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 exitOverriding 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 tokenCategory: 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 serverexit
usage: dx exit [-h]
Exit out of the interactive shell
optional arguments:
-h, --help show this help message and exitwhoami
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 usernameenv
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 variablesclearenv
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 folderstree
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 formatpwd
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 variablesselect
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 variablescp
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
promptingmv
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
promptingmkdir
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 neededrmdir
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 variablesrm
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 filesrmproject
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 messagesarchive
usage: dx archive [-h] [-a] [-q] [--all-copies] [-y] [--no-recurse]
path [path ...]
Requests for the specified set files or for the files in a single specified folder in ONE project to be archived on the platform.
For each file, if this is the last copy of a file to have archival requested, it will trigger the full archival of the object.
Otherwise, the file will be marked in an archival state denoting that archival has been requested.
The input paths should be either 1 folder path or up to 1000 files, and all path(s) need to be in the same project.
To specify which project to use, prepend the path or ID of the file/folder with the project ID or name and a colon.
EXAMPLES:
# archive 3 files in project "FirstProj" with project ID project-B0VK6F6gpqG6z7JGkbqQ000Q
$ dx archive FirstProj:file-B0XBQFygpqGK8ZPjbk0Q000Q FirstProj:/path/to/file1 project-B0VK6F6gpqG6z7JGkbqQ000Q:/file2
# archive 2 files in current project. Specifying file ids saves time by avoiding file name resolution.
$ dx select FirstProj
$ dx archive file-A00000ygpqGK8ZPjbk0Q000Q file-B00000ygpqGK8ZPjbk0Q000Q
# archive all files recursively in project-B0VK6F6gpqG6z7JGkbqQ000Q
$ dx archive project-B0VK6F6gpqG6z7JGkbqQ000Q:/
positional arguments:
path May refer to a single folder or specify up to 1000
files inside a project.
optional arguments:
-h, --help show this help message and exit
-a, --all Apply to all results with the same name without
prompting
-q, --quiet Do not print extra info messages
--all-copies If true, archive all the copies of files in projects
with the same billTo org.
See https://documentation.dnanexus.com/developer/api/d
ata-containers/projects#api-method-project-xxxx-archiv
e for details.
-y, --yes Do not ask for confirmation.
--no-recurse When `path` refers to a single folder, this flag
causes only files in the specified folder and not its
subfolders to be archived. This flag has no impact
when `path` input refers to a collection of files.
Output:
If -q option is not specified, prints "Tagged <count> file(s) for archival"unarchive
usage: dx unarchive [-h] [-a] [--rate {Standard,Bulk}] [-q] [-y] [--no-recurse] path [path ...]
Requests for a specified set files or for the files in a single specified folder in ONE project to be unarchived on the platform.
The requested copy will eventually be transitioned over to the live state while all other copies will move over to the archival state.
The input paths should be either 1 folder path or up to 1000 files, and all path(s) need to be in the same project.
To specify which project to use, prepend the path or ID of the file/folder with the project ID or name and a colon.
EXAMPLES:
# unarchive 3 files in project "FirstProj" with project ID project-B0VK6F6gpqG6z7JGkbqQ000Q
$ dx unarchive FirstProj:file-B0XBQFygpqGK8ZPjbk0Q000Q FirstProj:/path/to/file1 project-B0VK6F6gpqG6z7JGkbqQ000Q:/file2
# unarchive 2 files in current project. Specifying file ids saves time by avoiding file name resolution.
$ dx select FirstProj
$ dx unarchive file-A00000ygpqGK8ZPjbk0Q000Q file-B00000ygpqGK8ZPjbk0Q000Q
# unarchive all files recursively in project-B0VK6F6gpqG6z7JGkbqQ000Q
$ dx unarchive project-B0VK6F6gpqG6z7JGkbqQ000Q:/
positional arguments:
path May refer to a single folder or specify up to 1000 files inside a project.
optional arguments:
-h, --help show this help message and exit
-a, --all Apply to all results with the same name without prompting
--rate {Standard,Bulk}
The speed at which all files in this request are unarchived.
- Azure regions: {Standard}
- AWS regions: {Standard, Bulk}
-q, --quiet Do not print extra info messages
-y, --yes Do not ask for confirmation.
--no-recurse When `path` refers to a single folder, this flag causes only files in the
specified folder and not its subfolders to be unarchived. This flag has no
impact when `path` input refers to a collection of files.
Output:
If -q option is not specified, prints "Tagged <> file(s) for unarchival, totalling <> GB, costing <> "list database files
usage: dx list database files [-h] [--env-help] [--folder FOLDER] [--recurse]
[--csv] [--timeout TIMEOUT]
database
List files associated with a specific database
positional arguments:
database Data object ID or path of the database.
optional arguments:
-h, --help show this help message and exit
--env-help Display help message for overriding environment variables
--folder FOLDER Name of folder (directory) in which to start searching
for database files. This will typically match the name of
the table whose files are of interest. The default value
is "/" which will start the search at the root folder of
the database.
--recurse Look for files recursively down the directory structure.
Otherwise, by default, only look on one level.
--csv Write output as comma delimited fields, suitable as CSV
format.
--timeout TIMEOUT Number of seconds to wait before aborting the request. If
omitted, default timeout is 120 seconds.Category: data
View, download, and upload data
describe
usage: dx describe [-h] [--json] [--color {off,on,auto}]
[--delimiter [DELIMITER]] [--env-help] [--details]
[--verbose] [--name] [--multi] [--try T]
path
Describe a DNAnexus entity. Use this command to describe data objects by name
or ID, jobs, apps, users, organizations, etc. If using the "--json" flag, it
will thrown an error if more than one match is found (but if you would like a
JSON array of the describe hashes of all matches, then provide the "--multi"
flag). Otherwise, it will always display all results it finds.
NOTES:
- The project found in the path is used as a HINT when you are using an object
ID; you may still get a result if you have access to a copy of the object in
some other project, but if it exists in the specified project, its description
will be returned.
- When describing apps or applets, options marked as advanced inputs will be
hidden unless --verbose is provided
positional arguments:
path Object ID or path to an object (possibly in another
project) to describe.
optional arguments:
-h, --help show this help message and exit
--json Display return value in JSON
--color {off,on,auto}
Set when color is used (color=auto is used when stdout
is a TTY)
--delimiter [DELIMITER], --delim [DELIMITER]
Always use exactly one of DELIMITER to separate fields
to be printed; if no delimiter is provided with this
flag, TAB will be used
--env-help Display help message for overriding environment
variables
--details Include details of data objects
--verbose Include additional metadata
--name Only print the matching names, one per line
--multi If the flag --json is also provided, then returns a
JSON array of describe hashes of all matching results
--try T When describing a job that was restarted, describe job
try T. T=0 refers to the first try. Default is the
last job try.
--defaultSymlink When describing a project linked to a Symlink
Drive defined, return a mapping describing the drive,
in the form {"drive": "drive-xxxx", "container":
"containerOrBucketName", "prefix": "/"}
--symlinkPath When describing a symlinked file, return the path to the
file, including the name of the cloud storage container
where the file is stored, the folder name, if present, and the
filename proper.upload
usage: dx upload [-h] [--visibility {hidden,visible}] [--property KEY=VALUE]
[--type TYPE] [--tag TAG] [--details DETAILS] [-p]
[--brief | --verbose] [--env-help] [--path [PATH]] [-r]
[--wait] [--no-progress] [--buffer-size WRITE_BUFFER_SIZE]
[--singlethread]
filename [filename ...]
Upload local file(s) or directory. If "-" is provided, stdin will be used
instead. By default, the filename will be used as its new name. If
--path/--destination is provided with a path ending in a slash, the filename
will be used, and the folder path will be used as a destination. If it does
not end in a slash, then it will be used as the final name.
positional arguments:
filename Local file or directory to upload ("-" indicates stdin
input); provide multiple times to upload multiple
files or directories
optional arguments:
-h, --help show this help message and exit
--brief Display a brief version of the return value; for most
commands, prints a DNAnexus ID per line
--verbose If available, displays extra verbose output
--env-help Display help message for overriding environment
variables
--path [PATH], --destination [PATH]
DNAnexus path to upload file(s) to (default uses
current project and folder if not provided)
-r, --recursive Upload directories recursively
--wait Wait until the file has finished closing
--no-progress Do not show a progress bar
--buffer-size WRITE_BUFFER_SIZE
Set the write buffer size (in bytes)
--singlethread Enable singlethreaded uploading
metadata arguments:
--visibility {hidden,visible}
Whether the object is hidden or not
--property KEY=VALUE Key-value pair to add as a property; repeat as
necessary, e.g. "--property key1=val1 --property
key2=val2"
--type TYPE Type of the data object; repeat as necessary, e.g. "--
type type1 --type type2"
--tag TAG Tag of the data object; repeat as necessary, e.g. "--
tag tag1 --tag tag2"
--details DETAILS JSON to store as details
-p, --parents Create any parent folders necessarydownload
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
stdoutmake_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 stdouthead
usage: dx head [-h] [--color {off,on,auto}] [--env-help] [-n N] path
Print the first part of a file. By default, prints the first 10 lines.
positional arguments:
path File ID or name to access
optional arguments:
-h, --help show this help message and exit
--color {off,on,auto}
Set when color is used (color=auto is used when stdout
is a TTY)
--env-help Display help message for overriding environment
variables
-n N, --lines N Print the first N lines (default 10)new
usage: dx new [-h] class ...
