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

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

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)

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

usage: dx exit [-h]
​
Exit out of the interactive shell
​
optional arguments:
  -h, --help  show this help message and exit

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

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://wiki.dnanexus.com/Command-Line-Client/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

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.

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

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

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

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)

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

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

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

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

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

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

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

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

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

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

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)

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)

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 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

usage: dx new project [-h] [--brief | --verbose] [--env-help]
                      [--region REGION] [-s] [--bill-to BILL_TO] [--phi]
                      [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

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

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

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

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

usage: dx get [-h] [--env-help] [-o OUTPUT] [--no-ext] [--omit-resources] [-f]
              path
​
Download the contents of some types of data (records, apps, applets,
workflows, and files). 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.
  --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

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}]
                    [--state {open,closing,closed,any}]
                    [--visibility {hidden,visible,either}] [--name NAME]
                    [--type TYPE] [--link LINK] [--all-projects]
                    [--path PROJECT:FOLDER] [--norecurse]
                    [--mod-after MOD_AFTER] [--mod-before MOD_BEFORE]
                    [--created-after CREATED_AFTER]
                    [--created-before CREATED_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}
                        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
  --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)
  --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)
  --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)
  --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)
  --region REGION       Restrict the search to the provided region

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)
  --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)
  --region REGION       Restrict the search to the provided region

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

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

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

usage: dx add_types [-h] [--env-help] [-a] path type [type ...]
​
Add types to a data object. See https://wiki.dnanexus.com/pages/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

usage: dx remove_types [-h] [--env-help] [-a] path type [type ...]
​
Remove types from a data object. See https://wiki.dnanexus.com/pages/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

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

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

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

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

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

usage: dx build [-h] [--env-help] [--ensure-upload] [--force-symlinks] [--app]
                [--workflow] [--globalworkflow] [-d DESTINATION] [--dry-run]
                [--publish] [--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] [-y]
                [--extra-args EXTRA_ARGS] [--run ...] [--region REGION]
                [src_dir]
​
Build an applet, app, or workflow object from a local source directory. You
can use dx-app-wizard to generate a skeleton directory of an app/applet with
the necessary files.
​
positional arguments:
  src_dir               App, applet, or workflow source directory (default:
                        current directory)
​
optional arguments:
  -h, --help            show this help message and exit
  --env-help            Display help message for overriding environment
                        variables
  --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.
  --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)
​
options for creating apps:
  (Only valid when --app/--create-app is specified)
​
  --publish             Publish the resulting app and make it the default.
  -b USER_OR_ORG, --bill-to USER_OR_ORG
                        Entity (of the form user-NAME or org-ORGNAME) to bill
                        for the app.
  --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 in place.
  -y, --yes             Do not ask for confirmation for potentially dangerous
                        operations
  --region REGION       Enable the app in this region. This flag can be
                        specified multiple times to enable the app 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 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.

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

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:
  app         Name or ID of an app
  developer   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

usage: dx list users [-h] [--env-help] app
​
List the 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
​
optional arguments:
  -h, --help  show this help message and exit
  --env-help  Display help message for overriding environment variables

usage: dx list developers [-h] [--env-help] app
​
List the 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:
  app         Name or ID of an app
​
optional arguments:
  -h, --help  show this help message and exit
  --env-help  Display help message for overriding environment variables

usage: dx remove users [-h] [--env-help]
                       app authorizedUser [authorizedUser ...]
​
Remove users or orgs from 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 remove
​
optional arguments:
  -h, --help      show this help message and exit
  --env-help      Display help message for overriding environment variables

usage: dx remove developers [-h] [--env-help] app developer [developer ...]
​
Remove users or orgs from 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:
  app         Name or ID of an app
  developer   One or more users to remove
​
optional arguments:
  -h, --help  show this help message and exit
  --env-help  Display help message for overriding environment variables

usage: dx publish [-h] [--no-default] executable
​
Release a version of the executable (app or global workflow) to authorized
users.
​
positional arguments:
  executable    ID or name and version of an app/global workflow, e.g.
                myqc/1.0.0
​
optional arguments:
  -h, --help    show this help message and exit
  --no-default  Do not set a "default" alias on the published version

usage: dx install [-h] [--env-help] app
​
Install an app by name. To see a list of apps you can install, hit <TAB> twice
after "dx install" or run "dx find apps" to see a list of available apps.
​
positional arguments:
  app         ID or name of app to install
​
optional arguments:
  -h, --help  show this help message and exit
  --env-help  Display help message for overriding environment variables

