This page contains the help messages for each of the commands under dx
, grouped by their primary category.
usage: dx help [-h] [command_or_category] [subcommand]Displays the help message for the given command (and subcommand if given), ordisplays the list of all commands in the given category.CATEGORIESall All commandssession Manage your login sessionfs Navigate and organize your projects and filesdata View, download, and upload datametadata View and modify metadata for projects, data, and executionsworkflow View and modify workflowsexec Manage and run apps, applets, and workflowsorg Administer and operate on orgsother Miscellaneous advanced utilitiesEXAMPLETo find all commands related to running and monitoring a job and then displaythe 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 thelist of all available commands for the given categorysubcommand Display the help message for the given subcommand ofthe commandoptional arguments:-h, --help show this help message and exit
usage: dx command ... [--apiserver-host APISERVER_HOST][--apiserver-port APISERVER_PORT][--apiserver-protocol APISERVER_PROTOCOL][--project-context-id PROJECT_CONTEXT_ID][--workspace-id WORKSPACE_ID][--security-context SECURITY_CONTEXT][--auth-token AUTH_TOKEN]optional arguments:--apiserver-host APISERVER_HOSTAPI server host--apiserver-port APISERVER_PORTAPI server port--apiserver-protocol APISERVER_PROTOCOLAPI server protocol (http or https)--project-context-id PROJECT_CONTEXT_IDDefault project or project context ID--workspace-id WORKSPACE_IDWorkspace ID (for jobs only)--security-context SECURITY_CONTEXTJSON string of security context--auth-token AUTH_TOKENAuthentication token
Manage your login session
usage: dx login [-h] [--env-help] [--token TOKEN] [--noprojects] [--save][--timeout TIMEOUT]Log in interactively and acquire credentials. Use "--token" to log in with anexisting 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 futuresessions--timeout TIMEOUT Timeout for this login token (in seconds, or use suffixs, m, h, d, w, M, y)
usage: dx logout [-h] [--env-help] [--host HOST] [--port PORT][--protocol PROTOCOL]Log out and remove credentialsoptional arguments:-h, --help show this help message and exit--env-help Display help message for overriding environmentvariables--host HOST Log out of the given auth server host (port must alsobe given)--port PORT Log out of the given auth server port (host must alsobe given)--protocol PROTOCOL Used in conjunction with host and port arguments, givesthe protocol to use when contacting auth server
usage: dx exit [-h]Exit out of the interactive shelloptional arguments:-h, --help show this help message and exit
usage: dx whoami [-h] [--env-help] [--id]Print the username of the current user, in the form "user-USERNAME"optional arguments:-h, --help show this help message and exit--env-help Display help message for overriding environment variables--id Print user ID instead of username
usage: dx env [-h] [--env-help] [--bash] [--dx-flags]Prints all environment variables in use as they have been resolved fromenvironment variables and configuration files. For more details, seehttps://documentation.dnanexus.com/user/helpstrings-of-sdk-command-line-utilities#overriding-environment-variablesoptional arguments:-h, --help show this help message and exit--env-help Display help message for overriding environmentvariables--bash Prints a list of bash commands to export the environmentvariables--dx-flags Prints the dx options to override the environment variables
usage: dx clearenv [-h] [--reset]Clears all environment variables set by dx. More specifically, it removeslocal state stored in ~/.dnanexus_config/environment. Does not affect theenvironment 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 toavoid interference between multiple dx sessions when using shellenvironment variables.
Navigate and organize your projects and files
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 folderpositional arguments:path Folder (possibly in another project) to list thecontents of, default is the current directory in thecurrent project. Syntax: projectID:/folder/pathoptional arguments:-h, --help show this help message and exit--color {off,on,auto}Set when color is used (color=auto is used when stdoutis a TTY)--delimiter [DELIMITER], --delim [DELIMITER]Always use exactly one of DELIMITER to separate fieldsto be printed; if no delimiter is provided with thisflag, TAB will be used--env-help Display help message for overriding environmentvariables--brief Display a brief version of the return value; for mostcommands, prints a DNAnexus ID per line--verbose If available, displays extra verbose output-a, --all show hidden files-l, --long Alias for "verbose"--obj show only objects--folders show only folders--full show full paths of folders
usage: dx tree [-h] [--color {off,on,auto}] [--env-help] [-a] [-l] [path]List folders and objects in a treepositional arguments:path Folder (possibly in another project) to list thecontents of, default is the current directory in thecurrent project. Syntax: projectID:/folder/pathoptional arguments:-h, --help show this help message and exit--color {off,on,auto}Set when color is used (color=auto is used when stdoutis a TTY)--env-help Display help message for overriding environmentvariables-a, --all show hidden files-l, --long use a long listing format
usage: dx pwd [-h] [--env-help]Print current working directoryoptional arguments:-h, --help show this help message and exit--env-help Display help message for overriding environment variables
usage: dx select [-h] [--env-help] [--name NAME][--level {VIEW,UPLOAD,CONTRIBUTE,ADMINISTER}] [--public][project]Interactively list and select a project to switch to. By default, only listsprojects for which you have at least CONTRIBUTE permissions. Use --public tosee the list of public projects.positional arguments:project Name or ID of a project to switch to; if not provideda list will be provided for youoptional arguments:-h, --help show this help message and exit--env-help Display help message for overriding environmentvariables--name NAME Name of the project (wildcard patterns supported)--level {VIEW,UPLOAD,CONTRIBUTE,ADMINISTER}Minimum level of permissions expected--public Include ONLY public projects (will automatically set--level to VIEW)
usage: dx cd [-h] [--env-help] [path]Change the current working directorypositional arguments:path Folder (possibly in another project) to which to change thecurrent working directory, default is "/" in the current projectoptional arguments:-h, --help show this help message and exit--env-help Display help message for overriding environment variables
usage: dx cp [-h] [--env-help] [-a] source [source ...] destinationCopy objects and/or folders between different projects. Folders willautomatically be copied recursively. To specify which project to use as asource or destination, prepend the path or ID of the object/folder with theproject ID or name and a colon.EXAMPLESThe first example copies a file in a project called "FirstProj" to thecurrent directory of the current project. The second example copies theobject 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.gzpositional arguments:source Objects and/or folder names to copydestination Folder into which to copy the sources or new pathname (if onlyone source is provided). Must be in a differentproject/container than all source paths.optional arguments:-h, --help show this help message and exit--env-help Display help message for overriding environmentvariables-a, --all Apply to all results with the same name withoutprompting
usage: dx mv [-h] [--env-help] [-a] source [source ...] destinationMove or rename data objects and/or folders inside a single project. To copydata between different projects, use 'dx cp' instead.positional arguments:source Objects and/or folder names to movedestination Folder into which to move the sources or new pathname (if onlyone source is provided). Must be in the same project/containeras all source paths.optional arguments:-h, --help show this help message and exit--env-help Display help message for overriding environmentvariables-a, --all Apply to all results with the same name withoutprompting
usage: dx mkdir [-h] [--env-help] [-p] path [path ...]Create a new folderpositional arguments:path Paths to folders to createoptional arguments:-h, --help show this help message and exit--env-help Display help message for overriding environment variables-p, --parents no error if existing, create parent directories as needed
usage: dx rmdir [-h] [--env-help] path [path ...]Remove a folderpositional arguments:path Paths to folders to removeoptional arguments:-h, --help show this help message and exit--env-help Display help message for overriding environment variables
usage: dx rm [-h] [--env-help] [-a] [-r] [-f] path [path ...]Remove data objects and folders.positional arguments:path Paths to removeoptional arguments:-h, --help show this help message and exit--env-help Display help message for overriding environment variables-a, --all Apply to all results with the same name without prompting-r, --recursive Recurse into a directory-f, --force Force removal of files