Use this command with one of the available subcommands (classes) to create a
new project or data object from scratch. Not all data types are supported. See
'dx upload' for files and 'dx build' for applets.
positional arguments:
class
user Create a new user account
org Create new non-billable org
project Create a new project
record Create a new record
workflow Create a new workflow
optional arguments:
-h, --help show this help message and exitnew project
usage: dx new project [-h] [--brief | --verbose] [--env-help]
[--region REGION] [-s] [--bill-to BILL_TO] [--phi]
[--database-ui-view-only]
[name]
Create a new project
positional arguments:
name Name of the new project
optional arguments:
-h, --help show this help message and exit
--brief Display a brief version of the return value; for most
commands, prints a DNAnexus ID per line
--verbose If available, displays extra verbose output
--env-help Display help message for overriding environment
variables
--region REGION Region affinity of the new project
-s, --select Select the new project as current after creating
--bill-to BILL_TO ID of the user or org to which the project will be
billed. The default value is the billTo of the
requesting user.
--phi Add PHI protection to project
--database-ui-view-only
If set to true, viewers of the project will not be
able to access database data directly
--default-symlink DEFAULT_SYMLINK_MAPPING
Specifies default remote location for new files in the
project and all its execution containers. Mapping in the
form '{"drive": "drive-xxxx",
"container": "containerOrBucketName", "prefix": "/"}'
"drive" is the ID of the linked Symlink Drive.
"container" is the name of the cloud service container
where symlinked files are stored. "prefix," which is
optional, is the name of the folder, in the cloud service
container, where symlinked files are stored.
--monthly-compute-limit MONTHLY_COMPUTE_LIMIT
Monthly project spending limit for compute (in currency units)
--monthly-egress-bytes-limit MONTHLY_EGRESS_BYTES_LIMIT
Monthly project spending limit for egress (in bytes)new record
usage: dx new record [-h] [--visibility {hidden,visible}]
[--property KEY=VALUE] [--type TYPE] [--tag TAG]
[--details DETAILS] [-p] [--brief | --verbose]
[--env-help] [--init INIT] [--close]
[path]
Create a new record
positional arguments:
path DNAnexus path for the new data object (default uses
current project and folder if not provided)
optional arguments:
-h, --help show this help message and exit
--brief Display a brief version of the return value; for most
commands, prints a DNAnexus ID per line
--verbose If available, displays extra verbose output
--env-help Display help message for overriding environment
variables
--init INIT Path to record from which to initialize all metadata
--close Close the record immediately after creating it
metadata arguments:
--visibility {hidden,visible}
Whether the object is hidden or not
--property KEY=VALUE Key-value pair to add as a property; repeat as
necessary,
e.g. "--property key1=val1 --property key2=val2"
--type TYPE Type of the data object; repeat as necessary,
e.g. "--type type1 --type type2"
--tag TAG Tag of the data object; repeat as necessary,
e.g. "--tag tag1 --tag tag2"
--details DETAILS JSON to store as details
-p, --parents Create any parent folders necessarynew 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 necessaryclose
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 closewait
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
pathget
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 necessaryfind data
usage: dx find data [-h] [--brief | --verbose] [--json]
[--color {off,on,auto}] [--delimiter [DELIMITER]]
[--env-help] [--property KEY[=VALUE]] [--tag TAG]
[--class {record,file,applet,workflow,database}]
[--state {open,closing,closed,any}]
[--visibility {hidden,visible,either}] [--name NAME]
[--type TYPE] [--link LINK] [--all-projects]
[--path PROJECT:FOLDER] [--norecurse]
[--created-after CREATED_AFTER]
[--created-before CREATED_BEFORE] [--mod-after MOD_AFTER]
[--mod-before MOD_BEFORE] [--region REGION]
Finds data objects subject to the given search parameters. By default,
restricts the search to the current project if set. To search over all
projects (excluding public projects), use --all-projects (overrides --path and
--norecurse).
optional arguments:
-h, --help show this help message and exit
--brief Display a brief version of the return value; for most
commands, prints a DNAnexus ID per line
--verbose If available, displays extra verbose output
--json Display return value in JSON
--color {off,on,auto}
Set when color is used (color=auto is used when stdout
is a TTY)
--delimiter [DELIMITER], --delim [DELIMITER]
Always use exactly one of DELIMITER to separate fields
to be printed; if no delimiter is provided with this
flag, TAB will be used
--env-help Display help message for overriding environment
variables
--property KEY[=VALUE]
Key-value pair of a property or simply a property key;
if only a key is provided, matches a result that has
the key with any value; repeat as necessary, e.g. "--
property key1=val1 --property key2"
--tag TAG Tag to match; repeat as necessary, e.g. "--tag tag1
--tag tag2" will require both tags
--class {record,file,applet,workflow,database}
Data object class
--state {open,closing,closed,any}
State of the object
--visibility {hidden,visible,either}
Whether the object is hidden or not
--name NAME Name of the object
--type TYPE Type of the data object
--link LINK Object ID that the data object links to
--all-projects, --allprojects
Extend search to all projects (excluding public
projects)
--path PROJECT:FOLDER
Project and/or folder in which to restrict the results
--norecurse Do not recurse into subfolders
--created-after CREATED_AFTER
Date (e.g. 2012-01-01) or integer timestamp after
which the object was created (negative number means ms
in the past, or use suffix s, m, h, d, w, M, y)
Negative input example "--created-after=-2d"
--created-before CREATED_BEFORE
Date (e.g. 2012-01-01) or integer timestamp before
which the object was created (negative number means ms
in the past, or use suffix s, m, h, d, w, M, y)
Negative input example "--created-before=-2d"
--mod-after MOD_AFTER
Date (e.g. 2012-01-01) or integer timestamp after
which the object was last modified (negative number
means ms in the past, or use suffix s, m, h, d, w, M,
y) Negative input example "--mod-after=-2d"
--mod-before MOD_BEFORE
Date (e.g. 2012-01-01) or integer timestamp before
which the object was last modified (negative number
means ms in the past, or use suffix s, m, h, d, w, M,
y) Negative input example "--mod-before=-2d"
--region REGION Restrict the search to the provided regionfind projects
usage: dx find projects [-h] [--brief | --verbose] [--json]
[--delimiter [DELIMITER]] [--env-help]
[--property KEY[=VALUE]] [--tag TAG]
[--phi {true,false}] [--name NAME]
[--level {VIEW,UPLOAD,CONTRIBUTE,ADMINISTER}]
[--public] [--created-after CREATED_AFTER]
[--created-before CREATED_BEFORE] [--region REGION]
[--externalUploadRestricted {true,false}]
Finds projects subject to the given search parameters. Use the --public flag
to list all public projects.
optional arguments:
-h, --help show this help message and exit
--brief Display a brief version of the return value; for most
commands, prints a DNAnexus ID per line
--verbose If available, displays extra verbose output
--json Display return value in JSON
--delimiter [DELIMITER], --delim [DELIMITER]
Always use exactly one of DELIMITER to separate fields
to be printed; if no delimiter is provided with this
flag, TAB will be used
--env-help Display help message for overriding environment
variables
--property KEY[=VALUE]
Key-value pair of a property or simply a property key;
if only a key is provided, matches a result that has
the key with any value; repeat as necessary, e.g. "--
property key1=val1 --property key2"
--tag TAG Tag to match; repeat as necessary, e.g. "--tag tag1
--tag tag2" will require both tags
--phi {true,false} If set to true, only projects that contain PHI data
will be retrieved. If set to false, only projects that
do not contain PHI data will be retrieved.
--name NAME Name of the project
--level {VIEW,UPLOAD,CONTRIBUTE,ADMINISTER}
Minimum level of permissions expected
--public Include ONLY public projects (will automatically set
--level to VIEW)
--created-after CREATED_AFTER
Date (e.g. 2012-01-01) or integer timestamp after
which the project was created (negative number means
ms in the past, or use suffix s, m, h, d, w, M, y)
Negative input example "--created-after=-2d"
--created-before CREATED_BEFORE
Date (e.g. 2012-01-01) or integer timestamp after
which the project was created (negative number means
ms in the past, or use suffix s, m, h, d, w, M, y)
Negative input example "--created-before=-2d"
--region REGION Restrict the search to the provided region
--externalUploadRestricted {true,false}
If set to true, only externalUploadRestricted projects will
be retrieved. If set to false, only projects that are not
externalUploadRestricted will be retrieved.update project
usage: dx update project [-h] [--brief | --verbose] [--env-help] [--name NAME]
[--summary SUMMARY] [--description DESCRIPTION]
[--protected {true,false}]
[--restricted {true,false}]
[--download-restricted {true,false}]
[--containsPHI {true}]
[--database-ui-view-only {true,false}]
[--bill-to BILL_TO]
[ --external-upload-restricted {true,false}]
[--allowed-executables ALLOWED_EXECUTABLES
[ALLOWED_EXECUTABLES ...]