usage: dx uninstall [-h] [--env-help] app
​
Uninstall an app by name.
​
positional arguments:
  app         ID or name of app to uninstall
​
optional arguments:
  -h, --help  show this help message and exit
  --env-help  Display help message for overriding environment variables

usage: dx run [-i INPUT] [-j INPUT_JSON] [-f FILENAME] [--brief | --verbose]
              [--env-help] [--extra-args EXTRA_ARGS]
              [--instance-type INSTANCE_TYPE_OR_MAPPING]
              [--instance-type-help] [--property KEY=VALUE] [--tag TAG]
              [-d DEPENDS_ON] [-h] [--clone CLONE] [--alias ALIAS]
              [--destination PATH] [--batch-folders] [--project PROJECT]
              [--stage-output-folder STAGE_ID FOLDER]
              [--stage-relative-output-folder STAGE_ID FOLDER] [--name NAME]
              [--delay-workspace-destruction] [--priority {normal,high}] [-y]
              [--wait] [--watch] [--allow-ssh [ADDRESS]] [--ssh]
              [--ssh-proxy <address>:<port>]
              [--debug-on {AppError,AppInternalError,ExecutionError,All}]
              [--ignore-reuse | --ignore-reuse-stage STAGE_ID]
              [--rerun-stage STAGE_ID] [--batch-tsv FILE]
              [--instance-count INSTANCE_COUNT_OR_MAPPING] [--input-help]
              [executable]
​
Run an applet, app, or workflow.  To see a list of executables you can run,
hit <TAB> twice after "dx run" or run "dx find apps" or "dx find
globalworkflows" to see a list of available apps and global workflows.
​
If any inputs are required but not specified, an interactive mode for
selecting inputs will be launched.  Inputs can be set in multiple ways.  Run
"dx run --input-help" for more details.
​
Run "dx run --instance-type-help" to see a list of specifications for
computers available to run executables.
​
positional arguments:
  executable            Name or ID of an applet, app, or workflow to run; must
                        be provided if --clone is not set
​
optional arguments:
  -i INPUT, --input INPUT
                        An input to be added using "<input
                        name>[:<class>]=<input value>" (provide "class" if
                        there is no input spec; it can be any job IO class,
                        e.g. "string", "array:string", or "array"; if "class"
                        is "array" or not specified, the value will be
                        attempted to be parsed as JSON and is otherwise
                        treated as a string)
  -j INPUT_JSON, --input-json INPUT_JSON
                        The full input JSON (keys=input field names,
                        values=input field values)
  -f FILENAME, --input-json-file FILENAME
                        Load input JSON from FILENAME ("-" to use stdin)
  --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
  --extra-args EXTRA_ARGS
                        Arguments (in JSON format) to pass to the underlying
                        API method, overriding the default settings
  --instance-type INSTANCE_TYPE_OR_MAPPING
                        Specify instance type(s) for jobs this executable will
                        run; see --instance-type-help for more details
  --instance-type-help  Print help for specifying instance types
  --property KEY=VALUE  Key-value pair to add as a property; repeat as
                        necessary,
                         e.g. "--property key1=val1 --property key2=val2"
  --tag TAG             Tag for the resulting execution; repeat as necessary,
                         e.g. "--tag tag1 --tag tag2"
  -d DEPENDS_ON, --depends-on DEPENDS_ON
                        ID of job, analysis, or data object that must be in
                        the "done" or "closed" state, as appropriate, before
                        this executable can be run; repeat as necessary (e.g.
                        "--depends-on id1 ... --depends-on idN"). Cannot be
                        supplied when running workflows
  -h, --help            show this help message and exit
  --clone CLONE         Job or analysis ID or name from which to use as
                        default options (will use the exact same executable
                        ID, destination project and folder, job input,
                        instance type requests, and a similar name unless
                        explicitly overridden by command-line arguments)
  --alias ALIAS, --version ALIAS
                        Alias (tag) or version of the app to run (default:
                        "default" if an app)
  --destination PATH, --folder PATH
                        The full project:folder path in which to output the
                        results.  By default, the current working directory
                        will be used.
  --batch-folders       Output results to separate folders, one per batch,
                        using batch ID as the name of the output folder. The
                        batch output folder location will be relative to the
                        path set in --destination
  --project PROJECT     Project name or ID in which to run the executable.
                        This can also be specified together with the output
                        folder in --destination.
  --stage-output-folder STAGE_ID FOLDER
                        A stage identifier (ID, name, or index), and a folder
                        path to use as its output folder
  --stage-relative-output-folder STAGE_ID FOLDER
                        A stage identifier (ID, name, or index), and a
                        relative folder path to the workflow output folder to
                        use as the output folder
  --name NAME           Name for the job (default is the app or applet name)
  --delay-workspace-destruction
                        Whether to keep the job's temporary workspace around
                        for debugging purposes for 3 days after it succeeds or
                        fails
  --priority {normal,high}
                        Request a scheduling priority for all resulting jobs
  -y, --yes             Do not ask for confirmation
  --wait                Wait until the job is done before returning
  --watch               Watch the job after launching it; sets --priority high
  --allow-ssh [ADDRESS]
                        Configure the job to allow SSH access; sets --priority
                        high. If an argument is supplied, it is interpreted as
                        an IP or hostname mask to allow connections from, e.g.
                        "--allow-ssh 1.2.3.4 --allow-ssh berkeley.edu"
  --ssh                 Configure the job to allow SSH access and connect to
                        it after launching; sets --priority high
  --ssh-proxy <address>:<port>
                        SSH connect via proxy, argument supplied is used as
                        the proxy address and port
  --debug-on {AppError,AppInternalError,ExecutionError,All}
                        Configure the job to hold for debugging when any of
                        the listed errors occur
  --ignore-reuse        Disable job reuse for execution
  --ignore-reuse-stage STAGE_ID
                        A stage (using its ID, name, or index) for which job
                        reuse should be disabled, if a stage points to another
                        (nested) workflow the ignore reuse option will be
                        applied to the whole subworkflow. This option
                        overwrites any ignoreReuse fields set on app(let)s or
                        the workflow during build time; repeat as necessary
  --rerun-stage STAGE_ID
                        A stage (using its ID, name, or index) to rerun, or
                        "*" to indicate all stages should be rerun; repeat as
                        necessary
  --batch-tsv FILE      A file in tab separated value (tsv) format, with a
                        subset of the executable input arguments. A job will
                        be launched for each table row.
  --instance-count INSTANCE_COUNT_OR_MAPPING
                        Specify spark cluster instance count(s). It can be an
                        int or a mapping of the format '{"entrypoint": <number
                        of instances>}'
  --input-help          Print help and examples for how to specify inputs