usage: dx rmproject [-h] [--env-help] [-y] [-q] project [project ...]Delete projects and all their associated datapositional arguments:project Projects to removeoptional arguments:-h, --help show this help message and exit--env-help Display help message for overriding environment variables-y, --yes Do not ask for confirmation-q, --quiet Do not print purely informational messages
View, download, and upload data
usage: dx describe [-h] [--json] [--color {off,on,auto}][--delimiter [DELIMITER]] [--env-help] [--details][--verbose] [--name] [--multi]pathDescribe a DNAnexus entity. Use this command to describe data objects by nameor ID, jobs, apps, users, organizations, etc. If using the "--json" flag, itwill thrown an error if more than one match is found (but if you would like aJSON 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 objectID; you may still get a result if you have access to a copy of the object insome other project, but if it exists in the specified project, its descriptionwill be returned.- When describing apps or applets, options marked as advanced inputs will behidden unless --verbose is providedpositional arguments:path Object ID or path to an object (possibly in anotherproject) 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 stdoutis a TTY)--delimiter [DELIMITER], --delim [DELIMITER]Always use exactly one of DELIMITER to separate fieldsto be printed; if no delimiter is provided with thisflag, TAB will be used--env-help Display help message for overriding environmentvariables--details Include details of data objects--verbose Include all possible metadata--name Only print the matching names, one per line--multi If the flag --json is also provided, then returns aJSON array of describe hashes of all matching results
usage: dx upload [-h] [--visibility {hidden,visible}] [--property KEY=VALUE][--type TYPE] [--tag TAG] [--details DETAILS] [-p][--brief | --verbose] [--env-help] [--path [PATH]] [-r][--wait] [--no-progress] [--buffer-size WRITE_BUFFER_SIZE][--singlethread]filename [filename ...]Upload local file(s) or directory. If "-" is provided, stdin will be usedinstead. By default, the filename will be used as its new name. If--path/--destination is provided with a path ending in a slash, the filenamewill be used, and the folder path will be used as a destination. If it doesnot end in a slash, then it will be used as the final name.positional arguments:filename Local file or directory to upload ("-" indicates stdininput); provide multiple times to upload multiplefiles or directoriesoptional arguments:-h, --help show this help message and exit--brief Display a brief version of the return value; for mostcommands, prints a DNAnexus ID per line--verbose If available, displays extra verbose output--env-help Display help message for overriding environmentvariables--path [PATH], --destination [PATH]DNAnexus path to upload file(s) to (default usescurrent 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_SIZESet the write buffer size (in bytes)--singlethread Enable singlethreaded uploadingmetadata arguments:--visibility {hidden,visible}Whether the object is hidden or not--property KEY=VALUE Key-value pair to add as a property; repeat asnecessary, e.g. "--property key1=val1 --propertykey2=val2"--type TYPE Type of the data object; repeat as necessary, e.g. "--type type1 --type type2"--tag TAG Tag of the data object; repeat as necessary, e.g. "--tag tag1 --tag tag2"--details DETAILS JSON to store as details-p, --parents Create any parent folders necessary
usage: dx download [-h] [--env-help] [-o OUTPUT] [-f] [-r] [-a][--no-progress] [--lightweight] [--unicode]path [path ...]Download the contents of a file object or multiple objects. Use "-o -" todirect the output to stdout.positional arguments:path Data object ID or name, or folder to downloadoptional arguments:-h, --help show this help message and exit--env-help Display help message for overriding environmentvariables-o OUTPUT, --output OUTPUTLocal filename or directory to be used ("-" indicatesstdout output); if not supplied or a directory isgiven, 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 remotefile signatures match. If the signatures do not matchthe local file will be overwritten.-r, --recursive Download folders recursively-a, --all If multiple objects match the input, download all ofthem--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 tostdout
usage: dx make_download_url [-h] [--duration DURATION] [--filename FILENAME]pathCreates a pre-authenticated link that can be used to download a file withoutlogging in.positional arguments:path Data object ID or name to accessoptional 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 savethe file as (default is the filename)
usage: dx cat [-h] [--env-help] [--unicode] path [path ...]positional arguments:path File ID or name(s) to print to stdoutoptional arguments:-h, --help show this help message and exit--env-help Display help message for overriding environment variables--unicode Display the characters as text/unicode when writing to stdout
usage: dx head [-h] [--color {off,on,auto}] [--env-help] [-n N] pathPrint the first part of a file. By default, prints the first 10 lines.positional arguments:path File ID or name to accessoptional arguments:-h, --help show this help message and exit--color {off,on,auto}Set when color is used (color=auto is used when stdoutis a TTY)--env-help Display help message for overriding environmentvariables-n N, --lines N Print the first N lines (default 10)
usage: dx new [-h] class ...Use this command with one of the available subcommands (classes) to create anew project or data object from scratch. Not all data types are supported. See'dx upload' for files and 'dx build' for applets.positional arguments:classuser Create a new user accountorg Create new non-billable orgproject Create a new projectrecord Create a new recordworkflow Create a new workflowoptional arguments:-h, --help show this help message and exit
usage: dx new project [-h] [--brief | --verbose] [--env-help][--region REGION] [-s] [--bill-to BILL_TO] [--phi][name]Create a new projectpositional arguments:name Name of the new projectoptional arguments:-h, --help show this help message and exit--brief Display a brief version of the return value; for mostcommands, 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 bebilled. The default value is the billTo of the requestinguser.--phi Add PHI protection to project
usage: dx new record [-h] [--visibility {hidden,visible}][--property KEY=VALUE] [--type TYPE] [--tag TAG][--details DETAILS] [-p] [--brief | --verbose][--env-help] [--init INIT] [--close][path]Create a new recordpositional arguments:path DNAnexus path for the new data object (default usescurrent 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 mostcommands, prints a DNAnexus ID per line--verbose If available, displays extra verbose output--env-help Display help message for overriding environmentvariables--init INIT Path to record from which to initialize all metadata--close Close the record immediately after creating itmetadata arguments:--visibility {hidden,visible}Whether the object is hidden or not--property KEY=VALUE Key-value pair to add as a property; repeat asnecessary,e.g. "--property key1=val1 --property key2=val2"--type TYPE Type of the data object; repeat as necessary,e.g. "--type type1 --type type2"--tag TAG Tag of the data object; repeat as necessary,e.g. "--tag tag1 --tag tag2"--details DETAILS JSON to store as details-p, --parents Create any parent folders necessary
usage: dx new workflow [-h] [--visibility {hidden,visible}][--property KEY=VALUE] [--type TYPE] [--tag TAG][--details DETAILS] [-p] [--brief | --verbose][--env-help] [--title TITLE] [--summary SUMMARY][--description DESCRIPTION][--output-folder OUTPUT_FOLDER] [--init INIT][path]Create a new workflowpositional arguments:path DNAnexus path for the new data object (default usescurrent 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 mostcommands, prints a DNAnexus ID per line--verbose If available, displays extra verbose output--env-help Display help message for overriding environmentvariables--title TITLE Workflow title--summary SUMMARY Workflow summary--description DESCRIPTIONWorkflow description--output-folder OUTPUT_FOLDERDefault output folder for the workflow--init INIT Path to workflow or an analysis ID from which toinitialize all metadatametadata arguments:--visibility {hidden,visible}Whether the object is hidden or not--property KEY=VALUE Key-value pair to add as a property; repeat asnecessary,e.g. "--property key1=val1 --property key2=val2"--type TYPE Type of the data object; repeat as necessary,e.g. "--type type1 --type type2"--tag TAG Tag of the data object; repeat as necessary,e.g. "--tag tag1 --tag tag2"--details DETAILS JSON to store as details-p, --parents Create any parent folders necessary
