$icaanalysisdatasetslist--helpGetalistofanalysisdatasetstowhichyouhaveaccess.Usage:icaanalysisdatasetslist [flags]Flags: --analysis-run-id strings optional parameter. Set to filter the analysis datasets list and only include analysis datasets associated with the provided analysis runs
-h,--helphelpforlist--includestringsincludeoptions--max-itemsintmaximumnumberofitemstoreturn,use0fornolimit (default 50) --page-size int32 optimizes listing operations by limiting the number of items retrieved with each API call (default 1000)
--page-tokenstringpagetokenusedforretrievingpagedlistresults--sort-bystringspecifiestheordertolistitems (default "timeCreated Desc")
completion
$icacompletion--helpGeneratesbashcompletionscriptstoloadcompletionrunthefollowingonabashshellprompt.<(icacompletion)Toconfigureyourbashshelltoloadcompletionsforeachsessionaddtoyourbashrc# ~/.bashrc or ~/.profile.<(icacompletion)Usage:icacompletion [flags]Flags:-h,--helphelpforcompletion
Archives a gds file. Files in archived, archiving or unarchiving state will not be included in filter for batch action.
Usage:icafilesarchive [file idorgdspath,orgdspathfilterforbatchaction] [flags]Flags:-h,--helphelpforarchive--tierstringstoragetier [archive, deepArchive] (default "archive")
DownloadthespecifiedfileUsage:icafilesdownload [file idorgdspath,orgdspathfilterforbatchaction] [local path] [flags]Flags:-h,--helphelpfordownload--num-workersintnumberofworkerstoparallelize.DefaultcalculatedbasedonCPUsavailable.--tenant-idstringtenantidentifieroftheresource(s) --tenant-name string Optional field to reference shared resources in another tenant, mapping config in ~./ica/.tenants.yaml
files get
Getfileinfo,includingpresignedurlUsage:icafilesget [file idorgdspath] [flags]Flags:-h,--helphelpforget--tenant-idstringtenantidentifieroftheresource(s) --tenant-name string Optional field to reference shared resources in another tenant, mapping config in ~./ica/.tenants.yaml
files list
Getalistoffilestowhichyouhaveaccess.Afilterpathisrequiredofformgds://{volumeName}/{path}Usage:icafileslist [gdspath touseasfilter] [flags]Flags:--aclstringsCommadelimitedlistofaclsonwhichtofilterthelist --archive-status string filter by archive status comma seperated list of any of [None, Archived, Archiving, Unarchiving]. Default includes all
-h,--helphelpforlist --is-uploaded string filter for files that have either been uploaded or are not yet uploaded [true or false]. Default includes all
--max-itemsintmaximumnumberofitemstoreturn,use0fornolimit (default 50) --nonrecursive Optional field to specify that resources should not be returned recursively in and under the specified paths. Only returns resources directly in the specified paths
--page-size int32 optimizes listing operations by limiting the number of items retrieved with each API call (default 1000)
--page-tokenstringpagetokenusedforretrievingpagedlistresults--sort-bystringspecifiestheordertolistitems (default "timeCreated Desc")--tenant-idstringtenantidentifieroftheresource(s) --tenant-name string Optional field to reference shared resources in another tenant, mapping config in ~./ica/.tenants.yaml
--with-accessreturnobjectstoreaccess
Copy a folder from a source folder to another existing parent folder. Folders should be of the form gds://{volumeName}/{path}.