[ --unset-allowed-executables]
project_id
positional arguments:
project_id Project ID or project name
optional arguments:
-h, --help show this help message and exit
--brief Display a brief version of the return value; for most
commands, prints a DNAnexus ID per line
--verbose If available, displays extra verbose output
--env-help Display help message for overriding environment
variables
--name NAME New project name
--summary SUMMARY Project summary
--description DESCRIPTION
Project description
--protected {true,false}
Whether the project should be PROTECTED
--restricted {true,false}
Whether the project should be RESTRICTED
--download-restricted {true,false}
Whether the project should be DOWNLOAD RESTRICTED
--containsPHI {true} Flag to tell if project contains PHI
--database-ui-view-only {true,false}
Whether the viewers on the project can access the
database data directly
--bill-to BILL_TO Update the user or org ID of the billing account
--allowed-executables ALLOWED_EXECUTABLES [ALLOWED_EXECUTABLES ...]
Executable ID(s) this project is allowed to run. This
operation overrides any existing list of executables.
--unset-allowed-executables
Removes any restriction to run executables as set by
--allowed-executables
--external-upload-restricted {true,false}
Whether uploads of file and table data to the project
should be restrictedextract_dataset
usage: dx extract_dataset [-h] [-ddd] [--fields FIELDS]
[--fields-file FIELDS_FILE][--sql]
[--delim [DELIM]] [-o OUTPUT] [--list-fields] [--list-entities] [--entities ENTITIES]
path
Retrieves the data or generates SQL to retrieve the data from a dataset or
cohort for a set of entity.fields. Additionally, the dataset's dictionary can
be extracted independently or in conjunction with data. Note: A separate version of pandas may be required to install when using this functionality.
positional arguments:
path v3.0 Dataset or Cohort object ID (project-id:record-id
where "record-id" indicates the record ID in the
currently selected project) or name
optional arguments:
-h, --help show this help message and exit
-ddd, --dump-dataset-dictionary
If provided, the three dictionary files,
<record_name>.data_dictionary.csv,
<record_name>.entity_dictionary.csv, and
<record_name>.codings.csv will be generated. Files
will be comma delimited and written to the local
working directory, unless otherwise specified using
--delimiter and --output arguments. If stdout is
specified with the output argument, the data
dictionary, entity dictionary, and coding are output
in succession, without separators. If any of the
three dictionary files does not contain data (i.e. the
dictionary is empty), then that particular file will
not be created (or be output if the output is stdout).
--fields FIELDS
A comma-separated string where each value is the
phenotypic entity name and field name, separated by a
dot. For example: "<entity_name>.<field_name>,<entity
_name>.<field_name>". Internal spaces are permitted.
If multiple entities are provided, field values will
be automatically inner joined. If only the --fields
argument is provided, data will be retrieved and
returned. If both --fields and --sql arguments are
provided, a SQL statement to retrieve the specified
field data will be automatically generated and
returned. Alternatively, use --fields-file option when
the number of fields to be retrieved is large.
--fields-file FIELDS_FILE
A file with no header and one entry per line where
every entry is the phenotypic entity name and field
name, separated by a dot. For example:
<entity_name>.<field_name>. If multiple entities are
provided, field values will be automatically inner
joined. If only the --fields-file argument is
provided, data will be retrieved and returned. If both
--fields-file and --sql arguments are provided, a SQL
statement to retrieve the specified field data will be
automatically generated and returned. May not be used
in conjunction with the argument --fields.
--sql
If provided, a SQL statement (string) will be returned
to query the set of entity.fields, instead of
returning stored values from the set of entity.fields
--delim [DELIM], --delimiter [DELIM]
Always use exactly one of DELIMITER to separate fields
to be printed; if no delimiter is provided with this
flag, COMMA will be used
-o OUTPUT, --output OUTPUT
Local filename or directory to be used ("-" indicates
stdout output). If not supplied, output will create a
file with a default name in the current folder
--list-fields List the names and titles of all fields available in the dataset specified. When not specified together with "–-entities", it will return all the fields
from the main entity. Output will be a two column table, field names and field titles, separated by a tab, where field names will be of the format,
"<entity name>.<field name>" and field titles will be of the format, "<field title>".
--list-entities List the names and titles of all the entities available in the dataset specified. Output will be a two column table, entity names and entity titles,
separated by a tab.
--entities ENTITIES Similar output to "--list-fields", however using "--entities" will allow for specific entities to be specified. When multiple entities are specified,
use comma as the delimiter. For example: "--list-fields --entities entityA,entityB,entityC"extract_assay expression
usage: dx extract_assay expression [-h] [--list-assays]
[--retrieve-expression]
[--additional-fields-help]
[--assay-name ASSAY_NAME]
[--filter-json FILTER_JSON]
[--filter-json-file FILTER_JSON_FILE]
[--json-help] [--sql]
[--additional-fields ADDITIONAL_FIELDS [ADDITIONAL_FIELDS ...]]
[--expression-matrix] [--delim DELIM]
[--output OUTPUT]
[path]
Retrieve the selected data or generate SQL to retrieve the data from a
molecular expression assay in a dataset or cohort based on provided rules.
positional arguments:
path v3.0 Dataset or Cohort object ID, project-id:record-
id, where ":record-id" indicates the record-id in
current selected project, or name
options:
-h, --help show this help message and exit
--list-assays List molecular expression assays available for query
in the specified Dataset or Cohort object
--retrieve-expression
A flag to support, specifying criteria of molecular
expression to retrieve. Retrieves rows from the
expression table, optionally extended with sample and
annotation information where the extension is inline
without affecting row count. By default returns the
following set of fields; "sample_id", "feature_id",
and "value". Additional fields may be returned using "
--additional-fields". Must be used with either "--
filter-json" or "--filter-json-file". Specify "--json-
help" following this option to get detailed
information on the json format and filters. When
filtering, one, and only one of "location",
"annotation.feature_id", or "annotation.feature_name"
may be supplied. If a Cohort object is supplied,
returned samples will be initially filtered to match
the cohort-defined set of samples, and any additional
filters will only further refine the cohort-defined
set.
--additional-fields-help
List all fields available for output.
--assay-name ASSAY_NAME
Specify a specific molecular expression assay to
query. If the argument is not specified, the default
assay used is the first assay listed when using the
argument, "--list-assays"
--filter-json FILTER_JSON, -j FILTER_JSON
The full input JSON object as a string and
corresponding to "--retrieve-expression". Must be used
with "--retrieve-expression" flag. Either "--filter-
json" or "--filter-json-file" may be supplied, not
both.
--filter-json-file FILTER_JSON_FILE, -f FILTER_JSON_FILE
The full input JSON object as a file and corresponding
to "--retrieve-expression". Must be used with "--
retrieve-expression" flag. Either "--filter-json" or "
--filter-json-file" may be supplied, not both.
--json-help When set, return a json template of "--retrieve-
expression" and a list of filters with definitions.
--sql If the flag is provided, a SQL statement (as a string)
will be returned for the user to further query the
specified data, instead of returning actual data
values. Use of "--sql" is not supported when also
using the flag, --expression-matrix/-em
--additional-fields ADDITIONAL_FIELDS [ADDITIONAL_FIELDS ...]
A set of fields to return, in addition to the default
set; "sample_id", "feature_id", and "value". Fields
must be represented as field names and supplied as a
single string, where each field name is separated by a
single comma. For example, fieldA,fieldB,fieldC. Use "
--additional-fields-help" to get the full list of
output fields available.
--expression-matrix, -em
If the flag is provided with "--retrieve-expression",
the returned data will be a matrix of sample IDs
(rows) by feature IDs (columns), where each cell is
the respective pairwise value. The flag is not
compatible with "--additional-fields". Additionally,
the flag is not compatible with an "expression"
filter. If the underlying expression value is missing,
the value will be empty in returned data. Use of
--expression-matrix/-em is not supported when also
using the flag, "--sql".
--delim DELIM, --delimiter DELIM
Always use exactly one of DELIMITER to separate fields
to be printed; if no delimiter is provided with this
flag, COMMA will be used. If a file is specified and
no --delim argument is passed or is COMMA, the file
suffix will be ".csv". If a file is specified and the
--delim argument is TAB, the file suffix will be
".tsv". Otherwise, if a file is specified and "--
delim" is neither COMMA or TAB file suffix will be
".txt".
--output OUTPUT, -o OUTPUT
A local filename to be used, where "-" indicates
printing to STDOUT. If -o/--output is not supplied,
default behavior is to create a file with a
constructed name in the current folder.extract_assay germline
usage: dx extract_assay germline [-h] [--assay-name ASSAY_NAME]
(--list-assays |
--retrieve-allele [RETRIEVE_ALLELE] |
--retrieve-annotation [RETRIEVE_ANNOTATION] |
--retrieve-genotype [RETRIEVE_GENOTYPE])
[--infer-nocall | --infer-ref]
[--sql] [-o OUTPUT]
path
Query a Dataset or Cohort for an instance of a germline variant assay and retrieve data,
or generate SQL to retrieve data, as defined by user-provided filters.
positional arguments:
path
v3.0 Dataset or Cohort object ID (project-id:record-id,
where ":record-id" indicates the record-id in the currently
selected project) or name.
optional arguments:
-h, --help
Show this help message and exit.