usage: dx close [-h] [--env-help] [-a] [--wait] path [path ...]Close a remote data object or set of objects.positional arguments:path Path to a data object to closeoptional arguments:-h, --help show this help message and exit--env-help Display help message for overriding environment variables-a, --all Apply to all results with the same name without prompting--wait Wait for the object(s) to close
usage: dx wait [-h] [--env-help] [--from-file] path [path ...]Polls the state of specified data object(s) or job(s) until they are all inthe desired state. Waits until the "closed" state for a data object, and forany terminal state for a job ("terminated", "failed", or "done"). Exits with anon-zero code if a job reaches a terminal state that is not "done". Can alsoprovide a local file containing a list of data object(s) or job(s), one perline; 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 foroptional 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 inpath
usage: dx get [-h] [--env-help] [-o OUTPUT] [--filename FILENAME][--allow-all-files] [--recurse] [--no-ext] [--omit-resources][-f]pathDownload the contents of some types of data (records, apps, applets,workflows, files, and databases). Downloading an app, applet or a workflowwill attempt to reconstruct a source directory that can be used to rebuild itwith "dx build". Use "-o -" to direct the output to stdout.positional arguments:path Data object ID or name to accessoptional arguments:-h, --help show this help message and exit--env-help Display help message for overriding environmentvariables-o OUTPUT, --output OUTPUTlocal file path where the data is to be saved ("-"indicates stdout output for objects of class file andrecord). If not supplied, the object's name on theplatform will be used, along with any applicableextensions. For app(let) and workflow objects, ifOUTPUT does not exist, the object's source directorywill be created there; if OUTPUT is an existingdirectory, a new directory with the object's name willbe created inside it.--filename FILENAME When downloading from a database, name of the file orfolder to be downloaded. If omitted, all files in thedatabase will be downloaded, so use caution andinclude the --allow-all-files argument.--allow-all-files When downloading from a database, this allows allfiles in a database to be downloaded when --filenameargument is omitted.--recurse When downloading from a database, look for filesrecursively 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 thefilename--omit-resources When downloading an app(let), omit fetching theresources associated with the app(let).-f, --overwrite Overwrite the local file if necessary
usage: dx find data [-h] [--brief | --verbose] [--json][--color {off,on,auto}] [--delimiter [DELIMITER]][--env-help] [--property KEY[=VALUE]] [--tag TAG][--class {record,file,applet,workflow,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 allprojects (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 mostcommands, 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 stdoutis a TTY)--delimiter [DELIMITER], --delim [DELIMITER]Always use exactly one of DELIMITER to separate fieldsto be printed; if no delimiter is provided with thisflag, TAB will be used--env-help Display help message for overriding environmentvariables--property KEY[=VALUE]Key-value pair of a property or simply a property key;if only a key is provided, matches a result that hasthe 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, --allprojectsExtend search to all projects (excluding publicprojects)--path PROJECT:FOLDERProject and/or folder in which to restrict the results--norecurse Do not recurse into subfolders--created-after CREATED_AFTERDate (e.g. 2012-01-01) or integer timestamp afterwhich the object was created (negative number means msin the past, or use suffix s, m, h, d, w, M, y)Negative input example "--created-after=-2d"--created-before CREATED_BEFOREDate (e.g. 2012-01-01) or integer timestamp beforewhich the object was created (negative number means msin the past, or use suffix s, m, h, d, w, M, y)Negative input example "--created-before=-2d"--mod-after MOD_AFTERDate (e.g. 2012-01-01) or integer timestamp afterwhich the object was last modified (negative numbermeans ms in the past, or use suffix s, m, h, d, w, M,y) Negative input example "--mod-after=-2d"--mod-before MOD_BEFOREDate (e.g. 2012-01-01) or integer timestamp beforewhich the object was last modified (negative numbermeans ms in the past, or use suffix s, m, h, d, w, M,y) Negative input example "--mod-before=-2d"--region REGION Restrict the search to the provided region
usage: dx find projects [-h] [--brief | --verbose] [--json][--delimiter [DELIMITER]] [--env-help][--property KEY[=VALUE]] [--tag TAG][--phi {true,false}] [--name NAME][--level {VIEW,UPLOAD,CONTRIBUTE,ADMINISTER}][--public] [--created-after CREATED_AFTER][--created-before CREATED_BEFORE] [--region REGION]Finds projects subject to the given search parameters. Use the --public flagto list all public projects.optional arguments:-h, --help show this help message and exit--brief Display a brief version of the return value; for mostcommands, 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 fieldsto be printed; if no delimiter is provided with thisflag, TAB will be used--env-help Display help message for overriding environmentvariables--property KEY[=VALUE]Key-value pair of a property or simply a property key;if only a key is provided, matches a result that hasthe 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 datawill be retrieved. If set to false, only projects thatdo 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_AFTERDate (e.g. 2012-01-01) or integer timestamp afterwhich the project was created (negative number meansms in the past, or use suffix s, m, h, d, w, M, y)Negative input example "--created-after=-2d"--created-before CREATED_BEFOREDate (e.g. 2012-01-01) or integer timestamp afterwhich the project was created (negative number meansms 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
View and modify metadata for projects and data objects
See also dx describe and dx close.
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 modifydetails JSON to store as detailsoptional arguments:-h, --help show this help message and exit--env-help Display help message for overriding environmentvariables-a, --all Apply to all results with the same name withoutprompting-f DETAILS_FILE, --details-file DETAILS_FILEPath to local file containing JSON to store as details
usage: dx get_details [-h] [--env-help] pathGet the JSON details of a data object.positional arguments:path ID or path to data object to get details foroptional arguments:-h, --help show this help message and exit--env-help Display help message for overriding environment variables
usage: dx set_visibility [-h] [--env-help] [-a] path {hidden,visible}Set visibility on a data object.positional arguments:path ID or path to data object to modify{hidden,visible} Visibility that the object should haveoptional arguments:-h, --help show this help message and exit--env-help Display help message for overriding environment variables-a, --all Apply to all results with the same name without prompting
usage: dx add_types [-h] [--env-help] [-a] path type [type ...]Add types to a data object. Seehttps://documentation.dnanexus.com/developer/api/data-object-lifecycle/typesfor a list of DNAnexus types.positional arguments:path ID or path to data object to modifytype Types to addoptional arguments:-h, --help show this help message and exit--env-help Display help message for overriding environment variables-a, --all Apply to all results with the same name without prompting
usage: dx remove_types [-h] [--env-help] [-a] path type [type ...]Remove types from a data object. Seehttps://documentation.dnanexus.com/developer/api/data-object-lifecycle/typesfor a list of DNAnexus types.positional arguments:path ID or path to data object to modifytype Types to removeoptional arguments:-h, --help show this help message and exit--env-help Display help message for overriding environment variables-a, --all Apply to all results with the same name without prompting
usage: dx tag [-h] [--env-help] [-a] path tag [tag ...]Tag a project, data object, or execution. Note that a project context must beeither set or specified for data object IDs or paths.positional arguments:path ID or path to project, data object, or execution to modifytag Tags to addoptional arguments:-h, --help show this help message and exit--env-help Display help message for overriding environment variables-a, --all Apply to all results with the same name without prompting
usage: dx untag [-h] [--env-help] [-a] path tag [tag ...]Untag a project, data object, or execution. Note that a project context mustbe either set or specified for data object IDs or paths.positional arguments:path ID or path to project, data object, or execution to modifytag Tags to removeoptional arguments:-h, --help show this help message and exit--env-help Display help message for overriding environment variables-a, --all Apply to all results with the same name without prompting
