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

Category: data

View, download, and upload data

describe

usage: dx describe [-h] [--json] [--color {off,on,auto}]
[--delimiter [DELIMITER]] [--env-help] [--details]
[--verbose] [--name] [--multi]
path
Describe a DNAnexus entity. Use this command to describe data objects by name
or ID, jobs, apps, users, organizations, etc. If using the "--json" flag, it
will thrown an error if more than one match is found (but if you would like a
JSON array of the describe hashes of all matches, then provide the "--multi"
flag). Otherwise, it will always display all results it finds.
NOTES:
- The project found in the path is used as a HINT when you are using an object
ID; you may still get a result if you have access to a copy of the object in
some other project, but if it exists in the specified project, its description
will be returned.
- When describing apps or applets, options marked as advanced inputs will be
hidden unless --verbose is provided
positional arguments:
path Object ID or path to an object (possibly in another
project) to describe.
optional arguments:
-h, --help show this help message and exit
--json Display return value in JSON
--color {off,on,auto}
Set when color is used (color=auto is used when stdout
is a TTY)
--delimiter [DELIMITER], --delim [DELIMITER]
Always use exactly one of DELIMITER to separate fields
to be printed; if no delimiter is provided with this
flag, TAB will be used
--env-help Display help message for overriding environment
variables
--details Include details of data objects
--verbose Include all possible metadata
--name Only print the matching names, one per line
--multi If the flag --json is also provided, then returns a
JSON array of describe hashes of all matching results

upload

usage: dx upload [-h] [--visibility {hidden,visible}] [--property KEY=VALUE]
[--type TYPE] [--tag TAG] [--details DETAILS] [-p]
[--brief | --verbose] [--env-help] [--path [PATH]] [-r]
[--wait] [--no-progress] [--buffer-size WRITE_BUFFER_SIZE]
[--singlethread]
filename [filename ...]
Upload local file(s) or directory. If "-" is provided, stdin will be used
instead. By default, the filename will be used as its new name. If
--path/--destination is provided with a path ending in a slash, the filename
will be used, and the folder path will be used as a destination. If it does
not end in a slash, then it will be used as the final name.
positional arguments:
filename Local file or directory to upload ("-" indicates stdin
input); provide multiple times to upload multiple
files or directories
optional arguments:
-h, --help show this help message and exit
--brief Display a brief version of the return value; for most
commands, prints a DNAnexus ID per line
--verbose If available, displays extra verbose output
--env-help Display help message for overriding environment
variables
--path [PATH], --destination [PATH]
DNAnexus path to upload file(s) to (default uses
current project and folder if not provided)
-r, --recursive Upload directories recursively
--wait Wait until the file has finished closing
--no-progress Do not show a progress bar
--buffer-size WRITE_BUFFER_SIZE
Set the write buffer size (in bytes)
--singlethread Enable singlethreaded uploading
metadata arguments:
--visibility {hidden,visible}
Whether the object is hidden or not
--property KEY=VALUE Key-value pair to add as a property; repeat as
necessary, e.g. "--property key1=val1 --property
key2=val2"
--type TYPE Type of the data object; repeat as necessary, e.g. "--
type type1 --type type2"
--tag TAG Tag of the data object; repeat as necessary, e.g. "--
tag tag1 --tag tag2"
--details DETAILS JSON to store as details
-p, --parents Create any parent folders necessary

download

usage: dx download [-h] [--env-help] [-o OUTPUT] [-f] [-r] [-a]
[--no-progress] [--lightweight] [--unicode]
path [path ...]
Download the contents of a file object or multiple objects. Use "-o -" to
direct the output to stdout.
positional arguments:
path Data object ID or name, or folder to download
optional arguments:
-h, --help show this help message and exit
--env-help Display help message for overriding environment
variables
-o OUTPUT, --output OUTPUT
Local filename or directory to be used ("-" indicates
stdout output); if not supplied or a directory is
given, the object's name on the platform will be used,
along with any applicable extensions
-f, --overwrite Resume an interupted download if the local and remote
file signatures match. If the signatures do not match
the local file will be overwritten.
-r, --recursive Download folders recursively
-a, --all If multiple objects match the input, download all of
them
--no-progress Do not show a progress bar
--lightweight Skip some validation steps to make fewer API calls
--unicode Display the characters as text/unicode when writing to
stdout