--assay-name ASSAY_NAME
Specify the genetic variant assay to query.
If the argument is not specified, the default assay
used is the first assay listed when using the argument,
“--list-assays.”
--list-assays
List genetic variant assays available for query
in the specified Dataset or Cohort object.
--retrieve-allele [RETRIEVE_ALLELE]
A JSON object, either in a file (.json extension)
or as a string (‘<JSON object>’), specifying criteria of
alleles to retrieve. Returns a list of allele IDs with
additional information. Use --json-help with this option to
get detailed information on the JSON format and filters.
--retrieve-annotation [RETRIEVE_ANNOTATION]
A JSON object, either in a file (.json extension) or as a
string (‘<JSON object>’), specifying criteria to retrieve
corresponding alleles and their annotation. Use --json-help
with this option to get detailed information on the JSON
format and filters.
--retrieve-genotype [RETRIEVE_GENOTYPE]
A JSON object, either in a file (.json extension) or as a
string (‘<JSON object>’), specifying criteria of samples to
retrieve. Returns a list of genotypes and associated sample
IDs and allele IDs. Genotype types "ref" and "no-call" have
no allele ID, and "half" types where the genotype is half
reference and half no-call also have no allele ID. All other
genotype types have an allele ID, including "half" types where
the genotype is half alternate allele and half no-call. Use
--json-help with this option to get detailed information on
the JSON format and filters.
--infer-nocall
When using the "--retrieve-genotype" option, infer genotypes
with type "no-call" if they were excluded when the dataset
was created. This option is only valid if the exclusion
parameters at ingestion were set to "exclude_nocall=true",
"exclude_halfref=false", and "exclude_refdata=false".
--infer-ref
When using the "--retrieve-genotype" option, infer genotypes
with type "ref" if they were excluded when the dataset was
created. This option is only valid if the exclusion parameters
at ingestion were set to "exclude_nocall=false",
"exclude_halfref=false", and "exclude_refdata=true".
--sql
If the flag is provided, a SQL statement, returned as a string,
will be provided to query the specified data instead of
returning data.
-o OUTPUT, --output OUTPUT
A local filename or directory to be used, where "-" indicates
printing to STDOUT. If -o/--output is not supplied, default
behavior is to create a file with a constructed name in the
current folder.extract_assay somatic
usage: dx extract_assay somatic [-h] (--list-assays | --retrieve-meta-info |
--retrieve-variant [RETRIEVE_VARIANT])
[--additional-fields [ADDITIONAL_FIELDS]]
[--assay-name ASSAY_NAME]
[--include-normal-samples]
[--sql] [-o OUTPUT]
path
Query a Dataset or Cohort for an instance of a somatic variant assay and retrieve data,
or generate SQL to retrieve data, as defined by user-provided filters.
positional arguments:
path
v3.0 Dataset or Cohort object ID (project-id:record-id, where
":record-id" indicates the record-id in the currently
selected project) or name.
optional arguments:
-h, --help
Show this help message and exit.
--list-assays
List somatic variant assays available for query in the
specified Dataset or Cohort object.
--assay-name ASSAY_NAME
Specify the somatic variant assay to query.
If the argument is not specified, the default assay used
is the first assay listed when using the argument,
“--list-assays.”
--retrieve-variant [RETRIEVE_VARIANT]
A JSON object, either in a file (.json extension) or as a
string (‘<JSON object>’), specifying criteria of somatic
variants to retrieve. Retrieves rows from the variant table,
optionally extended with sample and annotation information
(the extension is inline without affecting row count).
By default returns the following set of fields;
“assay_sample_id”, “allele_id”, “CHROM”, “POS”, “REF”, and
“allele”. Additional fields may be returned using
--additional-fields. Use --json-help with this option to get detailed
information on the JSON format and filters. When filtering,
the user must supply one, and only one of “location”,
“annotation.symbol”, “annotation.gene”, “annotation.feature”,
“allele.allele_id”.
--additional-fields ADDITIONAL_FIELDS
A set of fields to return, in addition to the default set;
“assay_sample_id”, “allele_id”, “CHROM”, “POS”, “REF”,
“allele”. Fields must be represented as field names and
supplied as a single string, where each field name is
separated by a single comma. For example, “fieldA,fieldB,
fieldC.” Internal spaces are permitted.
Use --additional-fields-help with this option to get
detailed information and the full list of output fields available.
--include-normal-sample
Include variants associated with normal samples in the assay.
If no flag is supplied, variants from normal samples will not be supplied.
--retrieve-meta-info
List meta information, as it exists in the original VCF
headers for both INFO and FORMAT fields.
--sql
If the flag is provided, a SQL statement, returned as a
string, will be provided to query the specified data instead
of returning data.
-o OUTPUT, --output OUTPUT
A local filename or directory to be used, where "-" indicates
printing to STDOUT. If -o/--output is not supplied, default
behavior is to create a file with a constructed name in the
current folder.create_cohort
usage: dx create_cohort [--brief | --verbose] --from FROM
(--cohort-ids COHORT_IDS | --cohort-ids-file COHORT_IDS_FILE)
[-h]
[PATH]
Generates a new Cohort object on the platform from an existing Dataset or
Cohort object and using list of IDs.
positional arguments:
PATH DNAnexus path for the new data object. If not
provided, default behavior uses current project and
folder, and will name the object identical to the
assigned record-id.
optional arguments:
--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
--from FROM v3.0 Dataset or Cohort object ID, project-id:record-
id, where ":record-id" indicates the record-id in
current selected project, or name
--cohort-ids COHORT_IDS
A set of IDs used to subset the Dataset or Cohort
object as a comma-separated string. IDs must match
identically in the supplied Dataset. If a Cohort is
supplied instead of a Dataset, the intersection of
supplied and existing cohort IDs will be used to
create the new cohort.
--cohort-ids-file COHORT_IDS_FILE
A set of IDs used to subset the Dataset or Cohort
object in a file with one ID per line and no header.
IDs must match identically in the supplied Dataset. If
a Cohort is supplied instead of a Dataset, the
intersection of supplied and existing cohort IDs will
be used to create the new cohort.
-h, --help Return the docstring and exitCategory: 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 detailsget_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 variablesset_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 promptingadd_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 promptingremove_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 promptingtag
usage: dx tag [-h] [--env-help] [-a] [--try T] 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
--try T When modifying a job that was restarted, apply the change to try T of the restarted job. T=0 refers to
the first try. Default is the last job try.untag
usage: dx untag [-h] [--env-help] [-a] [--try T] 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
--try T When modifying a job that was restarted, apply the change to try T of the restarted job. T=0 refers to
the first try. Default is the last job try.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 promptingset_properties
usage: dx set_properties [-h] [--env-help] [-a] [--try T]
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
--try T When modifying a job that was restarted, apply the change to try T of the restarted job. T=0
refers to the first try. Default is the last job try.unset_properties
usage: dx unset_properties [-h] [--env-help] [-a] [--try T]
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
--try T When modifying a job that was restarted, apply the change to try T of the restarted job. T=0 refers
to the first try. Default is the last job try.Category: exec
Manage and run your apps, applets, and workflows.
build
usage: dx build [-h] [--env-help] [--brief | --verbose] [--ensure-upload]
[--force-symlinks] [--app] [--workflow] [--globalworkflow]
[-d DESTINATION] [--dry-run] [--publish] [--from _FROM]
[--remote] [--no-watch] [-f] [-a] [-v VERSION]
[-b USER_OR_ORG] [--no-check-syntax]
[--no-version-autonumbering] [--no-update]
[--no-dx-toolkit-autodep] [--no-parallel-build]
[--no-temp-build-project] [-y] [--extra-args EXTRA_ARGS]
[--run ...] [--region REGION] [--keep-open]
[src_dir]
Build an applet, app, or workflow object from a local source directory or an
app from an existing applet in the platform. You can use dx-app-wizard to
generate a skeleton directory of an app/applet with the necessary files.
positional arguments:
src_dir Source directory that contains dxapp.json or
dxworkflow.json. (default: current directory)
optional arguments:
-h, --help show this help message and exit
--env-help Display help message for overriding environment
variables
--brief Display a brief version of the return value; for most
commands, prints a DNAnexus ID per line
--verbose If available, displays extra verbose output
--ensure-upload If specified, will bypass computing checksum of
resources directory and upload it unconditionally; by
default, will compute checksum and upload only if it
differs from a previously uploaded resources bundle.
--force-symlinks If specified, will not attempt to dereference symbolic
links pointing outside of the resource directory. By
default, any symlinks within the resource directory
are kept as links while links to files outside the
resource directory are dereferenced (note that links
to directories outside of the resource directory will
cause an error).
--app, --create-app Create an app.
--workflow, --create-workflow
Create a workflow.
--globalworkflow, --create-globalworkflow
Create a global workflow.
--dry-run, -n Do not create an app(let): only perform local checks
and compilation steps, and show the spec of the
app(let) that would have been created.
--remote Build the app remotely by uploading the source
directory to the DNAnexus Platform and building it
there. This option is useful if you would otherwise
need to cross-compile the app(let) to target the
Execution Environment.
--no-watch Don't watch the real-time logs of the remote builder.
(This option only applicable if --remote was
specified).