usage: dx rename [-h] [--env-help] [-a] path nameRename a project or data object. To rename folders, use 'dx mv' instead. Notethat a project context must be either set or specified to rename a dataobject. 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 renamename New nameoptional arguments:-h, --help show this help message and exit--env-help Display help message for overriding environment variables-a, --all Apply to all results with the same name without prompting
usage: dx set_properties [-h] [--env-help] [-a]path propertyname=value [propertyname=value ...]Set properties of a project, data object, or execution. Note that a projectcontext must be either set or specified for data object IDs or paths.positional arguments:path ID or path to project, data object, or execution tomodifypropertyname=value Key-value pairs of property names and their new valuesoptional arguments:-h, --help show this help message and exit--env-help Display help message for overriding environmentvariables-a, --all Apply to all results with the same name withoutprompting
usage: dx unset_properties [-h] [--env-help] [-a]path propertyname [propertyname ...]Unset properties of a project, data object, or execution. Note that a projectcontext 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 modifypropertyname Property names to unsetoptional 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
Manage and run your apps, applets, and workflows
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] [-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 anapp from an existing applet in the platform. You can use dx-app-wizard togenerate a skeleton directory of an app/applet with the necessary files.positional arguments:src_dir App, applet, or workflow source directory (default:current directory)optional arguments:-h, --help show this help message and exit--env-help Display help message for overriding environmentvariables--brief Display a brief version of the return value; for mostcommands, prints a DNAnexus ID per line--verbose If available, displays extra verbose output--ensure-upload If specified, will bypass computing checksum ofresources directory and upload it unconditionally; bydefault, will compute checksum and upload only if itdiffers from a previously uploaded resources bundle.--force-symlinks If specified, will not attempt to dereference symboliclinks pointing outside of the resource directory. Bydefault, any symlinks within the resource directoryare kept as links while links to files outside theresource directory are dereferenced (note that linksto directories outside of the resource directory willcause an error).--app, --create-app Create an app.--workflow, --create-workflowCreate a workflow.--globalworkflow, --create-globalworkflowCreate a global workflow.--dry-run, -n Do not create an app(let): only perform local checksand compilation steps, and show the spec of theapp(let) that would have been created.--remote Build the app remotely by uploading the sourcedirectory to the DNAnexus Platform and building itthere. This option is useful if you would otherwiseneed to cross-compile the app(let) to target theExecution Environment.--no-watch Don't watch the real-time logs of the remote builder.(This option only applicable if --remote wasspecified).-v VERSION, --version VERSIONOverride the version number supplied in the manifest.--no-check-syntax Warn but do not fail when syntax problems are found(default is to fail on such errors)--no-dx-toolkit-autodepDo not auto-insert the dx-toolkit dependency (defaultis to add it if it would otherwise be absent from therunSpec)--no-parallel-build Build with make instead of make -jN.--extra-args EXTRA_ARGSArguments (in JSON format) to pass to the /applet/newAPI method, overriding all other settings--run ... Run the app or applet after building it (optionsfollowing this are passed to dx run; run at highpriority by default)--keep-open Do not close workflow after building it. Cannot beused when building apps, applets or global workflows.options for creating apps:(Only valid when --app/--create-app is specified)--publish Publish the resulting app and make it the default.--from _FROM ID of an applet to create an app from. Sourcedirectory cannot be given with this option-b USER_OR_ORG, --bill-to USER_OR_ORGEntity (of the form user-NAME or org-ORGNAME) to billfor the app.--no-version-autonumberingOnly attempt to create the version number supplied inthe manifest (that is, do not try to create anautonumbered version such as 1.2.3+git.ab1b1c1d if1.2.3 already exists and is published).--no-update Never update an existing unpublished app in place.-y, --yes Do not ask for confirmation for potentially dangerousoperations--region REGION Enable the app in this region. This flag can bespecified multiple times to enable the app in multipleregions. If --region is not specified, then theenabled region(s) will be determined by'regionalOptions' in dxapp.json, or the projectcontext.options for creating applets or workflows:(Only valid when --app/--create-app is NOT specified)-d DESTINATION, --destination DESTINATIONSpecifies the destination project, destination folder,and/or name for the applet, in the form[PROJECT_NAME_OR_ID:][/[FOLDER/][NAME]]. Overrides theproject, folder, and name fields of the dxapp.json ordxworkflow.json, if they were supplied.-f, --overwrite Remove existing applet(s) of the same name in thedestination folder. This option is not yet supportedfor workflows.-a, --archive Archive existing applet(s) of the same name in thedestination folder. This option is not yet supportedfor workflows.
usage: dx add users [-h] [--env-help] app authorizedUser [authorizedUser ...]Add users or orgs to the list of authorized users of an app. Publishedversions of the app will only be accessible to users represented by this listand to developers of the app. Unpublished versions are restricted to thedevelopers.positional arguments:app Name or ID of an appauthorizedUser One or more users or orgs to addoptional arguments:-h, --help show this help message and exit--env-help Display help message for overriding environment variables
usage: dx add developers [-h] [--env-help] app developer [developer ...]Add users or orgs to the list of developers for an app. Developers are able tobuild and publish new versions of the app, and add or remove others from thelist of developers and authorized users.positional arguments:app Name or ID of an appdeveloper One or more users or orgs to addoptional arguments:-h, --help show this help message and exit--env-help Display help message for overriding environment variables
usage: dx list users [-h] [--env-help] appList the authorized users of an app. Published versions of the app will onlybe accessible to users represented by this list and to developers of the app.Unpublished versions are restricted to the developerspositional arguments:app Name or ID of an appoptional arguments:-h, --help show this help message and exit--env-help Display help message for overriding environment variables
usage: dx list developers [-h] [--env-help] appList the developers for an app. Developers are able to build and publish newversions of the app, and add or remove others from the list of developers andauthorized users.positional arguments:app Name or ID of an appoptional arguments:-h, --help show this help message and exit--env-help Display help message for overriding environment variables
usage: dx remove users [-h] [--env-help]app authorizedUser [authorizedUser ...]Remove users or orgs from the list of authorized users of an app. Publishedversions of the app will only be accessible to users represented by this listand to developers of the app. Unpublished versions are restricted to thedeveloperspositional arguments:app Name or ID of an appauthorizedUser One or more users or orgs to removeoptional arguments:-h, --help show this help message and exit--env-help Display help message for overriding environment variables
usage: dx remove developers [-h] [--env-help] app developer [developer ...]Remove users or orgs from the list of developers for an app. Developers areable to build and publish new versions of the app, and add or remove othersfrom the list of developers and authorized users.positional arguments:app Name or ID of an appdeveloper One or more users to removeoptional arguments:-h, --help show this help message and exit--env-help Display help message for overriding environment variables
usage: dx publish [-h] [--no-default] executableRelease a version of the executable (app or global workflow) to authorizedusers.positional arguments:executable ID or name and version of an app/global workflow, e.g.myqc/1.0.0optional arguments:-h, --help show this help message and exit--no-default Do not set a "default" alias on the published version
usage: dx install [-h] [--env-help] appInstall an app by name. To see a list of apps you can install, hit <TAB> twiceafter "dx install" or run "dx find apps" to see a list of available apps.positional arguments:app ID or name of app to installoptional arguments:-h, --help show this help message and exit--env-help Display help message for overriding environment variables
