List of dx Commands

Below is a list of commands, with their usage overview, that are part of the dx-toolkit. You can view more details about each command, including the different options, by typing in the help command on the far right column for each command. The format for the help command is dx ___ -h .

Command	Usage	Help Command
add	Add one or more items to a list	dx add -h
add developers	Add developers for an app. Need to be a developer of an app to run it	dx add developers -h
add member	Grant a user membership to an org	dx add member -h
add stage	Add a stage to a workflow	dx add stage -h
add users	Add authorized users for an app. Need to be a developer of an app to run	dx add users -h
add_types	Add types to a data object	dx add_types -h
api	Call an API method	dx api -h
archive	Requests for the specified set files or for the files in a single specified folder in one project to be archived on the platform	dx archive -h
build	Create a new applet/app, or a workflow	dx build -h
build_asset	Build an asset bundle	dx build_asset -h
cat	Print file(s) to stdout	dx cat -h
cd	Change the current working directory	dx cd -h
clearenv	Clears all environment variables set by dx	dx clearenv -h
close	Close data object(s)	dx close -h
cp	Copy objects and/or folders between different projects	dx cp -h
create_cohort	Generates a new Cohort object on the platform from an existing Dataset or Cohort object and using list of IDs.	dx create_cohort -h
describe	Describe a remote object	dx describe -h
download	Download file(s)	dx download -h
env	Print all environment variables in use	dx env -h
exit	Exit out of the interactive shell	dx exit -h
extract_assay	Retrieve the selected data or generate SQL to retrieve the data from a genetic variant or somatic assay in a dataset or cohort based on provided rules.	dx extract_assay -h
extract_assay expression	Retrieve the selected data or generate SQL to retrieve the data from a genetic variant or somatic assay in a dataset or cohort based on provided rules.	dx extract_assay expression -h
extract_assay germline	Retrieve the selected data or generate SQL to retrieve the data from a genetic variant or somatic assay in a dataset or cohort based on provided rules.	dx extract_assay germline -h
extract_assay somatic	Retrieve the selected data or generate SQL to retrieve the data from a genetic variant or somatic assay in a dataset or cohort based on provided rules.	dx extract_assay somatic -h
extract_dataset	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. Listing options enable enumeration of the entities and their respective fields in the dataset.	dx extract_dataset -h
find	Search functionality over various DNAnexus entities	dx find -h
find analyses	List analyses in the current project	dx find analyses -h
find apps	List available apps	dx find apps -h
find data	List data objects in the current project	dx find data -h
find executions	List executions (jobs and analyses) in the current project	dx find executions -h
find globalworkflows	List available global workflows	dx find globalworkflows -h
find jobs	List jobs in the current project	dx find jobs -h
find 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.	dx find org -h
find org apps	List apps billed to the specified org	dx find org apps -h
find org members	List members in the specified org	dx find org members -h
find org projects	List projects billed to the specified org	dx find org projects -h
find orgs	List orgs	dx find orgs -h
find projects	List projects	dx find projects -h
generate_batch_inputs	Generate a batch plan (one or more TSV files) for batch execution	dx generate_batch_inputs -h
get	Download records, apps, applets, workflows, files, and databases.	dx get -h
get_details	Get details of a data object	dx get_details -h
head	Print part of a file	dx head -h
help	Display help messages and dx commands by category	dx help -h
install	Install an app	dx install -h
invite	Invite another user to a project or make it public	dx invite -h
list	Print the members of a list	dx list -h
list database	List entities associated with a specific database. For example, "dx list database files" lists database files associated with a specific database. Please execute "dx list database -h" for more information.	dx list database -h
list database files	List files associated with a specific database	dx list database files -h
list developers	List developers for an app	dx list developers -h
list stages	List the stages in a workflow	dx list stages -h
list users	List authorized users for an app	dx list users -h
login	Log in (interactively or with an existing API token)	dx login -h
logout	Log out and remove credentials	dx logout -h
ls	List folders and/or objects in a folder	dx ls -h
make_download_url	Create a file download link for sharing	dx make_download_url -h
mkdir	Create a new folder	dx mkdir -h
mv	Move or rename objects and/or folders inside a project	dx mv -h
new	Create a new project or data object	dx new -h
new org	Create new non-billable org	dx new org -h
new project	Create a new project	dx new project -h
new record	Create a new record	dx new record -h
new user	Create a new user account	dx new user -h
new workflow	Create a new workflow	dx new workflow -h
publish	Publish an app or a global workflow	dx publish -h
pwd	Print current working directory	dx pwd -h
remove	Remove one or more items to a list	dx remove -h
remove developers	Remove developers for an app	dx remove developers -h
remove member	Revoke the org membership of a user	dx remove member -h
remove stage	Remove a stage from a workflow	dx remove stage -h
remove users	Remove authorized users for an app	dx remove users -h
remove_types	Remove types from a data object	dx remove_types -h
rename	Rename a project or data object	dx rename -h
rm	Remove data objects and folders	dx rm -h
rmdir	Remove a folder	dx rmdir -h
rmproject	Delete a project	dx rmproject -h
run	Run an applet, app, or workflow	dx run -h
select	List and select a project to switch to	dx select -h
set_details	Set details on a data object	dx set_details -h
set_properties	Set properties of a project, data object, or execution	dx set_properties -h
set_visibility	Set visibility on a data object	dx set_visibility -h
setenv	Sets environment variables for the session	dx setenv -h
ssh	Connect to a running job via SSH	dx ssh -h
ssh_config	Configure SSH keys for your DNAnexus account	dx ssh_config -h
tag	Tag a project, data object, or execution	dx tag -h
terminate	Terminate jobs or analyses	dx terminate -h
tree	List folders and objects in a tree	dx tree -h
unarchive	Requests for the specified set files or for the files in a single specified folder in one project to be unarchived on the platform.	dx unarchive -h
uninstall	Uninstall an app	dx uninstall -h
uninvite	Revoke others' permissions on a project you administer	dx uninvite -h
unset_properties	Unset properties of a project, data object, or execution	dx unset_properties -h
untag	Untag a project, data object, or execution	dx untag -h
update	Update certain types of metadata	dx update -h
update member	Update the membership of a user in an org	dx update member -h
update org	Update information about an org	dx update org -h
update project	Updates a specified project with the specified options	dx update project -h
update stage	Update the metadata for a stage in a workflow	dx update stage -h
update workflow	Update the metadata for a workflow	dx update workflow -h
upload	Upload file(s) or directory	dx upload -h
wait	Wait for data object(s) to close or job(s) to finish	dx wait -h
watch	Watch logs of a job and its subjobs	dx watch -h
whoami	Print the username of the current user	dx whoami -h