Help: Specifying input for dx run
​
There are several ways to specify inputs.  In decreasing order of precedence,
they are:
​
  1) inputs given in the interactive mode
  2) inputs listed individually with the -i/--input command line argument
  3) JSON given in --input-json
  4) JSON given in --input-json-file
  5) if cloning a job with --clone, the input that the job was run with
     (this will get overridden completely if -j/--input-json or
      -f/--input-json-file are provided)
  6) default values set in a workflow or an executable's input spec
​
SPECIFYING INPUTS BY NAME
​
  Use the -i/--input flag to specify each input field by name and value.
​
    Syntax :  -i<input name>=<input value>
    Example:  dx run myApp -inum=34 -istr=ABC -ifiles=reads1.fq.gz -ifiles=reads2.fq.gz
​
  The example above runs an app called "myApp" with 3 inputs called num (class
  int), str (class string), and files (class array:file).  (For this method to
  work, the app must have an input spec so inputs can be interpreted
  correctly.)  The same input field can be used multiple times if the input
  class is an array.
​
  Job-based object references can also be provided using the <job id>:<output
  name> syntax:
​
    Syntax :  -i<input name>=<job id>:<output name>
    Example:  dx run mapper -ireads=job-B0fbxvGY00j9jqGQvj8Q0001:reads
​
  You can extract an element of an array output using the <job id>:<output
  name>.<element> syntax:
​
    Syntax :  -i<input name>=<job id>:<output name>.<element>
    Example:  dx run mapper -ireadsfile=job-B0fbxvGY00j9jqGQvj8Q0001:reads.1
              # Extracts second element of array output
​
  When executing workflows, stage inputs can be specified using the <stage
  key>.<input name>=<value> syntax:
​
    Syntax :  -i<stage key>.<input name>=<input value>
    Example:  dx run my_workflow -i0.reads="My reads file"
​
<stage key> may be either the ID of the stage, name of the stage, or the
number of the stage in the workflow (0 indicates first stage)
  If the workflow has explicit, workflow-level inputs, input values must be
  passed to these workflow-level input fields using the <workflow input
  name>=<value> syntax:
​
    Syntax :  -i<workflow input name>=<input value>
    Example:  dx run my_workflow -ireads="My reads file"
​
SPECIFYING JSON INPUT
​
  JSON input can be used directly using the -j/--input-json or
  -f/--input-json-file flags.  When running an app or applet, the keys should
  be the input field names for the app or applet.  When running a workflow,
  the keys should be the input field names for each stage, prefixed by the
  stage key and a period, e.g. "my_stage.reads" for the "reads" input of stage
  "my_stage".