usage: dx uninstall [-h] [--env-help] appUninstall an app by name.positional arguments:app ID or name of app to uninstalloptional arguments:-h, --help show this help message and exit--env-help Display help message for overriding environment variables
usage: dx run [-i INPUT] [-j INPUT_JSON] [-f FILENAME] [--brief | --verbose][--env-help] [--extra-args EXTRA_ARGS][--instance-type INSTANCE_TYPE_OR_MAPPING][--instance-type-help] [--property KEY=VALUE] [--tag TAG][-d DEPENDS_ON] [-h] [--clone CLONE] [--alias ALIAS][--destination PATH] [--batch-folders] [--project PROJECT][--stage-output-folder STAGE_ID FOLDER][--stage-relative-output-folder STAGE_ID FOLDER] [--name NAME][--delay-workspace-destruction] [--priority {normal,high}] [-y][--wait] [--watch] [--allow-ssh [ADDRESS]] [--ssh][--ssh-proxy <address>:<port>][--debug-on {AppError,AppInternalError,ExecutionError,All}][--ignore-reuse | --ignore-reuse-stage STAGE_ID][--rerun-stage STAGE_ID] [--batch-tsv FILE][--instance-count INSTANCE_COUNT_OR_MAPPING] [--input-help][--detach][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 findglobalworkflows" to see a list of available apps and global workflows.If any inputs are required but not specified, an interactive mode forselecting 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 forcomputers available to run executables.positional arguments:executable Name or ID of an applet, app, or workflow to run; mustbe provided if --clone is not setoptional arguments:-i INPUT, --input INPUTAn input to be added using "<inputname>[:<class>]=<input value>" (provide "class" ifthere 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 beattempted to be parsed as JSON and is otherwisetreated as a string)-j INPUT_JSON, --input-json INPUT_JSONThe full input JSON (keys=input field names,values=input field values)-f FILENAME, --input-json-file FILENAMELoad input JSON from FILENAME ("-" to use stdin)--brief Display a brief version of the return value; for mostcommands, prints a DNAnexus ID per line--verbose If available, displays extra verbose output--env-help Display help message for overriding environmentvariables--extra-args EXTRA_ARGSArguments (in JSON format) to pass to the underlyingAPI method, overriding the default settings--instance-type INSTANCE_TYPE_OR_MAPPINGSpecify instance type(s) for jobs this executable willrun; see --instance-type-help for more details--instance-type-help Print help for specifying instance types--property KEY=VALUE Key-value pair to add as a property; repeat asnecessary,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_ONID of job, analysis, or data object that must be inthe "done" or "closed" state, as appropriate, beforethis executable can be run; repeat as necessary (e.g."--depends-on id1 ... --depends-on idN"). Cannot besupplied when running workflows-h, --help show this help message and exit--clone CLONE Job or analysis ID or name from which to use asdefault options (will use the exact same executableID, destination project and folder, job input,instance type requests, and a similar name unlessexplicitly overridden by command-line arguments. Whenusing an analysis with --clone a workflow executablecannot be overriden and should not be provided.)--alias ALIAS, --version ALIASAlias (tag) or version of the app to run (default:"default" if an app)--destination PATH, --folder PATHThe full project:folder path in which to output theresults. By default, the current working directorywill be used.--batch-folders Output results to separate folders, one per batch,using batch ID as the name of the output folder. Thebatch output folder location will be relative to thepath set in --destination--project PROJECT Project name or ID in which to run the executable.This can also be specified together with the outputfolder in --destination.--stage-output-folder STAGE_ID FOLDERA stage identifier (ID, name, or index), and a folderpath to use as its output folder--stage-relative-output-folder STAGE_ID FOLDERA stage identifier (ID, name, or index), and arelative folder path to the workflow output folder touse as the output folder--name NAME Name for the job (default is the app or applet name)--delay-workspace-destructionWhether to keep the job's temporary workspace aroundfor debugging purposes for 3 days after it succeeds orfails--priority {normal,high}Request a scheduling priority for all resulting jobs. Will be overriden (set to high) when either --watch, --ssh, or --allow-ssh flags are used-y, --yes Do not ask for confirmation--wait Wait until the job is done before returning--watch Watch the job after launching it; sets --priority high--allow-ssh [ADDRESS]Configure the job to allow SSH access; sets --priorityhigh. If an argument is supplied, it is interpreted asan IP or hostname mask to allow connections from, e.g."--allow-ssh 1.2.3.4 --allow-ssh berkeley.edu"--ssh Configure the job to allow SSH access and connect toit after launching; sets --priority high--ssh-proxy <address>:<port>SSH connect via proxy, argument supplied is used asthe proxy address and port--debug-on {AppError,AppInternalError,ExecutionError,All}Configure the job to hold for debugging when any ofthe listed errors occur--ignore-reuse Disable job reuse for execution--ignore-reuse-stage STAGE_IDA stage (using its ID, name, or index) for which jobreuse should be disabled, if a stage points to another(nested) workflow the ignore reuse option will beapplied to the whole subworkflow. This optionoverwrites any ignoreReuse fields set on app(let)s orthe workflow during build time; repeat as necessary--rerun-stage STAGE_IDA stage (using its ID, name, or index) to rerun, or"*" to indicate all stages should be rerun; repeat asnecessary--batch-tsv FILE A file in tab separated value (tsv) format, with asubset of the executable input arguments. A job willbe launched for each table row.--instance-count INSTANCE_COUNT_OR_MAPPINGSpecify spark cluster instance count(s). It can be anint or a mapping of the format '{"entrypoint": <numberof instances>}'--input-help Print help and examples for how to specify inputs--detach When invoked from a job, detaches the new job from thecreator job so the new job will appear as a typicalroot execution. Setting DX_RUN_DETACH environmentvariable to 1 causes this option to be set by default.
Additional help on specifying inputs:
Help: Specifying input for dx runThere are several ways to specify inputs. In decreasing order of precedence,they are:1) inputs given in the interactive mode2) inputs listed individually with the -i/--input command line argument3) JSON given in --input-json4) JSON given in --input-json-file5) 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 specSPECIFYING INPUTS BY NAMEUse 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.gzThe example above runs an app called "myApp" with 3 inputs called num (classint), str (class string), and files (class array:file). (For this method towork, the app must have an input spec so inputs can be interpretedcorrectly.) The same input field can be used multiple times if the inputclass is an array.Job-based object references can also be provided using the <job id>:<outputname> syntax:Syntax : -i<input name>=<job id>:<output name>Example: dx run mapper -ireads=job-B0fbxvGY00j9jqGQvj8Q0001:readsYou can extract an element of an array output using the <job id>:<outputname>.<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 outputWhen executing workflows, stage inputs can be specified using the <stagekey>.<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 thenumber of the stage in the workflow (0 indicates first stage)If the workflow has explicit, workflow-level inputs, input values must bepassed to these workflow-level input fields using the <workflow inputname>=<value> syntax:Syntax : -i<workflow input name>=<input value>Example: dx run my_workflow -ireads="My reads file"SPECIFYING JSON INPUTJSON input can be used directly using the -j/--input-json or-f/--input-json-file flags. When running an app or applet, the keys shouldbe 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 thestage key and a period, e.g. "my_stage.reads" for the "reads" input of stage"my_stage".
usage: dx ssh [-h] [--env-help] [--ssh-proxy <address>:<port>] job_id ...Use an SSH client to connect to a job being executed on the DNAnexus platform.The job must be launched using "dx run --allow-ssh" or equivalent API options.Use "dx ssh_config" or the Profile page on the DNAnexus website to configureSSH for your DNAnexus account.positional arguments:job_id Name of job to connect tossh_args Command-line arguments to pass to the SSH clientoptional arguments:-h, --help show this help message and exit--env-help Display help message for overriding environmentvariables--ssh-proxy <address>:<port>SSH connect via proxy, argument supplied is used asthe proxy address and port
usage: dx ssh_config [-h] [--env-help] [--revoke] ...Configure SSH access credentials for your DNAnexus accountpositional arguments:ssh_keygen_args Command-line arguments to pass to ssh-keygenoptional 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 DNAnexusaccount; you will no longer be able to SSH into any jobs.
