Index of dx commands

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 {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 {Standard,Bulk}
                        The speed at which all files in this request are unarchived.
                          - Azure regions: {Standard}
                          - AWS regions: {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] [--try T]
                   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 additional 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
  --try T               When describing a job that was restarted, describe job
                        try T. T=0 refers to the first try. Default is the
                        last job try.
  --defaultSymlink      When describing a project linked to a Symlink
                        Drive defined, return a mapping describing the drive, 
                        in the form {"drive": "drive-xxxx", "container": 
                        "containerOrBucketName", "prefix": "/"}
  --symlinkPath         When describing a symlinked file, return the path to the
                        file, including the name of the cloud storage container
                        where the file is stored, the folder name, if present, and the
                        filename proper.

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
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
  --default-symlink DEFAULT_SYMLINK_MAPPING
                        Specifies default remote location for new files in the 
                        project and all its execution containers. Mapping in the 
                        form '{"drive": "drive-xxxx", 
                        "container": "containerOrBucketName", "prefix": "/"}'
                        "drive" is the ID of the linked Symlink Drive.
                        "container" is the name of the cloud service container 
                        where symlinked files are stored. "prefix," which is 
                        optional, is the name of the folder, in the cloud service 
                        container, where symlinked files are stored.
  --monthly-compute-limit MONTHLY_COMPUTE_LIMIT
                        Monthly project spending limit for compute (in currency units)
  --monthly-egress-bytes-limit MONTHLY_EGRESS_BYTES_LIMIT
                        Monthly project spending limit for egress (in bytes)

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]
                        [--externalUploadRestricted {true,false}]

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
  
--externalUploadRestricted {true,false}
                        If set to true, only externalUploadRestricted projects will 
                        be retrieved. If set to false, only projects that are not 
                        externalUploadRestricted will be retrieved.

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]
                         [ --external-upload-restricted {true,false}] 
                         [--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}