usage: dx ssh [-h] [--env-help] [--ssh-proxy <address>:<port>] job_id ...
​
Use an SSH client to connect to a job being executed on the DNAnexus platform.
The job must be launched using "dx run --allow-ssh" or equivalent API options.
Use "dx ssh_config" or the Profile page on the DNAnexus website to configure
SSH for your DNAnexus account.
​
positional arguments:
  job_id                Name of job to connect to
  ssh_args              Command-line arguments to pass to the SSH client
​
optional arguments:
  -h, --help            show this help message and exit
  --env-help            Display help message for overriding environment
                        variables
  --ssh-proxy <address>:<port>
                        SSH connect via proxy, argument supplied is used as
                        the proxy address and port

usage: dx ssh_config [-h] [--env-help] [--revoke] ...
​
Configure SSH access credentials for your DNAnexus account
​
positional arguments:
  ssh_keygen_args  Command-line arguments to pass to ssh-keygen
​
optional arguments:
  -h, --help       show this help message and exit
  --env-help       Display help message for overriding environment variables
  --revoke         Revoke SSH public key associated with your DNAnexus
                   account; you will no longer be able to SSH into any jobs.

usage: dx watch [-h] [--env-help] [--color {off,on,auto}]
                [-n NUM_RECENT_MESSAGES] [--tree]
                [-l {EMERG,ALERT,CRITICAL,ERROR,WARNING,NOTICE,INFO,DEBUG,STDERR,STDOUT}]
                [--get-stdout] [--get-stderr] [--get-streams]
                [--no-timestamps] [--job-ids] [--no-job-info] [-q] [-f FORMAT]
                [--no-wait]
                jobid
​
Monitors logging output from a running job
​
positional arguments:
  jobid                 ID of the job to watch
​
optional arguments:
  -h, --help            show this help message and exit
  --env-help            Display help message for overriding environment
                        variables
  --color {off,on,auto}
                        Set when color is used (color=auto is used when stdout
                        is a TTY)
  -n NUM_RECENT_MESSAGES, --num-recent-messages NUM_RECENT_MESSAGES
                        Number of recent messages to get
  --tree                Include the entire job tree
  -l {EMERG,ALERT,CRITICAL,ERROR,WARNING,NOTICE,INFO,DEBUG,STDERR,STDOUT}, --levels {EMERG,ALERT,CRITICAL,ERROR,WARNING,NOTICE,INFO,DEBUG,STDERR,STDOUT}
  --get-stdout          Extract stdout only from this job
  --get-stderr          Extract stderr only from this job
  --get-streams         Extract only stdout and stderr from this job
  --no-timestamps       Omit timestamps from messages
  --job-ids             Print job ID in each message
  --no-job-info         Omit job info and status updates
  -q, --quiet           Do not print extra info messages
  -f FORMAT, --format FORMAT
                        Message format. Available fields: job, level, msg,
                        date
  --no-wait, --no-follow
                        Exit after the first new message is received, instead
                        of waiting for all logs

usage: dx terminate [-h] [--env-help] jobid [jobid ...]
​
Terminate one or more jobs or analyses
​
positional arguments:
  jobid       ID of a job or analysis to terminate
​
optional arguments:
  -h, --help  show this help message and exit
  --env-help  Display help message for overriding environment variables

usage: dx find apps [-h] [--brief | --verbose] [--json]
                    [--delimiter [DELIMITER]] [--env-help] [--name NAME]
                    [--category CATEGORY] [--category-help] [-a]
                    [--unpublished] [--installed] [--billed-to BILLED_TO]
                    [--creator CREATOR] [--developer DEVELOPER]
                    [--created-after CREATED_AFTER]
                    [--created-before CREATED_BEFORE] [--mod-after MOD_AFTER]
                    [--mod-before MOD_BEFORE]
​
Finds apps subject to the given search parameters. Use --category to restrict
by a category; common categories are available as tab completions and can be
listed with --category-help.
​
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
  --name NAME           Name of the app
  --category CATEGORY   Category of the app
  --category-help       Print a list of common app categories
  -a, --all             Return all versions of each app
  --unpublished         Return only unpublished apps (if omitted, returns only
                        published apps)
  --installed           Return only installed apps
  --billed-to BILLED_TO
                        User or organization responsible for the app
  --creator CREATOR     Creator of the app version
  --developer DEVELOPER
                        Developer of the app
  --created-after CREATED_AFTER
                        Date (e.g. 2012-01-01) or integer timestamp after
                        which the app version was created (negative number
                        means ms in the past, or use suffix s, m, h, d, w, M,
                        y)
  --created-before CREATED_BEFORE
                        Date (e.g. 2012-01-01) or integer timestamp before
                        which the app version was created (negative number
                        means ms in the past, or use suffix s, m, h, d, w, M,
                        y)
  --mod-after MOD_AFTER
                        Date (e.g. 2012-01-01) or integer timestamp after
                        which the app was last modified (negative number means
                        ms in the past, or use suffix s, m, h, d, w, M, y)
  --mod-before MOD_BEFORE
                        Date (e.g. 2012-01-01) or integer timestamp before
                        which the app was last modified (negative number means
                        ms in the past, or use suffix s, m, h, d, w, M, y)