make_download_url

usage: dx make_download_url [-h] [--duration DURATION] [--filename FILENAME]
path
Creates a pre-authenticated link that can be used to download a file without
logging in.
positional arguments:
path Data object ID or name to access
optional arguments:
-h, --help show this help message and exit
--duration DURATION Time for which the URL will remain valid (in seconds,
or use suffix s, m, h, d, w, M, y). Default: 1 day
--filename FILENAME Name that the server will instruct the client to save
the file as (default is the filename)

cat

usage: dx cat [-h] [--env-help] [--unicode] path [path ...]
positional arguments:
path File ID or name(s) to print to stdout
optional arguments:
-h, --help show this help message and exit
--env-help Display help message for overriding environment variables
--unicode Display the characters as text/unicode when writing to stdout

head

usage: dx head [-h] [--color {off,on,auto}] [--env-help] [-n N] path
Print the first part of a file. By default, prints the first 10 lines.
positional arguments:
path File ID or name to access
optional arguments:
-h, --help show this help message and exit
--color {off,on,auto}
Set when color is used (color=auto is used when stdout
is a TTY)
--env-help Display help message for overriding environment
variables
-n N, --lines N Print the first N lines (default 10)

new

usage: dx new [-h] class ...
Use this command with one of the available subcommands (classes) to create a
new project or data object from scratch. Not all data types are supported. See
'dx upload' for files and 'dx build' for applets.
positional arguments:
class
user Create a new user account
org Create new 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]
[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

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}]
[--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

find projects

usage: dx find projects [-h] [--brief | --verbose] [--json]
[--delimiter [DELIMITER]] [--env-help]
[--property KEY[=VALUE]] [--tag TAG]
[--phi {true,false}] [--name NAME]
[--level {VIEW,UPLOAD,CONTRIBUTE,ADMINISTER}]
[--public] [--created-after CREATED_AFTER]
[--created-before CREATED_BEFORE] [--region REGION]
Finds projects subject to the given search parameters. Use the --public flag
to list all public projects.
optional arguments:
-h, --help show this help message and exit
--brief Display a brief version of the return value; for most
commands, prints a DNAnexus ID per line
--verbose If available, displays extra verbose output
--json Display return value in JSON
--delimiter [DELIMITER], --delim [DELIMITER]
Always use exactly one of DELIMITER to separate fields
to be printed; if no delimiter is provided with this
flag, TAB will be used
--env-help Display help message for overriding environment
variables
--property KEY[=VALUE]
Key-value pair of a property or simply a property key;
if only a key is provided, matches a result that has
the key with any value; repeat as necessary, e.g. "--
property key1=val1 --property key2"
--tag TAG Tag to match; repeat as necessary, e.g. "--tag tag1
--tag tag2" will require both tags
--phi {true,false} If set to true, only projects that contain PHI data
will be retrieved. If set to false, only projects that
do not contain PHI data will be retrieved.
--name NAME Name of the project
--level {VIEW,UPLOAD,CONTRIBUTE,ADMINISTER}
Minimum level of permissions expected
--public Include ONLY public projects (will automatically set
--level to VIEW)
--created-after CREATED_AFTER
Date (e.g. 2012-01-01) or integer timestamp after
which the project was created (negative number means
ms in the past, or use suffix s, m, h, d, w, M, y)
--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

Category: metadata

View and modify metadata for projects and data objects

See also dx describe and dx close.

set_details

usage: dx set_details [-h] [--env-help] [-a] [-f DETAILS_FILE] path [details]
Set the JSON details of a data object.
positional arguments:
path ID or path to data object to modify
details JSON to store as details
optional arguments:
-h, --help show this help message and exit
--env-help Display help message for overriding environment
variables
-a, --all Apply to all results with the same name without
prompting
-f DETAILS_FILE, --details-file DETAILS_FILE
Path to local file containing JSON to store as details

get_details

usage: dx get_details [-h] [--env-help] path
Get the JSON details of a data object.
positional arguments:
path ID or path to data object to get details for
optional arguments:
-h, --help show this help message and exit
--env-help Display help message for overriding environment variables