-v VERSION, --version VERSION
Override the version number supplied in the manifest.
This option needs to be specified when using --from
option.
--no-check-syntax Warn but do not fail when syntax problems are found
(default is to fail on such errors)
--no-dx-toolkit-autodep
Do not auto-insert the dx-toolkit dependency (default
is to add it if it would otherwise be absent from the
runSpec)
--no-parallel-build Build with make instead of make -jN.
--extra-args EXTRA_ARGS
Arguments (in JSON format) to pass to the /applet/new
API method, overriding all other settings
--run ... Run the app or applet after building it (options
following this are passed to dx run; run at high
priority by default)
--keep-open Do not close workflow after building it. Cannot be
used when building apps, applets or global workflows.
options for creating apps or globalworkflows:
(Only valid when --app/--create-app/--globalworkflow/--create-
globalworkflow is specified)
--publish Publish the resulting app/globalworkflow and make it
the default.
--from _FROM ID or path of the source applet/workflow to create an
app/globalworkflow from. Source directory src_dir
cannot be given when using this option
-b USER_OR_ORG, --bill-to USER_OR_ORG
Entity (of the form user-NAME or org-ORGNAME) to bill
for the app/globalworkflow.
--no-version-autonumbering
Only attempt to create the version number supplied in
the manifest (that is, do not try to create an
autonumbered version such as 1.2.3+git.ab1b1c1d if
1.2.3 already exists and is published).
--no-update Never update an existing unpublished
app/globalworkflow in place.
--no-temp-build-project
When building an app in a single region, build its
applet in the current project instead of a temporary
project.
-y, --yes Do not ask for confirmation for potentially dangerous
operations
--region REGION Enable the app/globalworkflow in this region. This
flag can be specified multiple times to enable the
app/globalworkflow in multiple regions. If --region is
not specified, then the enabled region(s) will be
determined by 'regionalOptions' in dxapp.json, or the
project context.
options for creating applets or workflows:
(Only valid when --app/--create-app/--globalworkflow/--create-
globalworkflow is NOT specified)
-d DESTINATION, --destination DESTINATION
Specifies the destination project, destination folder,
and/or name for the applet, in the form
[PROJECT_NAME_OR_ID:][/[FOLDER/][NAME]]. Overrides the
project, folder, and name fields of the dxapp.json or
dxworkflow.json, if they were supplied.
-f, --overwrite Remove existing applet(s) of the same name in the
destination folder. This option is not yet supported
for workflows.
-a, --archive Archive existing applet(s) of the same name in the
destination folder. This option is not yet supported
for workflows.add users
usage: dx add users [-h] [--env-help] app authorizedUser [authorizedUser ...]
Add users or orgs to the list of authorized users of an app. Published
versions of the app will only be accessible to users represented by this list
and to developers of the app. Unpublished versions are restricted to the
developers.
positional arguments:
app Name or ID of an app
authorizedUser One or more users or orgs to add
optional arguments:
-h, --help show this help message and exit
--env-help Display help message for overriding environment variablesadd 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 variableslist 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 variableslist 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 variablesremove 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 variablesremove 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 variablespublish
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 versioninstall
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 variablesuninstall
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 variablesrun
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-by-executable DOUBLE_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 {low,normal,high}]
[--head-job-on-demand] [-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]
[--detach] [--cost-limit cost_limit] [-r RANK]
[--max-tree-spot-wait-time MAX_TREE_SPOT_WAIT_TIME]
[--max-job-spot-wait-time MAX_JOB_SPOT_WAIT_TIME]
[--detailed-job-metrics]
[--preserve-job-outputs | --preserve-job-outputs-folder JOB_OUTPUTS_FOLDER]
[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
When running an app or applet, the mapping lists
executable's entry points or "*" as keys, and instance
types to use for these entry points as values.
When
running a workflow, the specified instance types can
be prefixed by a stage name or stage index followed by
"=" to apply to a specific stage, or apply to all
workflow stages without such prefix.
The instance
type corresponding to the "*" key is applied to all
entry points not explicitly mentioned in the
--instance-type mapping. Specifying a single instance
type is equivalent to using it for all entry points,
so "--instance-type mem1_ssd1_v2_x2" is same as
"--instance-type '{"*":"mem1_ssd1_v2_x2"}'.
Note that
"dx run" calls within the execution subtree may
override the values specified at the root of the
execution tree.
See dx run --instance-type-help for
details.
--instance-type-by-executable DOUBLE_MAPPING
Specifies instance types by app or applet id, then by
entry point within the executable.
The order of
priority for this specification is:
*
--instance-type, systemRequirements and
stageSystemRequirements specified at runtime
*
stage's systemRequirements, systemRequirements
supplied to /app/new and /applet/new at
workflow/app/applet build time
*
systemRequirementsByExecutable specified in downstream
executions (if any)
See dx run --instance-type-help
for 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. When
using an analysis with --clone a workflow executable
cannot be overriden and should not be provided.)
--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 {low,normal,high}
Request a scheduling priority for all resulting jobs.
Defaults to high when --watch, --ssh, or --allow-ssh
flags are used.
--head-job-on-demand Requests that the head job of an app or applet be run
in an on-demand instance. Note that
--head-job-on-demand option will override the
--priority setting for the head job
-y, --yes Do not ask for confirmation
--wait Wait until the job is done before returning
--watch Watch the job after launching it. Defaults --priority to high.
--allow-ssh [ADDRESS]
Configure the job to allow SSH access. Defaults
--priority to high. If an argument is supplied, it is
interpreted as an IP range, e.g. "--allow-ssh
1.2.3.4". If no argument is supplied then the client
IP visible to the DNAnexus API server will be used by
default
--ssh Configure the job to allow SSH access and connect to
it after launching. Defaults --priority to 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
--detach When invoked from a job, detaches the new job from the
creator job so the new job will appear as a typical
root execution. Setting DX_RUN_DETACH environment
variable to 1 causes this option to be set by default.
--cost-limit cost_limit
Maximum cost of the job before termination. In case of
workflows it is cost of the entire analysis job. For
batch run, this limit is applied per job.
-r RANK, --rank RANK Set the rank of the root execution, integer between
-1024 and 1023. Requires executionRankEnabled license
feature for the billTo. Default is 0.
--max-tree-spot-wait-time MAX_TREE_SPOT_WAIT_TIME
The amount of time allocated to each path in the root
execution's tree to wait for Spot (in seconds, or use
suffix s, m, h, d, w, M, y)
--max-job-spot-wait-time MAX_JOB_SPOT_WAIT_TIME
The amount of time allocated to each job in the root
execution's tree to wait for Spot (in seconds, or use
suffix s, m, h, d, w, M, y)
--detailed-job-metrics
Collect CPU, memory, network and disk metrics every 60
seconds
--preserve-job-outputs
Copy cloneable outputs of every non-reused job
entering "done" state in this root execution R into
the "intermediateJobOutputs" subfolder under R's
output folder. As R's root job or root analysis'
stages complete, R's regular outputs will be moved to
R's regular output folder.
--preserve-job-outputs-folder JOB_OUTPUTS_FOLDER
Similar to --preserve-job-outputs, copy cloneable
outputs of every non-reused job entering "done" state
in this root execution to the specified folder in the
project. JOB_OUTPUTS_FOLDER starting with '/' refers
to an absolute path within the project, otherwise, it
refers to a subfolder under root execution's output
folder.run --input-help
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".run --instance-type-help
Help: Specifying instance types for dx run
Instance types can be requested with --instance-type-by-executable and
--instance-type arguments, with --instance-type-by-executable specification
taking priority over --instance-type, workflow's stageSystemRequirements, and
specifications provided during app and applet creation.
--instance-type specifications do not propagate to subjobs and sub-analyses
launched from a job with a /executable-xxxx/run call, but
--instance-type-by-executable do (where executable refers to an app, applet or
workflow).
When running an app or an applet, --instance-type lets you specify the
instance type to be used by each entry point.
A single instance type can be requested to be used by all entry points by
providing the instance type name. Different instance types can also be
requested for different entry points of an app or applet by providing a JSON
string mapping from function names to instance types, e.g.
{"main": "mem2_hdd2_v2_x2", "other_function": "mem1_ssd1_v2_x2"}
When running a workflow, --instance-type lets you specify instance types for
each entry point of each workflow stage by prepending the request with "<stage
identifier>=" (where a stage identifier is an ID, a numeric index, or a unique
stage name) and repeating the argument for as many stages as desired. If no
stage identifier is provided, the value is applied as a default for all
stages.
Examples
1. Run the main entry point of applet-xxxx on mem1_ssd1_v2_x2, and all other
entry points on mem1_ssd1_v2_x4
dx run applet-xxxx --instance-type '{"main": "mem1_ssd1_v2_x2",
"*": "mem1_ssd1_v2_x4"}'
2. Runs all entry points of the first stage with mem2_hdd2_v2_x2, the main
entry point of the second stage with mem1_ssd1_v2_x4, the stage named "BWA"
with mem1_ssd1_v2_x2, and all other stages with mem2_hdd2_v2_x4
dx run workflow-xxxx \
--instance-type 0=mem2_hdd2_v2_x2 \
--instance-type 1='{"main": "mem1_ssd1_v2_x4"}' \
--instance-type BWA=mem1_ssd1_v2_x2 \
--instance-type mem2_hdd2_v2_x4
--instance-type-by-executable argument is a JSON string with a double mapping
that specifies instance types by app or applet id, then by entry point within
the executable.This specification applies across the entire nested execution
tree and is propagated across /executable-xxxx/run calls issued with the
execution tree.