usage: dx find jobs [-h] [--id ID] [--name NAME] [--user USER]
                    [--project PROJECT] [--all-projects] [--app EXECUTABLE]
                    [--state STATE] [--origin ORIGIN] [--parent PARENT]
                    [--created-after CREATED_AFTER]
                    [--created-before CREATED_BEFORE] [--no-subjobs]
                    [--root-execution ROOT_EXECUTION] [-n N] [-o]
                    [--brief | --verbose] [--json] [--color {off,on,auto}]
                    [--delimiter [DELIMITER]] [--env-help]
                    [--property KEY[=VALUE]] [--tag TAG]
                    [--trees | --origin-jobs | --all-jobs]
​
Finds jobs subject to the given search parameters. By default, output is
formatted to show the last several job trees that you've run in the current
project.
​
optional arguments:
  -h, --help            show this help message and exit
  --id ID               Show only the job tree or job containing this job ID
  --name NAME           Restrict the search by job name (accepts wildcards "*"
                        and "?")
  --user USER           Username who launched the job (use "self" to ask for
                        your own jobs)
  --project PROJECT     Project context (output project), default is current
                        project if set
  --all-projects, --allprojects
                        Extend search to all projects
  --app EXECUTABLE, --applet EXECUTABLE, --executable EXECUTABLE
                        Applet or App ID that job is running
  --state STATE         State of the job, e.g. "done", "failed"
  --origin ORIGIN       Job ID of the top-level job
  --parent PARENT       Job ID of the parent job; implies --all-jobs
  --created-after CREATED_AFTER
                        Date (e.g. 2012-01-01) or integer timestamp after
                        which the job was last created (negative number means
                        ms in the past, or use suffix s, m, h, d, w, M, y)
  --created-before CREATED_BEFORE
                        Date (e.g. 2012-01-01) or integer timestamp before
                        which the job was last created (negative number means
                        ms in the past, or use suffix s, m, h, d, w, M, y)
  --no-subjobs          Do not show any subjobs
  --root-execution ROOT_EXECUTION, --root ROOT_EXECUTION
                        Execution ID of the top-level (user-initiated) job or
                        analysis
  -n N, --num-results N
                        Max number of results (trees or jobs, as according to
                        the search mode) to return (default 10)
  -o, --show-outputs    Show job outputs in results
  --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
​
Search mode:
  --trees               Show entire job trees for all matching results
                        (default)
  --origin-jobs         Search and display only top-level origin jobs
  --all-jobs            Search for jobs at all depths matching the query (no
                        tree structure shown)

usage: dx generate_batch_inputs [-h] [-i INPUT] [--path PROJECT:FOLDER]
                                [-o OUTPUT_PREFIX]
​
Generate a table of input files matching desired regular expressions for each
input.
​
optional arguments:
  -h, --help            show this help message and exit
  -i INPUT, --input INPUT
                        An input to be batch-processed "-i<input name>=<input
                        pattern>" where <input_pattern> is a regular
                        expression with a group corresponding to the desired
                        region to match (e.g. "-iinputa=SRR(.*)_1.gz"
                        "-iinputb=SRR(.*)_2.gz")
  --path PROJECT:FOLDER
                        Project and/or folder to which the search for input
                        files will be restricted
  -o OUTPUT_PREFIX, --output_prefix OUTPUT_PREFIX
                        Prefix for output file