usage: dx watch [-h] [--env-help] [--color {off,on,auto}][-n NUM_RECENT_MESSAGES] [--tree][-l {EMERG,ALERT,CRITICAL,ERROR,WARNING,NOTICE,INFO,DEBUG,STDERR,STDOUT}][--get-stdout] [--get-stderr] [--get-streams][--no-timestamps] [--job-ids] [--no-job-info] [-q] [-f FORMAT][--no-wait]jobidMonitors logging output from a running jobpositional arguments:jobid ID of the job to watchoptional arguments:-h, --help show this help message and exit--env-help Display help message for overriding environmentvariables--color {off,on,auto}Set when color is used (color=auto is used when stdoutis a TTY)-n NUM_RECENT_MESSAGES, --num-recent-messages NUM_RECENT_MESSAGESNumber of recent messages to get--tree Include the entire job tree-l {EMERG,ALERT,CRITICAL,ERROR,WARNING,NOTICE,INFO,DEBUG,STDERR,STDOUT}, --levels {EMERG,ALERT,CRITICAL,ERROR,WARNING,NOTICE,INFO,DEBUG,STDERR,STDOUT}--get-stdout Extract stdout only from this job--get-stderr Extract stderr only from this job--get-streams Extract only stdout and stderr from this job--no-timestamps Omit timestamps from messages--job-ids Print job ID in each message--no-job-info Omit job info and status updates-q, --quiet Do not print extra info messages-f FORMAT, --format FORMATMessage format. Available fields: job, level, msg,date--no-wait, --no-followExit after the first new message is received, insteadof waiting for all logs
usage: dx terminate [-h] [--env-help] jobid [jobid ...]Terminate one or more jobs or analysespositional arguments:jobid ID of a job or analysis to terminateoptional arguments:-h, --help show this help message and exit--env-help Display help message for overriding environment variables
usage: dx find apps [-h] [--brief | --verbose] [--json][--delimiter [DELIMITER]] [--env-help] [--name NAME][--category CATEGORY] [--category-help] [-a][--unpublished] [--installed] [--billed-to BILLED_TO][--creator CREATOR] [--developer DEVELOPER][--created-after CREATED_AFTER][--created-before CREATED_BEFORE] [--mod-after MOD_AFTER][--mod-before MOD_BEFORE]Finds apps subject to the given search parameters. Use --category to restrictby a category; common categories are available as tab completions and can belisted with --category-help.optional arguments:-h, --help show this help message and exit--brief Display a brief version of the return value; for mostcommands, 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 fieldsto be printed; if no delimiter is provided with thisflag, TAB will be used--env-help Display help message for overriding environmentvariables--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 onlypublished apps)--installed Return only installed apps--billed-to BILLED_TOUser or organization responsible for the app--creator CREATOR Creator of the app version--developer DEVELOPERDeveloper of the app--created-after CREATED_AFTERDate (e.g. 2012-01-01) or integer timestamp afterwhich the app version was created (negative numbermeans ms in the past, or use suffix s, m, h, d, w, M,y) Negative input example "--created-after=-2d"--created-before CREATED_BEFOREDate (e.g. 2012-01-01) or integer timestamp beforewhich the app version was created (negative numbermeans ms in the past, or use suffix s, m, h, d, w, M,y) Negative input example "--created-before=-2d"--mod-after MOD_AFTERDate (e.g. 2012-01-01) or integer timestamp afterwhich the app was last modified (negative number meansms in the past, or use suffix s, m, h, d, w, M, y)Negative input example "--mod-after=-2d"--mod-before MOD_BEFOREDate (e.g. 2012-01-01) or integer timestamp beforewhich the app was last modified (negative number meansms in the past, or use suffix s, m, h, d, w, M, y)Negative input example "--mod-before=-2d"
usage: dx find jobs [-h] [--id ID] [--name NAME] [--user USER][--project PROJECT] [--all-projects] [--app EXECUTABLE][--state STATE] [--origin ORIGIN] [--parent PARENT][--created-after CREATED_AFTER][--created-before CREATED_BEFORE] [--no-subjobs][--root-execution ROOT_EXECUTION] [-n N] [-o][--brief | --verbose] [--json] [--color {off,on,auto}][--delimiter [DELIMITER]] [--env-help][--property KEY[=VALUE]] [--tag TAG][--trees | --origin-jobs | --all-jobs]Finds jobs subject to the given search parameters. By default, output isformatted to show the last several job trees that you've run in the currentproject.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 foryour own jobs)--project PROJECT Project context (output project), default is currentproject if set--all-projects, --allprojectsExtend search to all projects--app EXECUTABLE, --applet EXECUTABLE, --executable EXECUTABLEApplet 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_AFTERDate (e.g. 2012-01-01) or integer timestamp afterwhich the job was last created (negative number meansms in the past, or use suffix s, m, h, d, w, M, y)--created-before CREATED_BEFOREDate (e.g. 2012-01-01) or integer timestamp beforewhich the job was last created (negative number meansms 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_EXECUTIONExecution ID of the top-level (user-initiated) job oranalysis-n N, --num-results NMax number of results (trees or jobs, as according tothe search mode) to return (default 10)-o, --show-outputs Show job outputs in results--brief Display a brief version of the return value; for mostcommands, 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 stdoutis a TTY)--delimiter [DELIMITER], --delim [DELIMITER]Always use exactly one of DELIMITER to separate fieldsto be printed; if no delimiter is provided with thisflag, TAB will be used--env-help Display help message for overriding environmentvariables--property KEY[=VALUE]Key-value pair of a property or simply a property key;if only a key is provided, matches a result that hasthe 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 tagsSearch 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 (notree structure shown)
usage: dx generate_batch_inputs [-h] [-i INPUT] [--path PROJECT:FOLDER][-o OUTPUT_PREFIX]Generate a table of input files matching desired regular expressions for eachinput.optional arguments:-h, --help show this help message and exit-i INPUT, --input INPUTAn input to be batch-processed "-i<input name>=<inputpattern>" where <input_pattern> is a regularexpression with a group corresponding to the desiredregion to match (e.g. "-iinputa=SRR(.*)_1.gz""-iinputb=SRR(.*)_2.gz")--path PROJECT:FOLDERProject and/or folder to which the search for inputfiles will be restricted-o OUTPUT_PREFIX, --output_prefix OUTPUT_PREFIXPrefix for output file
Tools to help org admins manage their orgs
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_idGrant a user membership to an orgpositional arguments:org_id ID of the orgusername_or_user_id Username or ID of useroptional arguments:-h, --help show this help message and exit--brief Display a brief version of the return value; for mostcommands, prints a DNAnexus ID per line--verbose If available, displays extra verbose output--env-help Display help message for overriding environmentvariables--level {ADMIN,MEMBER}Org membership level that will be granted to thespecified user--allow-billable-activitiesGrant the specified user "allowBillableActivities" inthe 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 specifieduser will receive to projects explicitly shared withthe org; default CONTRIBUTE--no-email Disable org invitation email notification to thespecified user
usage: dx remove member [-h] [--brief | --verbose] [--env-help][--keep-explicit-project-permissions][--keep-explicit-app-permissions] [-y]org_id username_or_user_idRevoke the org membership of a userpositional arguments:org_id ID of the orgusername_or_user_id Username or ID of useroptional arguments:-h, --help show this help message and exit--brief Display a brief version of the return value; for mostcommands, prints a DNAnexus ID per line--verbose If available, displays extra verbose output--env-help Display help message for overriding environmentvariables--keep-explicit-project-permissionsDisable revocation of explicit project permissions ofthe specified user to projects billed to the org;implicit project permissions (i.e. those granted tothe specified user via his membership in this org)will always be revoked--keep-explicit-app-permissionsDisable revocation of explicit app developer and userpermissions of the specified user to apps billed tothe org; implicit app permissions (i.e. those grantedto the specified user via his membership in this org)will always be revoked-y, --yes Do not ask for confirmation