set_visibility

usage: dx set_visibility [-h] [--env-help] [-a] path {hidden,visible}
Set visibility on a data object.
positional arguments:
path ID or path to data object to modify
{hidden,visible} Visibility that the object should have
optional arguments:
-h, --help show this help message and exit
--env-help Display help message for overriding environment variables
-a, --all Apply to all results with the same name without prompting

add_types

usage: dx add_types [-h] [--env-help] [-a] path type [type ...]
Add types to a data object. See
https://documentation.dnanexus.com/developer/api/data-object-lifecycle/types
for a list of DNAnexus types.
positional arguments:
path ID or path to data object to modify
type Types to add
optional arguments:
-h, --help show this help message and exit
--env-help Display help message for overriding environment variables
-a, --all Apply to all results with the same name without prompting

remove_types

usage: dx remove_types [-h] [--env-help] [-a] path type [type ...]
Remove types from a data object. See
https://documentation.dnanexus.com/developer/api/data-object-lifecycle/types
for a list of DNAnexus types.
positional arguments:
path ID or path to data object to modify
type Types to remove
optional arguments:
-h, --help show this help message and exit
--env-help Display help message for overriding environment variables
-a, --all Apply to all results with the same name without prompting

tag

usage: dx tag [-h] [--env-help] [-a] path tag [tag ...]
Tag a project, data object, or execution. Note that a project context must be
either set or specified for data object IDs or paths.
positional arguments:
path ID or path to project, data object, or execution to modify
tag Tags to add
optional arguments:
-h, --help show this help message and exit
--env-help Display help message for overriding environment variables
-a, --all Apply to all results with the same name without prompting

untag

usage: dx untag [-h] [--env-help] [-a] path tag [tag ...]
Untag a project, data object, or execution. Note that a project context must
be either set or specified for data object IDs or paths.
positional arguments:
path ID or path to project, data object, or execution to modify
tag Tags to remove
optional arguments:
-h, --help show this help message and exit
--env-help Display help message for overriding environment variables
-a, --all Apply to all results with the same name without prompting

rename

usage: dx rename [-h] [--env-help] [-a] path name
Rename a project or data object. To rename folders, use 'dx mv' instead. Note
that a project context must be either set or specified to rename a data
object. To specify a project or a project context, append a colon character
":" after the project ID or name.
positional arguments:
path Path to project or data object to rename
name New name
optional arguments:
-h, --help show this help message and exit
--env-help Display help message for overriding environment variables
-a, --all Apply to all results with the same name without prompting

set_properties

usage: dx set_properties [-h] [--env-help] [-a]
path propertyname=value [propertyname=value ...]
Set properties of a project, data object, or execution. Note that a project
context must be either set or specified for data object IDs or paths.
positional arguments:
path ID or path to project, data object, or execution to
modify
propertyname=value Key-value pairs of property names and their new values
optional arguments:
-h, --help show this help message and exit
--env-help Display help message for overriding environment
variables
-a, --all Apply to all results with the same name without
prompting

unset_properties

usage: dx unset_properties [-h] [--env-help] [-a]
path propertyname [propertyname ...]
Unset properties of a project, data object, or execution. Note that a project
context must be either set or specified for data object IDs or paths.
positional arguments:
path ID or path to project, data object, or execution to modify
propertyname Property names to unset
optional arguments:
-h, --help show this help message and exit
--env-help Display help message for overriding environment variables
-a, --all Apply to all results with the same name without prompting

Category: exec

Manage and run your apps, applets, and workflows

build

usage: dx build [-h] [--env-help] [--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.

add users

usage: dx add users [-h] [--env-help] app authorizedUser [authorizedUser ...]
Add users or orgs to the list of authorized users of an app. Published
versions of the app will only be accessible to users represented by this list
and to developers of the app. Unpublished versions are restricted to the
developers.
positional arguments:
app Name or ID of an app
authorizedUser One or more users or orgs to add
optional arguments:
-h, --help show this help message and exit
--env-help Display help message for overriding environment variables

add developers

usage: dx add developers [-h] [--env-help] app developer [developer ...]
Add users or orgs to the list of developers for an app. Developers are able to
build and publish new versions of the app, and add or remove others from the
list of developers and authorized users.
positional arguments:
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

list users

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

list developers

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

remove users

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

remove developers

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

publish

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

install

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

uninstall

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

run

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

Additional help on specifying 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".

ssh

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

ssh_config

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.

watch

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

terminate

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

find apps

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)

find jobs

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)

generate_batch_inputs

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

Category: orgs

Tools to help org admins manage their orgs

add member

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

remove member

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

update org

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

update member

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

find org members

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

find org projects

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

find org apps

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

find orgs

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

Category: other

Miscellaneous advanced utilities

invite

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

uninvite

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

api

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://documentation.dnanexus.com/developer/api
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)

upgrade

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

Helpstrings of SDK Command-Line Utilities

Below is a list of some of the various command-line utilities available in the SDK and some brief documentation for their usage.