usage: dx add member [-h] [--brief | --verbose] [--env-help] --level
                     {ADMIN,MEMBER} [--allow-billable-activities]
                     [--no-app-access]
                     [--project-access {ADMINISTER,CONTRIBUTE,UPLOAD,VIEW,NONE}]
                     [--no-email]
                     org_id username_or_user_id
​
Grant a user membership to an org
​
positional arguments:
  org_id                ID of the org
  username_or_user_id   Username or ID of user
​
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
  --level {ADMIN,MEMBER}
                        Org membership level that will be granted to the
                        specified user
  --allow-billable-activities
                        Grant the specified user "allowBillableActivities" in
                        the org
  --no-app-access       Disable "appAccess" for the specified user in the org
  --project-access {ADMINISTER,CONTRIBUTE,UPLOAD,VIEW,NONE}
                        The default implicit maximum permission the specified
                        user will receive to projects explicitly shared with
                        the org; default CONTRIBUTE
  --no-email            Disable org invitation email notification to the
                        specified user

usage: dx remove member [-h] [--brief | --verbose] [--env-help]
                        [--keep-explicit-project-permissions]
                        [--keep-explicit-app-permissions] [-y]
                        org_id username_or_user_id
​
Revoke the org membership of a user
​
positional arguments:
  org_id                ID of the org
  username_or_user_id   Username or ID of user
​
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
  --keep-explicit-project-permissions
                        Disable revocation of explicit project permissions of
                        the specified user to projects billed to the org;
                        implicit project permissions (i.e. those granted to
                        the specified user via his membership in this org)
                        will always be revoked
  --keep-explicit-app-permissions
                        Disable revocation of explicit app developer and user
                        permissions of the specified user to apps billed to
                        the org; implicit app permissions (i.e. those granted
                        to the specified user via his membership in this org)
                        will always be revoked
  -y, --yes             Do not ask for confirmation

usage: dx update [-h] target ...
​
Use this command with one of the available targets listed below to update
their metadata that are not covered by the other subcommands.
​
positional arguments:
  target
    org       Update information about an org
    workflow  Update the metadata for a workflow
    stage     Update the metadata for a stage in a workflow
    member    Update the membership of a user in an org
    project   Updates a specified project with the specified options
​
optional arguments:
  -h, --help  show this help message and exit

usage: dx update [-h] target ...
​
Use this command with one of the available targets listed below to update
their metadata that are not covered by the other subcommands.
​
positional arguments:
  target
    org       Update information about an org
    workflow  Update the metadata for a workflow
    stage     Update the metadata for a stage in a workflow
    member    Update the membership of a user in an org
    project   Updates a specified project with the specified options
​
optional arguments:
  -h, --help  show this help message and exit

usage: dx find org [-h] entities ...
​
List entities within a specific org.
​
positional arguments:
  entities
    members   List members in the specified org
    projects  List projects billed to the specified org
    apps      List apps billed to the specified org
​
optional arguments:
  -h, --help  show this help message and exit

usage: dx find org [-h] entities ...
​
List entities within a specific org.
​
positional arguments:
  entities
    members   List members in the specified org
    projects  List projects billed to the specified org
    apps      List apps billed to the specified org
​
optional arguments:
  -h, --help  show this help message and exit

usage: dx find org [-h] entities ...
​
List entities within a specific org.
​
positional arguments:
  entities
    members   List members in the specified org
    projects  List projects billed to the specified org
    apps      List apps billed to the specified org
​
optional arguments:
  -h, --help  show this help message and exit

usage: dx find orgs [-h] [--brief | --verbose] [--env-help]
                    [--delimiter [DELIMITER]] [--json] --level {ADMIN,MEMBER}
                    [--with-billable-activities | --without-billable-activities]
​
Finds orgs subject to the given search parameters.
​
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
  --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
  --json                Display return value in JSON
  --level {ADMIN,MEMBER}
                        Restrict the result set to contain only orgs in which
                        the requesting user has at least the specified
                        membership level
  --with-billable-activities
                        Restrict the result set to contain only orgs in which
                        the requesting user can perform billable activities;
                        mutually exclusive with --without-billable-activities
  --without-billable-activities
                        Restrict the result set to contain only orgs in which
                        the requesting user **cannot** perform billable
                        activities; mutually exclusive with --with-billable-
                        activities

usage: dx invite [-h] [--env-help] [--no-email]
                 invitee [project] [{VIEW,UPLOAD,CONTRIBUTE,ADMINISTER}]
​
Invite a DNAnexus entity to a project. If the invitee is not recognized as a
DNAnexus ID, it will be treated as a username, i.e. "dx invite alice : VIEW"
is equivalent to inviting the user with user ID "user-alice" to view your
current default project.
​
positional arguments:
  invitee               Entity to invite
  project               Project to invite the invitee to
  {VIEW,UPLOAD,CONTRIBUTE,ADMINISTER}
                        Permissions level the new member should have
​
optional arguments:
  -h, --help            show this help message and exit
  --env-help            Display help message for overriding environment
                        variables
  --no-email            Disable email notifications to invitee