More examples
3. Force every job in the execution tree to use mem2_ssd1_v2_x2
dx run workflow-xxxx --instance-type-by-executable '{"*": {"*": "mem2_ssd1_v2_x2"}}'
4. Force every job in the execution tree executing applet-xyz1 to use
mem2_ssd1_v2_x2
dx run workflow-xxxx --instance-type-by-executable '{"applet-xyz1":{"*": "mem2_ssd1_v2_x2"}}'
5. Force every job executing applet-xyz1 to use mem2_ssd1_v2_x4 for the main
entry point and mem2_ssd1_v2_x2 for all other entry points.Also force the
collect entry point of all executables other than applet-xyz1 to use
mem2_ssd1_v2_x8.Other entry points of executable other than applet-xyz1 may be
overridden by lower-priority mechanisms
dx run workflow-xxxx --instance-type-by-executable \
'{"applet-xyz1": {"main": "mem2_ssd1_v2_x4", "*": "mem2_ssd1_v2_x2"},
"*": {"collect": "mem2_ssd1_v2_x8"}}'
6. Force every job executing applet-xxxx to use mem2_ssd1_v2_x2 for all entry
points in the entire execution tree. Also force stage 0 executable to run on
mem2_ssd1_v2_x4, unless stage 0 invokes applet-xxxx, in which case
applet-xxxx's jobs will use mem2_ssd1_v2_x2 as specified by
--instance-type-by-executable.
dx run workflow-xxxx \
--instance-type-by-executable '{"applet-xxxx": {"*": "mem2_ssd1_v2_x2"}}' \
--instance-type 0=mem2_ssd1_v2_x4
See "Requesting Instance Types" in DNAnexus documentation for more details.ssh
usage: dx ssh [-h] [--env-help] [--ssh-proxy <address>:<port>]
[--no-firewall-update | --allow-ssh [ADDRESS]]
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
--no-firewall-update Do not update the allowSSH allowed IP ranges before
connecting with ssh
--allow-ssh [ADDRESS]
Configure the job to allow SSH access. from an IP
range, e.g. "--allow-ssh 1.2.3.4". If no argument is
supplied then the client IP visible to the DNAnexus
API server will be used by defaultssh_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 | --try T]
[-l {EMERG,ALERT,CRITICAL,ERROR,WARNING,NOTICE,INFO,DEBUG,STDERR,STDOUT,METRICS}]
[--get-stdout] [--get-stderr] [--get-streams]
[--no-timestamps] [--job-ids] [--no-job-info] [-q] [-f FORMAT]
[--no-wait] [--metrics {interspersed,none,top,csv}]
[--metrics-help]
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
--try T Allows to watch older tries of a restarted job. T=0 refers to the first try. Default is the
last job try.
-l {EMERG,ALERT,CRITICAL,ERROR,WARNING,NOTICE,INFO,DEBUG,STDERR,STDOUT,METRICS}, --levels {EMERG,ALERT,CRITICAL,ERROR,WARNING,NOTICE,INFO,DEBUG,STDERR,STDOUT,METRICS}
--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
--metrics {interspersed,none,top,csv}
Select display mode for detailed job metrics if they
were collected and are available based on retention
policy; see --metrics-help for details
--metrics-help Print help for displaying detailed job metricswatch --metrics-help
Help: Displaying detailed job metrics
Detailed job metrics describe job's consumption of CPU, memory, disk, network, etc
at 60 second intervals.
If collection of job metrics was enabled for a job (e.g with
dx run --detailed-job-metrics), the metrics can be displayed by "dx watch" for
15 days from the time the job started running.
Note that all reported data-related values are in base 2 units - i.e. 1 MB = 1024 * 1024 bytes.
The "interspersed" default mode shows METRICS job log messages interspersed with other
jog log messages.
The "none" mode omits all METRICS messages from "dx watch" output.
The "top" mode interactively shows the latest METRICS message at the top of the screen
and updates it for running jobs instead of showing every METRICS message interspersed
with the currently-displayed job log messages.
For completed jobs, this mode does not show any metrics.
Built-in help describing key bindings is available by pressing "?".
The "csv" mode outputs the following columns with headers in csv format to stdout:
- timestamp: An integer number representing the number of milliseconds since the Unix epoch.
- cpuCount: A number of CPUs available on the instance that ran the job.
- cpuUsageUser: The percentage of cpu time spent in user mode on the instance during the metric collection period.
- cpuUsageSystem: The percentage of cpu time spent in system mode on the instance during the metric collection period.
- cpuUsageIowait: The percentage of cpu time spent in waiting for I/O operations to complete on the instance during the metric collection period.
- cpuUsageIdle: The percentage of cpu time spent in waiting for I/O operations to complete on the instance during the metric collection period.
- memoryUsedBytes: Bytes of memory used (calculated as total - free - buffers - cache - slab_reclaimable + shared_memory).
- memoryTotalBytes: Total memory available on the instance that ran the job.
- diskUsedBytes: Bytes of storage allocated to the AEE that are used by the filesystem.
- diskTotalBytes: Total bytes of disk space available to the job within the AEE.
- networkOutBytes: Total network bytes transferred out from AEE since the job started. Includes "dx upload" bytes.
- networkInBytes: Total network bytes transferred into AEE since the job started. Includes "dx download" bytes.
- diskReadBytes: Total bytes read from the AEE-accessible disks since the job started.
- diskWriteBytes: Total bytes written to the AEE-accessible disks since the job started.
- diskReadOpsCount: Total disk read operation count against AEE-accessible disk since the job started.
- diskWriteOpsCount: Total disk write operation count against AEE-accessible disk since the job started.
Note 1: cpuUsageUser, cpuUsageSystem, cpuUsageIowait, cpuUsageIdle and memoryUsedBytes metrics reflect usage by processes inside and outside of the AEE which include DNAnexus services responsible for proxying DNAnexus data.
Note 2: cpuUsageUser + cpuUsageSystem + cpuUsageIowait + cpuUsageIdle + cpuUsageSteal = 100. cpuUsageSteal is unreported, but can be derived from the other 4 quantities given that they add up to 100.
Note 3: cpuUsage numbers are rounded to 2 decimal places.
Note 4: networkOutBytes may be larger than job's egressReport which does not include "dx upload" bytes.
The format of METRICS job log lines is defined as follows using the example below:
2023-03-15 12:23:44 some-job-name METRICS ** CPU usr/sys/idl/wai: 24/11/1/64% (4 cores) * Memory: 1566/31649MB * Storage: 19/142GB * Net: 10↓/0↑MBps * Disk: r/w 20/174 MBps iops r/w 8/1300
"2023-03-15 12:23:44" is the metrics collection time.
"METRICS" is a type of job log line containing detailed job metrics.
"CPU usr/sys/idl/wai: 24/11/1/64%" maps to cpuUsageUser, cpuUsageSystem, cpuUsageIdle, cpuUsageIowait values.
"(4 cores)" maps to cpuCount.
"Memory: 1566/31649MB" maps to memoryUsedBytes and memoryTotalBytes.
"Storage: 19/142GB" maps to diskUsedBytes and diskTotalBytes.
"Net: 10↓/0↑MBps" is derived from networkOutBytes and networkInBytes cumulative totals by subtracting previous measurement from the measurement at the metric collection time, and dividing the difference by the time span between the two measurements.
"Disk: r/w 20/174 MBps iops r/w 8/1300" is derived similar to "Net:" from diskReadBytes, diskWriteBytes, diskReadOpsCount, and diskWriteOpsCount.
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 variablesfind
usage: dx find [-h] category ...
Search functionality over various DNAnexus entities.
positional arguments:
category
apps List available apps
globalworkflows
List available global workflows
jobs List jobs in the current project
analyses List analyses in the current project
executions List executions (jobs and analyses) in the current project
data List data objects in the current project
projects List projects
org List entities within a specific org.
"dx find org members" lists members in the specified org
"dx find org projects" lists projects billed to the specified org
"dx find org apps" lists apps billed to the specified org
Please execute "dx find org -h" for more information.
orgs List orgs
optional arguments:
-h, --help show this help message and exitfind 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) Negative input example "--created-after=-2d"
--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) Negative input example "--created-before=-2d"
--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)
Negative input example "--mod-after=-2d"
--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)
Negative input example "--mod-before=-2d"
find globalworkflows
usage: dx find globalworkflows [-h] [--brief | --verbose] [--json] [--delimiter [DELIMITER]]
[--env-help] [--name NAME] [--category CATEGORY]
[--category-help] [-a] [--unpublished]
[--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 global workflows 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 workflow
--category CATEGORY Category of the workflow
--category-help Print a list of common global workflow categories
-a, --all Return all versions of each workflow
--unpublished Return only unpublished workflows (if omitted, returns only
published workflows)
--billed-to BILLED_TO
User or organization responsible for the workflow
--creator CREATOR Creator of the workflow version
--developer DEVELOPER
Developer of the workflow
--created-after CREATED_AFTER
Date (e.g. --created-after="2021-12-01" or --created-
after="2021-12-01 19:01:33") or integer Unix epoch timestamp in
milliseconds (e.g. --created-after=1642196636000) after which the
workflow was created. You can also specify negative numbers to
indicate a time period in the past suffixed by s, m, h, d, w, M or y
to indicate seconds, minutes, hours, days, weeks, months or years
(e.g. --created-after=-2d for workflows created in the last 2 days).
