-dx-toolkit-autodep] [--no-parallel-build]
                [--no-temp-build-project] [-y] [--extra-args EXTRA_ARGS]
                [--run ...] [--region REGION] [--keep-open]
                [src_dir]
​
Build an applet, app, or workflow object from a local source directory or an
app from an existing applet in the platform. You can use dx-app-wizard to
generate a skeleton directory of an app/applet with the necessary files.
​
positional arguments:
  src_dir               Source directory that contains dxapp.json or
                        dxworkflow.json. (default: current directory)
​
optional arguments:
  -h, --help            show this help message and exit
  --env-help            Display help message for overriding environment
                        variables
  --brief               Display a brief version of the return value; for most
                        commands, prints a DNAnexus ID per line
  --verbose             If available, displays extra verbose output
  --ensure-upload       If specified, will bypass computing checksum of
                        resources directory and upload it unconditionally; by
                        default, will compute checksum and upload only if it
                        differs from a previously uploaded resources bundle.
  --force-symlinks      If specified, will not attempt to dereference symbolic
                        links pointing outside of the resource directory. By
                        default, any symlinks within the resource directory
                        are kept as links while links to files outside the
                        resource directory are dereferenced (note that links
                        to directories outside of the resource directory will
                        cause an error).
  --app, --create-app   Create an app.
  --workflow, --create-workflow
                        Create a workflow.
  --globalworkflow, --create-globalworkflow
                        Create a global workflow.
  --dry-run, -n         Do not create an app(let): only perform local checks
                        and compilation steps, and show the spec of the
                        app(let) that would have been created.
  --remote              Build the app remotely by uploading the source
                        directory to the DNAnexus Platform and building it
                        there. This option is useful if you would otherwise
                        need to cross-compile the app(let) to target the
                        Execution Environment.
  --no-watch            Don't watch the real-time logs of the remote builder.
                        (This option only applicable if --remote was
                        specified).
  -v VERSION, --version VERSION
                        Override the version number supplied in the manifest.
                        This option needs to be specified when using --from
                        option.
  --no-check-syntax     Warn but do not fail when syntax problems are found
                        (default is to fail on such errors)
  --no-dx-toolkit-autodep
                        Do not auto-insert the dx-toolkit dependency (default
                        is to add it if it would otherwise be absent from the
                        runSpec)
  --no-parallel-build   Build with make instead of make -jN.
  --extra-args EXTRA_ARGS
                        Arguments (in JSON format) to pass to the /applet/new
                        API method, overriding all other settings
  --run ...             Run the app or applet after building it (options
                        following this are passed to dx run; run at high
                        priority by default)
  --keep-open           Do not close workflow after building it. Cannot be
                        used when building apps, applets or global workflows.
​
options for creating apps or globalworkflows:
  (Only valid when --app/--create-app/--globalworkflow/--create-
  globalworkflow is specified)
​
  --publish             Publish the resulting app/globalworkflow and make it
                        the default.
  --from _FROM          ID or path of the source applet/workflow to create an
                        app/globalworkflow from. Source directory src_dir
                        cannot be given when using this option
  -b USER_OR_ORG, --bill-to USER_OR_ORG
                        Entity (of the form user-NAME or org-ORGNAME) to bill
                        for the app/globalworkflow.
  --no-version-autonumbering
                        Only attempt to create the version number supplied in
                        the manifest (that is, do not try to create an
                        autonumbered version such as 1.2.3+git.ab1b1c1d if
                        1.2.3 already exists and is published).
  --no-update           Never update an existing unpublished
                        app/globalworkflow in place.
  --no-temp-build-project
                        When building an app in a single region, build its
                        applet in the current project instead of a temporary
                        project.
  -y, --yes             Do not ask for confirmation for potentially dangerous
                        operations
  --region REGION       Enable the app/globalworkflow in this region. This
                        flag can be specified multiple times to enable the
                        app/globalworkflow in multiple regions. If --region is
                        not specified, then the enabled region(s) will be
                        determined by 'regionalOptions' in dxapp.json, or the
                        project context.
​
options for creating applets or workflows:
  (Only valid when --app/--create-app/--globalworkflow/--create-
  globalworkflow is NOT specified)
​
  -d DESTINATION, --destination DESTINATION
                        Specifies the destination project, destination folder,
                        and/or name for the applet, in the form
                        [PROJECT_NAME_OR_ID:][/[FOLDER/][NAME]]. Overrides the
                        project, folder, and name fields of the dxapp.json or
                        dxworkflow.json, if they were supplied.
  -f, --overwrite       Remove existing applet(s) of the same name in the
                        destination folder. This option is not yet supported
                        for workflows.
  -a, --archive         Archive existing applet(s) of the same name in the
                        destination folder. This option is not yet supported
                        for workflows.
add users
usage: dx add users [-h] [--env-help] app authorizedUser [authorizedUser ...]
​
Add users or orgs to the list of authorized users of an app. Published
versions of the app will only be accessible to users represented by this list
and to developers of the app. Unpublished versions are restricted to the
developers.
​
positional arguments:
  app             Name or ID of an app
  authorizedUser  One or more users or orgs to add
​
optional arguments:
  -h, --help      show this help message and exit
  --env-help      Display help message for overriding environment variables
add developers
usage: dx add developers [-h] [--env-help] app developer [developer ...]
​
Add users or orgs to the list of developers for an app. Developers are able to
build and publish new versions of the app, and add or remove others from the
list of developers and authorized users.
​
positional arguments:
  a