General purpose dx utilities

dx

usage: dx [-h] [--version] command ...
DNAnexus Command-Line Client, API v1.0.0, client v0.289.1
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://documentation.dnanexus.com/getting-started/tutorials/cli-quickstart#quickstart-for-cli
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

dx-app-wizard

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

dx-build-report-html

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

dx-docker

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

dx-fetch-bundled-depends

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

dx-generate-dxapp

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.

dx-jobutil-add-output

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
usage: dx-jobutil-dxlink [-h] object
Creates a DNAnexus link from an object ID or "<project ID>:<object ID>"
string. The result is of the form {"$dnanexus_link": "<object ID>"} or
{"$dnanexus_link": {"project": <project ID>, "id": <object ID>}}, as
appropriate.
positional arguments:
object Data object ID or "<Project ID>:<Data object ID>" to package
into a DNAnexus link
optional arguments:
-h, --help show this help message and exit

dx-jobutil-new-job

usage: dx-jobutil-new-job [-h] [-i INPUT] [-j INPUT_JSON] [-f FILENAME]
[--instance-type INSTANCE_TYPE_OR_MAPPING]
[--instance-type-help] [--extra-args EXTRA_ARGS]
[--property KEY=VALUE] [--tag TAG] [--name NAME]
[--depends-on [JOB_OR_OBJECT_ID [JOB_OR_OBJECT_ID ...]]]
function
Creates a new job to run the named function with the specified input. If
successful, prints the ID of the new job.
positional arguments:
function Name of the function to run
optional arguments:
-h, --help show this help message and exit
-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)
--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
--extra-args EXTRA_ARGS
Arguments (in JSON format) to pass to the underlying
API method, overriding the default settings
--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"
--name NAME Name for the new job (default is the current job name,
plus ":<function>")
--depends-on [JOB_OR_OBJECT_ID [JOB_OR_OBJECT_ID ...]]
Job and/or data object IDs that must finish or close
before the new job should be run. WARNING: For proper
parsing, do not use this flag directly before the
*function* parameter.
usage: dx-jobutil-parse-link [-h] [--no-project] dxlink
Parse a dxlink JSON hash into an object ID or project:object-id tuple
positional arguments:
dxlink Link to parse
optional arguments:
-h, --help show this help message and exit
--no-project Ignore project ID in an extended dxlink - just print the
object ID

dx-jobutil-report-error

usage: dx-jobutil-report-error [-h] message [{AppInternalError,AppError}]
Creates job_error.json in your home directory, a JSON file to include the
error type and message for the running job. There are two types of errors you
may report: 1) AppError (the default) for recognized actionable errors, and 2)
AppInternalError for unexpected application errors.
positional arguments:
message Error message for the job
{AppInternalError,AppError}
Error type
optional arguments:
-h, --help show this help message and exit

dx-log-stream

usage: dx-log-stream [-h] [-l {critical,error,warning,info,debug}]
[-s {DX_APP,DX_APP_STREAM}]
Redirects stdin to a DNAnexus log socket in the execution environment.
Valid logging levels:
┌─────────────────────────┬────────────────┬────────────┐
│ --source │ --level │ Appears as │
├─────────────────────────┼────────────────┼────────────┤
│ DX_APP_STREAM (default) │ info (default) │ STDOUT │
│ DX_APP_STREAM (default) │ error │ STDERR │
├─────────────────────────┼────────────────┼────────────┤
│ DX_APP │ debug │ DEBUG │
│ DX_APP │ info (default) │ INFO │
│ DX_APP │ warning │ WARNING │
│ DX_APP │ error │ ERROR │
│ DX_APP │ critical │ CRITICAL │
└─────────────────────────┴────────────────┴────────────┘
optional arguments:
-h, --help show this help message and exit
-l {critical,error,warning,info,debug}, --level {critical,error,warning,info,debug}
Logging level to use
-s {DX_APP,DX_APP_STREAM}, --source {DX_APP,DX_APP_STREAM}
Source ID to use

dx-notebook-reconnect

usage: dx-notebook-reconnect [-h] [--port PORT] job_id
Reconnect to a notebook job
positional arguments:
job_id Job-id of the notebook job to reconnect to.
optional arguments:
-h, --help show this help message and exit
--port PORT Local port to use for connecting.