usage: dx update [-h] target ...Use this command with one of the available targets listed below to updatetheir metadata that are not covered by the other subcommands.positional arguments:targetorg Update information about an orgworkflow Update the metadata for a workflowstage Update the metadata for a stage in a workflowmember Update the membership of a user in an orgproject Updates a specified project with the specified optionsoptional arguments:-h, --help show this help message and exit
usage: dx update [-h] target ...Use this command with one of the available targets listed below to updatetheir metadata that are not covered by the other subcommands.positional arguments:targetorg Update information about an orgworkflow Update the metadata for a workflowstage Update the metadata for a stage in a workflowmember Update the membership of a user in an orgproject Updates a specified project with the specified optionsoptional arguments:-h, --help show this help message and exit
usage: dx find org [-h] entities ...List entities within a specific org.positional arguments:entitiesmembers List members in the specified orgprojects List projects billed to the specified orgapps List apps billed to the specified orgoptional arguments:-h, --help show this help message and exit
usage: dx find org [-h] entities ...List entities within a specific org.positional arguments:entitiesmembers List members in the specified orgprojects List projects billed to the specified orgapps List apps billed to the specified orgoptional arguments:-h, --help show this help message and exit
usage: dx find org [-h] entities ...List entities within a specific org.positional arguments:entitiesmembers List members in the specified orgprojects List projects billed to the specified orgapps List apps billed to the specified orgoptional arguments:-h, --help show this help message and exit
usage: dx find orgs [-h] [--brief | --verbose] [--env-help][--delimiter [DELIMITER]] [--json] --level {ADMIN,MEMBER}[--with-billable-activities | --without-billable-activities]Finds orgs subject to the given search parameters.optional arguments:-h, --help show this help message and exit--brief Display a brief version of the return value; for mostcommands, prints a DNAnexus ID per line--verbose If available, displays extra verbose output--env-help Display help message for overriding environmentvariables--delimiter [DELIMITER], --delim [DELIMITER]Always use exactly one of DELIMITER to separate fieldsto be printed; if no delimiter is provided with thisflag, TAB will be used--json Display return value in JSON--level {ADMIN,MEMBER}Restrict the result set to contain only orgs in whichthe requesting user has at least the specifiedmembership level--with-billable-activitiesRestrict the result set to contain only orgs in whichthe requesting user can perform billable activities;mutually exclusive with --without-billable-activities--without-billable-activitiesRestrict the result set to contain only orgs in whichthe requesting user **cannot** perform billableactivities; mutually exclusive with --with-billable-activities
Miscellaneous advanced utilities
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 aDNAnexus 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 yourcurrent default project.positional arguments:invitee Entity to inviteproject Project to invite the invitee to{VIEW,UPLOAD,CONTRIBUTE,ADMINISTER}Permissions level the new member should haveoptional arguments:-h, --help show this help message and exit--env-help Display help message for overriding environmentvariables--no-email Disable email notifications to invitee
usage: dx uninvite [-h] [--env-help] entity [project]Revoke others' permissions on a project you administer. If the entity is notrecognized as a DNAnexus ID, it will be treated as a username, i.e. "dxuninvite alice :" is equivalent to revoking the permissions of the user withuser ID "user-alice" to your current default project.positional arguments:entity Entity to uninviteproject Project to revoke permissions fromoptional arguments:-h, --help show this help message and exit--env-help Display help message for overriding environment variables
usage: dx api [-h] [--env-help] [--input INPUT] resource method [input_json]Call an API method directly. The JSON response from the API server will bereturned if successful. No name resolution is performed; DNAnexus IDs mustalways be provided. The API specification can be found athttps://documentation.dnanexus.com/developer/apiEXAMPLEIn 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 entityID such as "record-xxxx". Use "app-name/1.0.0" to refer toversion "1.0.0" of the app named "name".method Method name for the resource as documented by the APIspecificationinput_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 environmentvariables--input INPUT Load JSON input from FILENAME ("-" to use stdin)
usage: dx upgrade [-h] [args [args ...]]Upgrades dx-toolkit (the DNAnexus SDK and this program) to the latestrecommended version, or to a specified version and platform.positional arguments:argsoptional arguments:-h, --help show this help message and exit
Below is a list of some of the various command-line utilities available in the SDK and some brief documentation for their usage.
usage: dx [-h] [--version] command ...DNAnexus Command-Line Client, API v1.0.0, client v0.306.0dx is a command-line client for interacting with the DNAnexus platform. Youcan log in, navigate, upload, organize and share your data, launch analyses,and more. For a quick tour of what the tool can do, seehttps://documentation.dnanexus.com/getting-started/tutorials/cli-quickstart#quickstart-for-cliFor a breakdown of dx commands by category, run "dx help".dx exits with exit code 3 if invalid input is provided or an invalid operationis requested, and exit code 1 if an internal error is encountered. The latterusually indicate bugs in dx; please report them athttps://github.com/dnanexus/dx-toolkit/issuesoptional arguments:-h, --help show this help message and exit--env-help Display help message for overriding environmentvariables--version show program's version number and exit
usage: dx-app-wizard [-h] [--json-file JSON_FILE] [--language LANGUAGE][--template {basic,parallelized,scatter-process-gather}][name]Create a source code directory for a DNAnexus app. You will be prompted forvarious metadata for the app as well as for its input and outputspecifications.positional arguments:name Name of your appoptional arguments:-h, --help show this help message and exit--json-file JSON_FILEUse the metadata and IO spec found in the given file--language LANGUAGE Programming language of your app--template {basic,parallelized,scatter-process-gather}Execution pattern of your app
usage: dx-docker [-h] [-q] {pull,run,add-to-applet,create-asset} ...positional arguments:{pull,run,add-to-applet,create-asset}pull Pulls a docker image for use in DNAnexusrun Runs a docker image in a containeradd-to-applet Adds a local Docker image to an appletcreate-asset Caches a local Docker image as an asset in theDNAnexus platform (subject to change)optional arguments:-h, --help show this help message and exit-q, --quiet Suppress printing pull progress to stderr
usage: dx-fetch-bundled-depends [-h]Downloads the contents of runSpec.bundledDepends of a job running in theexecution environment.optional arguments:-h, --help show this help message and exit
usage: dx-generate-dxapp [-h] [-m TARGET_MODULE] [-f TARGET_FUNCTION][-x TARGET_EXECUTABLE] [-s SUBCOMMAND][-o OUTPUT_FILE][-p OUTPUT_PARAMS [OUTPUT_PARAMS ...]][-r OUTPUT_PARAM_REGEXP] [-n {bash,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_MODULEThe fully-qualified module that contains the targetmethod.-f TARGET_FUNCTION, --target-function TARGET_FUNCTIONThe main function that is called by the targetexecutable. This should bewhere the ArgumentParser isconfigured.-x TARGET_EXECUTABLE, --target-executable TARGET_EXECUTABLEThe name of the executable. This is used in thedxapp.json runSpec.-s SUBCOMMAND, --subcommand SUBCOMMANDSubcommand to pass to the target method, if required.-o OUTPUT_FILE, --output-file OUTPUT_FILEThe output dxapp.json file. If not specified, outputwill go to stdout.-p OUTPUT_PARAMS [OUTPUT_PARAMS ...], --output-params OUTPUT_PARAMS [OUTPUT_PARAMS ...]Names of output parameters (in case they can't beautodetected).-r OUTPUT_PARAM_REGEXP, --output-param-regexp OUTPUT_PARAM_REGEXPRegular expression that identifies output parameternames.-n {bash,python3}, --interpreter {bash,python3}Type of script that will wrap the executable.-i INSTANCE_TYPE, --instance-type INSTANCE_TYPEAWS instance type to use.-t TIMEOUT, --timeout TIMEOUTMax runtime of this app (in hours).--distribution DISTRIBUTIONDistribution to use for the machine image.--release RELEASE Distribution release to use for the machine image.--runspec-version RUNSPEC_VERSIONVersion of the application execution environmentinside the runSpec block.