Usage:icafolderscopy [source_folder gdspath] [target_parent_folder gdspath] [flags]Flags:-h,--helphelpforcopy--tenant-idstringtenantidentifieroftheresource(s) --tenant-name string Optional field to reference shared resources in another tenant, mapping config in ~/.ica/.tenants.yaml
Usage:icafoldersget [folder id] [flags]Flags:-h,--helphelpforget--tenant-idstringtenantidentifieroftheresource(s) --tenant-name string Optional field to reference shared resources in another tenant, mapping config in ~./ica/.tenants.yaml
Usage:icafolderslist [gdspath touseasfilter] [flags]Flags:--aclstringsCommadelimitedlistofaclsonwhichtofilterthelist-h,--helphelpforlist--max-itemsintmaximumnumberofitemstoreturn,use0fornolimit (default 50) --nonrecursive Optional field to specify that resources should not be returned recursively in and under the specified paths. Only returns resources directly in the specified paths
--page-size int32 optimizes listing operations by limiting the number of items retrieved with each API call (default 1000)
--page-tokenstringpagetokenusedforretrievingpagedlistresults--sort-bystringspecifiestheordertolistitems (default "timeCreated Desc")--tenant-idstringtenantidentifieroftheresource(s) --tenant-name string Optional field to reference shared resources in another tenant, mapping config in ~./ica/.tenants.yaml
ListalltoolsUsage:icaga4ghtrstoolslist [flags]Flags:--authorstringTheauthorofthetool--descriptionstringThedescriptionofthetool.-h,--helphelpforlist--idstringAuniqueidentifierofthetool,scopedtothisregistry--limitint32Amountofrecordstoreturninagivenpage.Bydefaultitis1000 (default 1000)--namestringThenameoftheimage. --offset string Start index of paging. Pagination results can be based on numbers or other values chosen by the registry implementor (for example, SHA values). If this exceeds the current result set return an empty set. If not specified in the request this will start at the beginning of the results.
--organizationstringTheorganizationintheregistrythatpublishedtheimage.--registrystringTheimageregistrythatcontainstheimage--toolnamestringuniqueidentifierofthetool,scopedtothisregistry
ga4gh trs tools versions
TherootcommandforGA4GH-compliantactionsthatactonthetoolversions.Usage:icaga4ghtrstoolsversions [flags]icaga4ghtrstoolsversions [command]AvailableCommands: descriptor Get the tool descriptor (CWL/WDL) for the specified tool. Get additional tool descriptor files (CWL/WDL) relative to the main file.
dockerfileGetthedockerfileforthespecifiedimage.getListonespecifictoolversion,actsasananchorforselfreferenceslistListversionsofatooltestsGetanarrayoftestJSONssuitableforusewiththisdescriptortype.Flags:-h,--helphelpforversions
ga4gh trs tools versions descriptor
Get the tool descriptor (CWL/WDL) for the specified tool. Get additional tool descriptor files (CWL/WDL) relative to the main file.
Usage:icaga4ghtrstoolsversionsdescriptor [tool id] [version id] [type] [optional relative-path] [flags]Flags:-h,--helphelpfordescriptor
Runaworkflow.Usage:icaga4ghwesrunscreate [flags]Flags:-h,--helphelpforcreate --workflow-attachment stringArray The workflow_attachment array may be used to upload files that are required to execute the workflow, including the primary workflow, tools imported by the workflow, other files referenced by the workflow, or files which are part of the input. Specify one flag for each file to include.
--workflow-engine-parametersstring --workflow-params string The workflow_params JSON object specifies input parameters, such as input files. The exact format of the JSON object depends on the conventions of the workflow language being used. Input files should either be absolute URLs, or relative URLs corresponding to files uploaded using workflow_attachment.
--workflow-type string The workflow_type is the type of workflow language and must be CWL or WDL currently (or another alternative supported by this WES instance).
--workflow-type-version string The workflow_type_version is the version of the workflow language submitted and must be one supported by this WES instance.
--workflow-url string The workflow_url is either an absolute URL to a workflow file that is accessible by the WES endpoint, or a relative URL corresponding to one of the files attached using workflow_attachment
List the workflow runs
Usage:
ica ga4gh wes runs list [flags]
Flags:
-h, --help help for list
--page-size int The preferred number of workflow runs to return in a page (default 10)
--page-token string Token to use to indicate where to start getting results. If unspecified, return the first page of results.
ga4gh wes runs status
Get quick status info about a workflow run
Usage:
ica ga4gh wes runs status [flags]
Flags:
-h, --help help for status
ga4gh wes service-info
Get information about the GA4GH-compliant Workflow Execution Service
Usage:
ica ga4gh wes service-info [flags]
Flags:
-h, --help help for service-info
help
Help provides help for any command in the application.
Simply type ica help [path to command] for full details.
Usage:
ica help [command] [flags]
Flags:
-h, --help help for help
login
This command logs the end user into the cli and starts their session. User can use their credentials or pass a session token they have already obtained.