--created-before CREATED_BEFORE
Date (e.g. --created-before="2021-12-01" or --created-
before="2021-12-01 19:01:33") or integer Unix epoch timestamp in
milliseconds (e.g. --created-before=1642196636000) before which the
workflow was created. You can also specify negative numbers to
indicate a time period in the past suffixed by s, m, h, d, w, M or y
to indicate seconds, minutes, hours, days, weeks, months or years
(e.g. --created-before=-2d for workflows created earlier than 2 days
ago)
--mod-after MOD_AFTER
Date (e.g. --mod-after="2021-12-01" or --mod-after="2021-12-01
19:01:33") or integer Unix epoch timestamp in milliseconds (e.g.
--mod-after=1642196636000) after which the workflow was created. You
can also specify negative numbers to indicate a time period in the
past suffixed by s, m, h, d, w, M or y to indicate seconds, minutes,
hours, days, weeks, months or years (e.g. --mod-after=-2d for
workflows modified in the last 2 days)
--mod-before MOD_BEFORE
Date (e.g. --mod-before="2021-12-01" or --mod-before="2021-12-01
19:01:33") or integer Unix epoch timestamp in milliseconds (e.g.
--mod-before=1642196636000) before which the workflow was created.
You can also specify negative numbers to indicate a time period in
the past suffixed by s, m, h, d, w, M or y to indicate seconds,
minutes, hours, days, weeks, months or years (e.g. --mod-before=-2d
for workflows modified earlier than 2 days ago)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] [--include-restarted]
[--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
--include-restarted If specified, results will include restarted jobs and job trees rooted in
restarted jobs
--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)find analyses
usage: dx find analyses [-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] [--include-restarted] [--brief | --verbose]
[--json] [--color {off,on,auto}] [--delimiter [DELIMITER]]
[--env-help] [--property KEY[=VALUE]] [--tag TAG]
[--trees | --origin-jobs | --all-jobs]
Finds analyses 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. --created-after="2021-12-01" or
--created-after="2021-12-01 19:01:33") or integer Unix epoch
timestamp in milliseconds (e.g. --created-after=1642196636000) after
which the job was last created. You can also specify negative
numbers to indicate a time period in the past suffixed by s, m, h,
d, w, M or y to indicate seconds, minutes, hours, days, weeks,
months or years (e.g. --created-after=-2d for executions created in
the last 2 days)
--created-before CREATED_BEFORE
Date (e.g. --created-before="2021-12-01" or
--created-before="2021-12-01 19:01:33") or integer Unix epoch
timestamp in milliseconds (e.g. --created-before=1642196636000)
before which the job was last created. You can also specify negative
numbers to indicate a time period in the past suffixed by s, m, h,
d, w, M or y to indicate seconds, minutes, hours, days, weeks,
months or years (e.g. --created-before=-2d for executions created
earlier than 2 days ago)
--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
--include-restarted if specified, results will include restarted jobs and job trees rooted in
restarted jobs
--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)find executions
usage: dx find executions [-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] [--include-restarted]
[--brief | --verbose] [--json] [--color {off,on,auto}]
[--delimiter [DELIMITER]] [--env-help] [--property KEY[=VALUE]]
[--tag TAG] [--trees | --origin-jobs | --all-jobs]
Finds executions (jobs and analyses) 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. --created-after="2021-12-01" or
--created-after="2021-12-01 19:01:33") or integer Unix epoch
timestamp in milliseconds (e.g. --created-after=1642196636000) after
which the job was last created. You can also specify negative
numbers to indicate a time period in the past suffixed by s, m, h,
d, w, M or y to indicate seconds, minutes, hours, days, weeks,
months or years (e.g. --created-after=-2d for executions created in
the last 2 days)
--created-before CREATED_BEFORE
Date (e.g. --created-before="2021-12-01" or
--created-before="2021-12-01 19:01:33") or integer Unix epoch
timestamp in milliseconds (e.g. --created-before=1642196636000)
before which the job was last created. You can also specify negative
numbers to indicate a time period in the past suffixed by s, m, h,
d, w, M or y to indicate seconds, minutes, hours, days, weeks,
months or years (e.g. --created-before=-2d for executions created
earlier than 2 days ago)
--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
--include-restarted if specified, results will include restarted jobs and job trees rooted in
restarted jobs
--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 fileCategory: 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 userremove 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 confirmationupdate org
usage: dx update org [-h] [--brief | --verbose] [--env-help] [--name NAME]
[--member-list-visibility {ADMIN,MEMBER,PUBLIC}]
[--project-transfer-ability {ADMIN,MEMBER}]
[--saml-idp SAML_IDP]
[--detailed-job-metrics-collect-default {true,false}]
[--enable-job-reuse | --disable-job-reuse]
[--job-logs-forwarding-json JLF]
org_id
Update information about an org
positional arguments:
org_id ID of the org
optional arguments:
-h, --help show this help message and exit
--brief Display a brief version of the return value; for most
commands, prints a DNAnexus ID per line
--verbose If available, displays extra verbose output
--env-help Display help message for overriding environment
variables
--name NAME New name of the org
--member-list-visibility {ADMIN,MEMBER,PUBLIC}
New org membership level that is required to be able
to view the membership level and/or permissions of any
other member in the specified org (corresponds to the
memberListVisibility org policy)
--project-transfer-ability {ADMIN,MEMBER}
New org membership level that is required to be able
to change the billing account of a project that is
billed to the specified org, to some other entity
(corresponds to the restrictProjectTransfer org
policy)
--saml-idp SAML_IDP New SAML identity provider
--detailed-job-metrics-collect-default {true,false}
If set to true, jobs launched in the projects billed
to this org will collect detailed job metrics by
default
--enable-job-reuse Enable job reuse for projects where the org is the
billTo
--disable-job-reuse Disable job reuse for projects where the org is the
billTo
--job-logs-forwarding-json JLF
JLF is a JSON string with url and token enabling
forwarding of job logs to Splunk, e.g.
'{"url":"https://http-inputs-
acme.splunkcloud.com/event/collector","token":"splunk-
hec-token"}'update member
usage: dx update member [-h] [--brief | --verbose] [--env-help] [--level {ADMIN,MEMBER}]
[--allow-billable-activities {true,false}] [--app-access {true,false}]
[--project-access {ADMINISTER,CONTRIBUTE,UPLOAD,VIEW,NONE}]
org_id username_or_user_id
Update the membership of a user in 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}
The new org membership level of the specified user
--allow-billable-activities {true,false}
The new "allowBillableActivities" membership permission of the specified user in the org; default
false if demoting the specified user from ADMIN to MEMBER
--app-access {true,false}
The new "appAccess" membership permission of the specified user in the org; default true if
demoting the specified user from ADMIN to MEMBER
--project-access {ADMINISTER,CONTRIBUTE,UPLOAD,VIEW,NONE}
The new default implicit maximum permission the specified user will receive to projects explicitly
shared with the org; default CONTRIBUTE if demoting the specified user from ADMIN to MEMBERfind org members
usage: dx find org members [-h] [--brief | --verbose] [--json] [--delimiter [DELIMITER]] [--env-help]
[--level {ADMIN,MEMBER}]
org_id
Finds members in the specified org subject to the given search parameters
positional arguments:
org_id Org ID
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
--level {ADMIN,MEMBER}
Restrict the result set to contain only members at the specified membership level.
find org entities
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 exitusage: dx find org [-h] entities ...find org projects
usage: dx find org projects [-h] [--brief | --verbose] [--json] [--delimiter [DELIMITER]] [--env-help]
[--property KEY[=VALUE]] [--tag TAG] [--phi {true,false}] [--name NAME] [--ids IDS [IDS ...]]
[--public-only | --private-only] [--created-after CREATED_AFTER]
[--created-before CREATED_BEFORE] [--region REGION]
org_id
Finds projects billed to the specified org subject to the given search parameters. You must be an ADMIN of the specified
org to use this command. It allows you to identify projects billed to the org that have not been shared with you
explicitly.
positional arguments:
org_id Org ID
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 projects
--ids IDS [IDS ...] Possible project IDs. May be specified like "--ids project-1 project-2"
--public-only Include only public projects
--private-only Include only private projects
--created-after CREATED_AFTER
Date (e.g. --created-after="2021-12-01" or --created-after="2021-12-01 19:01:33") or integer Unix
epoch timestamp in milliseconds (e.g. --created-after=1642196636000) after which the project was
created. You can also specify negative numbers to indicate a time period in the past suffixed by s,
m, h, d, w, M or y to indicate seconds, minutes, hours, days, weeks, months or years (e.g.
--created-after=-2d for projects created in the last 2 days).