usage: dx-jobutil-add-output [-h] [--class [CLASSNAME]] [--array] name valueReads and modifies job_output.json in your home directory to be a JSON hashwith key *name* and value *value*.If --class is not provided or is set to "auto", auto-detection of the outputformat will occur. In particular, it will treat it as a number, hash, orboolean if it can be successfully parsed as such. If it is a string whichmatches the pattern for a data object ID, it will encapsulate it in a DNAnexuslink hash; otherwise it is treated as a simple string.Use --array to append to an array of values or prepend "array:" to the --classargument.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 theautomatic parsing which will recognize anything starting with a job ID as ajob-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_outputAnalysis references can be specified similarly with --class=analysisref andformatted 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_outputpositional arguments:name Name of the output field namevalue Value of the output fieldoptional arguments:-h, --help show this help message and exit--class [CLASSNAME] Class of output for formatting purposes, e.g. "int";default "auto"--array Output field is an array
usage: dx-jobutil-dxlink [-h] objectCreates 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>}}, asappropriate.positional arguments:object Data object ID or "<Project ID>:<Data object ID>" to packageinto a DNAnexus linkoptional arguments:-h, --help show this help message and exit
usage: dx-jobutil-new-job [-h] [-i INPUT] [-j INPUT_JSON] [-f FILENAME][--instance-type INSTANCE_TYPE_OR_MAPPING][--instance-type-help] [--extra-args EXTRA_ARGS][--property KEY=VALUE] [--tag TAG] [--name NAME][--depends-on [JOB_OR_OBJECT_ID [JOB_OR_OBJECT_ID ...]]]functionCreates a new job to run the named function with the specified input. Ifsuccessful, prints the ID of the new job.positional arguments:function Name of the function to runoptional arguments:-h, --help show this help message and exit-i INPUT, --input INPUTAn input to be added using "<inputname>[:<class>]=<input value>" (provide "class" ifthere 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 beattempted to be parsed as JSON and is otherwisetreated as a string)-j INPUT_JSON, --input-json INPUT_JSONThe full input JSON (keys=input field names,values=input field values)-f FILENAME, --input-json-file FILENAMELoad input JSON from FILENAME ("-" to use stdin)--instance-type INSTANCE_TYPE_OR_MAPPINGSpecify instance type(s) for jobs this executable willrun; see --instance-type-help for more details--instance-type-help Print help for specifying instance types--extra-args EXTRA_ARGSArguments (in JSON format) to pass to the underlyingAPI method, overriding the default settings--property KEY=VALUE Key-value pair to add as a property; repeat asnecessary, e.g. "--property key1=val1 --propertykey2=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 closebefore the new job should be run. WARNING: For properparsing, do not use this flag directly before the*function* parameter.
usage: dx-jobutil-parse-link [-h] [--no-project] dxlinkParse a dxlink JSON hash into an object ID or project:object-id tuplepositional arguments:dxlink Link to parseoptional arguments:-h, --help show this help message and exit--no-project Ignore project ID in an extended dxlink - just print theobject ID
usage: dx-jobutil-report-error [-h] message [{AppInternalError,AppError}]Creates job_error.json in your home directory, a JSON file to include theerror type and message for the running job. There are two types of errors youmay 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 typeoptional arguments:-h, --help show this help message and exit
usage: dx-log-stream [-h] [-l {critical,error,warning,info,debug}][-s {DX_APP,DX_APP_STREAM}]Redirects stdin to a DNAnexus log socket in the execution environment.Valid logging levels:┌─────────────────────────┬────────────────┬────────────┐│ --source │ --level │ Appears as │├─────────────────────────┼────────────────┼────────────┤│ DX_APP_STREAM (default) │ info (default) │ STDOUT ││ DX_APP_STREAM (default) │ error │ STDERR │├─────────────────────────┼────────────────┼────────────┤│ DX_APP │ debug │ DEBUG ││ DX_APP │ info (default) │ INFO ││ DX_APP │ warning │ WARNING ││ DX_APP │ error │ ERROR ││ DX_APP │ critical │ CRITICAL │└─────────────────────────┴────────────────┴────────────┘optional arguments:-h, --help show this help message and exit-l {critical,error,warning,info,debug}, --level {critical,error,warning,info,debug}Logging level to use-s {DX_APP,DX_APP_STREAM}, --source {DX_APP,DX_APP_STREAM}Source ID to use
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, ifan 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.TXTIf an input is an array of files, then all files will be placed into numberedsubdirectories under a parent directory named for the input. For example, ifthe input key is FOO, and the inputs are {A, B, C}.vcf then, the directorystructure will be:$HOME/in/FOO/0/A.vcf1/B.vcf2/C.vcfZero padding is used to ensure argument order. For example, if there are 12input files {A, B, C, D, E, F, G, H, I, J, K, L}.txt, the directory structurewill be:$HOME/in/FOO/00/A.vcf...11/L.vcfThis allows using shell globbing (FOO/*/*.vcf) to get all the files in theinput order.optional arguments:-h, --help show this help message and exit--except EXCLUDE Do not mount the input with this name. (May be usedmultiple times.)--verbose Start dxfuse with '-verbose 2' logging
usage: dx-notebook-reconnect [-h] [--port PORT] job_idReconnect to a notebook jobpositional 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.
usage: dx-print-bash-vars [-h]Parses $HOME/job_input.json and prints the bash variables that would beavailable in the execution environment.optional arguments:-h, --help show this help message and exit
Usage: dx-verify-file [options] -r <remote_file1_id> -l <local_file1> [-r <remote_file2_id> -l <local_file2> ...]Available options:-h [ --help ] Produce a help message--version Print the version-e [ --env ] Print environment information-a [ --auth-token ] arg Specify the authentication token-r [ --remote-file ] arg ID of the remote file-l [ --local-file ] arg Local file path--read-threads arg (=1) Number of parallel disk read threads--md5-threads arg (=1) Number of parallel MD5 compute threads-v [ --verbose ] Verbose logging
usage: dx-download-all-inputs [-h] [--except EXCLUDE] [--parallel][--sequential]Note: this is a utility for use by bash apps running in the DNAnexus Platform.Downloads all files that were supplied as inputs to the app. By convention,if an input parameter "FOO" has value{"$dnanexus_link": "file-xxxx"}and filename INPUT.TXT, then the linked file will be downloaded into the path:$HOME/in/FOO/INPUT.TXTIf an input is an array of files, then all files will be placed into numberedsubdirectories under a parent directory named for the input. For example, ifthe input key is FOO, and the inputs are {A, B, C}.vcf then, the directorystructure will be:$HOME/in/FOO/0/A.vcf1/B.vcf2/C.vcfZero padding is used to ensure argument order. For example, if there are 12input files {A, B, C, D, E, F, G, H, I, J, K, L}.txt, the directory structurewill be:$HOME/in/FOO/00/A.vcf...11/L.vcfThis allows using shell globbing (FOO/*/*.vcf) to get all the files in theinput order.optional arguments:-h, --help show this help message and exit--except EXCLUDE Do not download the input with this name. (May be usedmultiple times.)--parallel Download the files in parallel--sequential Download the files sequentially
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 $HOME/out, as describedbelow. It also adds relevant entries into the job_output.json file.By convention, only directories with names equal to output parameter names areexpected to be found in the output directory, and any file(s) found in thosesubdirectories will be uploaded as the corresponding outputs. For example, afile with the path$HOME/out/FOO/OUTPUT.TXTwill be uploaded, and the key "FOO" will be added to the job_output.json filewith value{"$dnanexus_link": "file-xxxx"}where "file-xxxx" is the ID of the newly uploaded file. If multiple files arefound, they will be added as an array output (in unspecified order). Ifsubdirectories are found under $HOME/out/FOO, then they are uploaded in theirentirety to the workspace, and values are added to FOO in the job_output.jsonfile. For example, the path:$HOME/out/FOO/BAR/XXX.TXTwill 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 usedmultiple times.)--parallel Upload the files in parallel--sequential Upload the files sequentially--clearJSON CLEARJSONClears the output JSON file prior to starting upload.--wait-on-close Wait for files to close, default is not to wait--xattr-properties Get filesystem attributes and set them as properties on each file uploaded