dx-print-bash-vars

usage: dx-print-bash-vars [-h]
Parses $HOME/job_input.json and prints the bash variables that would be
available in the execution environment.
optional arguments:
-h, --help show this help message and exit

dx-verify-file

Usage: dx-verify-file [options] -r <remote_file1_id> -l <local_file1> [-r <remote_file2_id> -l <local_file2> ...]
Available options:
-h [ --help ] Produce a help message
--version Print the version
-e [ --env ] Print environment information
-a [ --auth-token ] arg Specify the authentication token
-r [ --remote-file ] arg ID of the remote file
-l [ --local-file ] arg Local file path
--read-threads arg (=1) Number of parallel disk read threads
--md5-threads arg (=1) Number of parallel MD5 compute threads
-v [ --verbose ] Verbose logging

Utilities useful in writing bash apps and applets

dx-download-all-inputs

usage: dx-download-all-inputs [-h] [--except EXCLUDE] [--parallel]
[--sequential]
Note: this is a utility for use by bash apps running in the DNAnexus Platform.
Downloads all files that were supplied as inputs to the app. By convention,
if an input parameter "FOO" has value
{"$dnanexus_link": "file-xxxx"}
and filename INPUT.TXT, then the linked file will be downloaded into the path:
$HOME/in/FOO/INPUT.TXT
If an input is an array of files, then all files will be placed into numbered
subdirectories under a parent directory named for the input. For example, if
the input key is FOO, and the inputs are {A, B, C}.vcf then, the directory
structure will be:
$HOME/in/FOO/0/A.vcf
1/B.vcf
2/C.vcf
Zero padding is used to ensure argument order. For example, if there are 12
input files {A, B, C, D, E, F, G, H, I, J, K, L}.txt, the directory structure
will be:
$HOME/in/FOO/00/A.vcf
...
11/L.vcf
This allows using shell globbing (FOO/*/*.vcf) to get all the files in the
input order.
optional arguments:
-h, --help show this help message and exit
--except EXCLUDE Do not download the input with this name. (May be used
multiple times.)
--parallel Download the files in parallel
--sequential Download the files sequentially

dx-upload-all-outputs

usage: dx-upload-all-outputs [-h] [--except EXCLUDE] [--parallel]
[--sequential] [--clearJSON CLEARJSON]
[--wait-on-close] [--xattr-properties]
Note: this is a utility for use by bash apps running in the DNAnexus Platform.
Uploads all files and subdirectories in the directory $HOME/out, as described
below. It also adds relevant entries into the job_output.json file.
By convention, only directories with names equal to output parameter names are
expected to be found in the output directory, and any file(s) found in those
subdirectories will be uploaded as the corresponding outputs. For example, a
file with the path
$HOME/out/FOO/OUTPUT.TXT
will be uploaded, and the key "FOO" will be added to the job_output.json file
with value
{"$dnanexus_link": "file-xxxx"}
where "file-xxxx" is the ID of the newly uploaded file. If multiple files are
found, they will be added as an array output (in unspecified order). If
subdirectories are found under $HOME/out/FOO, then they are uploaded in their
entirety to the workspace, and values are added to FOO in the job_output.json
file. For example, the path:
$HOME/out/FOO/BAR/XXX.TXT
will be uploaded to /BAR/XXX.TXT.
optional arguments:
-h, --help show this help message and exit
--except EXCLUDE Do not upload the input with this name. (May be used
multiple times.)
--parallel Upload the files in parallel
--sequential Upload the files sequentially
--clearJSON CLEARJSON
Clears the output JSON file prior to starting upload.
--wait-on-close Wait for files to close, default is not to wait
--xattr-properties Get filesystem attributes and set them as properties on each file uploaded