--created-before CREATED_BEFORE
Date (e.g. --created-before="2021-12-01" or --created-before="2021-12-01 19:01:33") or integer Unix
epoch timestamp in milliseconds (e.g. --created-before=1642196636000) before which the project was
created. You can also specify negative numbers to indicate a time period in the past suffixed by s,
m, h, d, w, M or y to indicate seconds, minutes, hours, days, weeks, months or years (e.g.
--created-before=-2d for projects created earlier than 2 days ago)
--region REGION Restrict the search to the provided region
find org apps
dx find org apps -h
[--developer DEVELOPER] [--created-after CREATED_AFTER] [--created-before CREATED_BEFORE]
[--mod-after MOD_AFTER] [--mod-before MOD_BEFORE]
org_id
Finds apps billed to the specified org subject to the given search parameters. You must be an ADMIN of the specified org to
use this command. It allows you to identify apps billed to the org that have not been shared with you explicitly.
positional arguments:
org_id Org ID
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 apps
--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 all apps)
--installed Return only installed apps
--creator CREATOR Creator of the app version
--developer DEVELOPER
Developer of the app
--created-after CREATED_AFTER
Date (e.g. --created-after="2021-12-01" or --created-after="2021-12-01 19:01:33") or integer Unix
epoch timestamp in milliseconds (e.g. --created-after=1642196636000) after which the app was
created. You can also specify negative numbers to indicate a time period in the past suffixed by s,
m, h, d, w, M or y to indicate seconds, minutes, hours, days, weeks, months or years (e.g.
--created-after=-2d for apps created in the last 2 days).
--created-before CREATED_BEFORE
Date (e.g. --created-before="2021-12-01" or --created-before="2021-12-01 19:01:33") or integer Unix
epoch timestamp in milliseconds (e.g. --created-before=1642196636000) before which the app was
created. You can also specify negative numbers to indicate a time period in the past suffixed by s,
m, h, d, w, M or y to indicate seconds, minutes, hours, days, weeks, months or years (e.g.
--created-before=-2d for apps created earlier than 2 days ago)
--mod-after MOD_AFTER
Date (e.g. 2012-01-01) or integer timestamp after which the app was last modified (negative number
means seconds in the past, or use suffix s, m, h, d, w, M, y) Negative input example "--mod-
after=-2d"
--mod-before MOD_BEFORE
Date (e.g. 2012-01-01) or integer timestamp before which the app was last modified (negative number
means seconds in the past, or use suffix s, m, h, d, w, M, y) Negative input example "--mod-
before=-2d"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-
activitiesCategory: 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 inviteeuninvite
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 variablesapi
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
dx upgrade is removed in v0.379.0. See this documentation for guidance on installing and upgrading dxpy using pip3.
add stage
usage: dx add stage [-h] [-i INPUT] [-j INPUT_JSON] [-f FILENAME] [--brief | --verbose] [--env-help]
[--instance-type INSTANCE_TYPE_OR_MAPPING] [--instance-type-help] [--alias ALIAS] [--name NAME]
[--id STAGE_ID] [--output-folder OUTPUT_FOLDER | --relative-output-folder RELATIVE_OUTPUT_FOLDER]
workflow executable
Add a stage to a workflow. Default inputs for the stage can also be set at the same time.
positional arguments:
workflow Name or ID of a workflow
executable Name or ID of an executable to add as a stage in the workflow
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)
--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
--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
--alias ALIAS, --version ALIAS, --tag ALIAS
Tag or version of the app to add if the executable is an app (default: "default" if an app)
--name NAME Stage name
--id STAGE_ID Stage ID
--output-folder OUTPUT_FOLDER
Path to the output folder for the stage (interpreted as an absolute path)
--relative-output-folder RELATIVE_OUTPUT_FOLDER
A relative folder path for the stage (interpreted as relative to the workflow's output
folder)remove stage
usage: dx remove stage [-h] [--brief | --verbose] [--env-help] workflow stage
Remove a stage from a workflow. The stage should be indicated either by an integer (0-indexed, i.e. "0" for the first
stage), or a stage ID.
positional arguments:
workflow Name or ID of a workflow
stage Stage (index or ID) of the workflow to remove
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 variablesCategory: orgsupdate stage
usage: dx update stage [-h] [-i INPUT] [-j INPUT_JSON] [-f FILENAME] [--brief | --verbose] [--env-help]
[--instance-type INSTANCE_TYPE_OR_MAPPING] [--instance-type-help] [--executable EXECUTABLE]
[--alias ALIAS] [--force] [--name NAME | --no-name]
[--output-folder OUTPUT_FOLDER | --relative-output-folder RELATIVE_OUTPUT_FOLDER]
workflow stage
Update the metadata for a stage in a workflow
positional arguments:
workflow Name or ID of a workflow
stage Stage (index or ID) of the workflow to update
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)
--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
--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
--executable EXECUTABLE
Name or ID of an executable to replace in the stage
--alias ALIAS, --version ALIAS, --tag ALIAS
Tag or version of the app to use if replacing the stage executable with an app (default:
"default" if an app)
--force Whether to replace the executable even if it the new one cannot be verified as compatible
with the previous version
--name NAME Stage name
--no-name Unset the stage name
--output-folder OUTPUT_FOLDER
Path to the output folder for the stage (interpreted as an absolute path)
--relative-output-folder RELATIVE_OUTPUT_FOLDER
A relative folder path for the stage (interpreted as relative to the workflow's output
folder)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 v0.322.1
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 exitdx-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 appdx-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 exitdx-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,python3}]
[-i INSTANCE_TYPE] [-t TIMEOUT]
[--distribution DISTRIBUTION] [--release RELEASE]
[--runspec-version RUNSPEC_VERSION]
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,python3}, --interpreter {bash,python3}
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.
--runspec-version RUNSPEC_VERSION
Version of the application execution environment
inside the runSpec block.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 arraydx-jobutil-dxlink
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 exitdx-jobutil-new-job
usage: dx-jobutil-new-job [-h] [-i INPUT] [-j INPUT_JSON] [-f FILENAME]
[--instance-type INSTANCE_TYPE_OR_MAPPING]
[--instance-type-by-executable DOUBLE_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 ...]]]
[--head-job-on-demand]
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
When running an app or applet, the mapping lists
executable's entry points or "*" as keys, and instance
types to use for these entry points as values. When
running a workflow, the specified instance types can
be prefixed by a stage name or stage index followed by
"=" to apply to a specific stage, or apply to all
workflow stages without such prefix. The instance type
corresponding to the "*" key is applied to all entry
points not explicitly mentioned in the --instance-type
mapping. Specifying a single instance type is
equivalent to using it for all entry points, so "--
instance-type mem1_ssd1_v2_x2" is same as "--instance-
type '{"*":"mem1_ssd1_v2_x2"}'. Note that "dx run"
calls within the execution subtree may override the
values specified at the root of the execution tree.
See dx run --instance-type-help for details.
--instance-type-by-executable DOUBLE_MAPPING
Specifies instance types by app or applet id, then by
entry point within the executable. The order of
priority for this specification is: * --instance-type,
systemRequirements and stageSystemRequirements
specified at runtime * stage's systemRequirements,
systemRequirements supplied to /app/new and
/applet/new at workflow/app/applet build time *
systemRequirementsByExecutable specified in downstream
executions (if any) See dx run --instance-type-help
for 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.
--head-job-on-demand Whether the head job should be run on an on-demand
instancedx-jobutil-parse-link
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 IDdx-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 exitdx-jobutil-get-identity-token
usage: dx-jobutil-get-identity-token [-h] --aud AUD [--subject_claims <subject_claims>]
calls job-xxxx/getIdentityToken and retrieves a JWT token based on aud and subject claims input
optional arguments:
-h, --help show this help message and exit
--aud AUD Audience URI the JWT is intended for
--subject_claims <subject_claims>
Defines the subject claims to be validated by the cloud providerdx-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 usedx-mount-all-inputs
usage: dx-mount-all-inputs [-h] [--except EXCLUDE] [--verbose]
Note: this is a utility for use by bash apps running in the DNAnexus Platform.
Mounts 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 mounted 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 mount the input with this name. (May be used
multiple times.)
--verbose Start dxfuse with '-verbose 2' loggingdx-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 $HOME/job_input.json and prints the bash variables that would be
available in the execution environment.
optional arguments:
-h, --help show this help message and exitdx-verify-file
Usage: dx-verify-file [options] -r <remote_file1_id> -l <local_file1> [-r <remote_file2_id> -l <local_file2> ...]
Available options:
-h [ --help ] Produce a help message
--version Print the version
-e [ --env ] Print environment information
-a [ --auth-token ] arg Specify the authentication token
-r [ --remote-file ] arg ID of the remote file
-l [ --local-file ] arg Local file path
--read-threads arg (=1) Number of parallel disk read threads
--md5-threads arg (=1) Number of parallel MD5 compute threads
-v [ --verbose ] Verbose loggingUtilities useful in writing bash apps and applets
dx-download-all-inputs
usage: dx-download-all-inputs [-h] [--except EXCLUDE] [--parallel]
[--sequential]
Note: this is a utility for use by bash apps running in the DNAnexus Platform.
Downloads all files that were supplied as inputs to the app. By convention,
if an input parameter "FOO" has value
{"$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 sequentiallydx-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 uploadedLast updated