usage: dx uninvite [-h] [--env-help] entity [project]
​
Revoke others' permissions on a project you administer. If the entity is not
recognized as a DNAnexus ID, it will be treated as a username, i.e. "dx
uninvite alice :" is equivalent to revoking the permissions of the user with
user ID "user-alice" to your current default project.
​
positional arguments:
  entity      Entity to uninvite
  project     Project to revoke permissions from
​
optional arguments:
  -h, --help  show this help message and exit
  --env-help  Display help message for overriding environment variables

usage: dx api [-h] [--env-help] [--input INPUT] resource method [input_json]
​
Call an API method directly.  The JSON response from the API server will be
returned if successful.  No name resolution is performed; DNAnexus IDs must
always be provided.  The API specification can be found at
​
https://wiki.dnanexus.com/API-Specification-v1.0.0/Introduction
​
EXAMPLE
​
  In the following example, a project's description is changed.
​
  $ dx api project-B0VK6F6gpqG6z7JGkbqQ000Q update '{"description": "desc"}'
  {
      "id": "project-B0VK6F6gpqG6z7JGkbqQ000Q"
  }
​
positional arguments:
  resource       One of "system", a class name (e.g. "record"), or an entity
                 ID such as "record-xxxx".  Use "app-name/1.0.0" to refer to
                 version "1.0.0" of the app named "name".
  method         Method name for the resource as documented by the API
                 specification
  input_json     JSON input for the method (if not given, "{}" is used)
​
optional arguments:
  -h, --help     show this help message and exit
  --env-help     Display help message for overriding environment
                 variables
  --input INPUT  Load JSON input from FILENAME ("-" to use stdin)

usage: dx upgrade [-h] [args [args ...]]
​
Upgrades dx-toolkit (the DNAnexus SDK and this program) to the latest
recommended version, or to a specified version and platform.
​
positional arguments:
  args
​
optional arguments:
  -h, --help  show this help message and exit

usage: dx [-h] [--version] command ...
​
DNAnexus Command-Line Client, API v1.0.0, client v0.285.0
​
dx is a command-line client for interacting with the DNAnexus platform.  You
can log in, navigate, upload, organize and share your data, launch analyses,
and more.  For a quick tour of what the tool can do, see
​
  https://wiki.dnanexus.com/Command-Line-Client/Quickstart
​
For a breakdown of dx commands by category, run "dx help".
​
dx exits with exit code 3 if invalid input is provided or an invalid operation
is requested, and exit code 1 if an internal error is encountered.  The latter
usually indicate bugs in dx; please report them at
​
  https://github.com/dnanexus/dx-toolkit/issues
​
optional arguments:
  -h, --help  show this help message and exit
  --env-help  Display help message for overriding environment
              variables
  --version   show program's version number and exit

usage: dx-app-wizard [-h] [--json-file JSON_FILE] [--language LANGUAGE]
                     [--template {basic,parallelized,scatter-process-gather}]
                     [name]
​
Create a source code directory for a DNAnexus app. You will be prompted for
various metadata for the app as well as for its input and output
specifications.
​
positional arguments:
  name                  Name of your app
​
optional arguments:
  -h, --help            show this help message and exit
  --json-file JSON_FILE
                        Use the metadata and IO spec found in the given file
  --language LANGUAGE   Programming language of your app
  --template {basic,parallelized,scatter-process-gather}
                        Execution pattern of your app

usage: dx-build-report-html [-h] [-r REMOTE] [--local LOCAL] [-w WIDTH]
                            [-g HEIGHT]
                            src [src ...]
​
Constructs and saves/uploads an HTML report from HTML and/or linked images
​
positional arguments:
  src                   Source image or HTML file(s)
​
optional arguments:
  -h, --help            show this help message and exit
  -r REMOTE, --remote REMOTE
                        Destination route. Can be: (1) a project ID, (2) a
                        path, with or without object name (e.g.
                        /PATH/REPORT_NAME), (3) project ID + path (e.g.
                        PROJECT:/PATH/REPORT_NAME)
  --local LOCAL         Local file to save baked HTML to
  -w WIDTH, --width WIDTH
                        Width of the final report, in pixels
  -g HEIGHT, --height HEIGHT
                        Height of the final report, in pixels

usage: dx-docker [-h] [-q] {pull,run,add-to-applet,create-asset} ...
​
positional arguments:
  {pull,run,add-to-applet,create-asset}
    pull                Pulls a docker image for use in DNAnexus
    run                 Runs a docker image in a container
    add-to-applet       Adds a local Docker image to an applet
    create-asset        Caches a local Docker image as an asset in the
                        DNAnexus platform (subject to change)
​
optional arguments:
  -h, --help            show this help message and exit
  -q, --quiet           Suppress printing pull progress to stderr

usage: dx-fetch-bundled-depends [-h]
​
Downloads the contents of runSpec.bundledDepends of a job running in the
execution environment.
​
optional arguments:
  -h, --help  show this help message and exit

usage: dx-generate-dxapp [-h] [-m TARGET_MODULE] [-f TARGET_FUNCTION]
                         [-x TARGET_EXECUTABLE] [-s SUBCOMMAND]
                         [-o OUTPUT_FILE]
                         [-p OUTPUT_PARAMS [OUTPUT_PARAMS ...]]
                         [-r OUTPUT_PARAM_REGEXP] [-n {bash,python2.7}]
                         [-i INSTANCE_TYPE] [-t TIMEOUT]
                         [--distribution DISTRIBUTION] [--release RELEASE]
​
optional arguments:
  -h, --help            show this help message and exit
  -m TARGET_MODULE, --target-module TARGET_MODULE
                        The fully-qualified module that contains the target
                        method.
  -f TARGET_FUNCTION, --target-function TARGET_FUNCTION
                        The main function that is called by the target
                        executable. This should bewhere the ArgumentParser is
                        configured.
  -x TARGET_EXECUTABLE, --target-executable TARGET_EXECUTABLE
                        The name of the executable. This is used in the
                        dxapp.json runSpec.
  -s SUBCOMMAND, --subcommand SUBCOMMAND
                        Subcommand to pass to the target method, if required.
  -o OUTPUT_FILE, --output-file OUTPUT_FILE
                        The output dxapp.json file. If not specified, output
                        will go to stdout.
  -p OUTPUT_PARAMS [OUTPUT_PARAMS ...], --output-params OUTPUT_PARAMS [OUTPUT_PARAMS ...]
                        Names of output parameters (in case they can't be
                        autodetected).
  -r OUTPUT_PARAM_REGEXP, --output-param-regexp OUTPUT_PARAM_REGEXP
                        Regular expression that identifies output parameter
                        names.
  -n {bash,python2.7}, --interpreter {bash,python2.7}
                        Type of script that will wrap the executable.
  -i INSTANCE_TYPE, --instance-type INSTANCE_TYPE
                        AWS instance type to use.
  -t TIMEOUT, --timeout TIMEOUT
                        Max runtime of this app (in hours).
  --distribution DISTRIBUTION
                        Distribution to use for the machine image.
  --release RELEASE     Distribution release to use for the machine image.

usage: dx-jobutil-add-output [-h] [--class [CLASSNAME]] [--array] name value
​
Reads and modifies job_output.json in your home directory to be a JSON hash
with key *name* and value  *value*.
​
If --class is not provided or is set to "auto", auto-detection of the output
format will occur.  In particular, it will treat it as a number, hash, or
boolean if it can be successfully parsed as such.  If it is a string which
matches the pattern for a data object ID, it will encapsulate it in a DNAnexus
link hash; otherwise it is treated as a simple string.
​
Use --array to append to an array of values or prepend "array:" to the --class
argument.
​
To use the output of another job as part of your output, use --class=jobref
(which will throw an error if it is not formatted correctly), or use the
automatic parsing which will recognize anything starting with a job ID as a
job-based object reference.  You should format the value as follows:
​
  Format: <job ID>:<output field name>
  Example: dx-jobutil-add-output myoutput --class=jobref \
             job-B2JKYqK4Zg2K915yQxPQ0024:other_output
​
Analysis references can be specified similarly with --class=analysisref and
formatted as:
​
  Format: <analysis ID>:<stage ID>.<output field name>
          <analysis ID>:<exported output field name>
  Example: dx-jobutil-add-output myoutput --class=analysisref \
             analysis-B2JKYqK4Zg2K915yQxPQ0024:some_output
​
positional arguments:
  name                 Name of the output field name
  value                Value of the output field
​
optional arguments:
  -h, --help           show this help message and exit
  --class [CLASSNAME]  Class of output for formatting purposes, e.g. "int";
                       default "auto"
  --array              Output field is an array