Usage:
ica login [username] [flags]
Flags:
--api-key string api-key for authentication
--auth-url string single-sign on authentication server address (default "login.illumina.com")
-d, --domain string Optionally pass the domain name you are logging into
-h, --help help for login
--local-port int local port for single-sign on authentication flow (default 8282)
--project-id string project ID to set current project context
--project-name string project name to set current project context
--session-token string session token for authentication
--sso use single-sign on
--workgroup-id string workgroup ID to set current workgroup context
--workgroup-name string workgroup name to set current workgroup context
logout
This command logs the end user out of the cli by revoking the session. Additionally, it will prompt the user to revoke and remove the JWT token from the session config
Usage:
ica logout [flags]
Flags:
-h, --help help for logout
projects
This is the root command for actions that act on projects
Usage:
ica projects [flags]
ica projects [command]
Available Commands:
enter Enter project context
exit Exit project context
list List projects
Flags:
-h, --help help for projects
--page-token string page token used for retrieving paged list results
projects enter
This command sets the user to the project context.
Usage:
ica projects enter [project name] [flags]
Flags:
-h, --help help for enter
--session-token string session token for authentication
projects exit
This command switches the user back to their personal context
Usage:
ica projects exit [flags]
Flags:
-h, --help help for exit
--session-token string session token for authentication
projects list
This command lists the projects for the current user
Usage:
ica projects list [flags]
Flags:
-h, --help help for list
samples
The root command for actions that act on samples in GSS
Usage:
ica samples [flags]
ica samples [command]
Available Commands:
analysisdatasets Get list of analysisdatasets for a sample
get Get sample info
list Get list of samples
registerdata Register data for a sample
Flags:
-h, --help help for samples
samples analysisdatasets
Get a list of analysis datasets for a samples to which you have access.
Usage:
ica samples analysisdatasets [sample id] [flags]
Flags:
-h, --help help for analysisdatasets
--include strings include options
--max-items int maximum number of items to return, use 0 for no limit (default 50)
--page-size int32 optimizes listing operations by limiting the number of items retrieved with each API call (default 1000)
--page-token string page token used for retrieving paged list results
--sort-by string specifies the order to list items (default "timeCreated Desc")
--type strings analysis dataset types requested
samples get
Get sample info
Usage:
ica samples get [sample id] [flags]
Flags:
-h, --help help for get
samples list
Get a list of samples to which you have access.
Usage:
ica samples list [flags]
Flags:
-h, --help help for list
--max-items int maximum number of items to return, use 0 for no limit (default 50)
--name string filter by name
--page-size int32 optimizes listing operations by limiting the number of items retrieved with each API call (default 1000)
--page-token string page token used for retrieving paged list results
--project-name string filter by projectName
--sort-by string specifies the order to list items (default "timeCreated Desc")
samples registerdata
Register data for a sample
Usage:
ica samples registerdata [flags]
Flags:
--analysis-datasets string path to JSON list of one or more analysis datasets that should be associated with the analysis
--external-analysis-run-id string Optional external ID for the analysis run
--external-project-id string optional external ID for the project associated with the sample (only when a new sample is being created)
--external-sample-id string optional external ID to associate with the sample (only when a new sample is being created)
-h, --help help for registerdata
--project-name string projectName of the sample (when IDentifying sample by Name+ProjectName)
--sample-id string optional Sample ID of the sample (if name based matching is not being used)
--sample-name string optional name of the sample (when IDentifying sample by Name+ProjectName)
--skip-copy-files-to-project-volume optional. If true, skip copying files to the project volume if the ProjectName matches a known project context
--total-dataset-count int32 total number of datasets that are being registered as part of the same ExternalAnalysisRunId
--total-sample-count int32 total number of samples that are being registered as part of the same ExternalAnalysisRunId
subscriptions
The root command for actions that act on subscriptions in ENS.
Usage:
ica subscriptions [flags]
ica subscriptions [command]
Available Commands:
create Create a subscription
delete Delete subscription info
get Get subscription info
list Get list of subscriptions
Flags:
-h, --help help for subscriptions
subscriptions create
Create a subscription in ENS
Usage:
ica subscriptions create [optional path to createSubscriptionRequest] [flags]
Flags:
--actions strings Actions which will be subscribed to for the event type
--aws-sns-topic string ARN for the AWS SNS topic
--aws-sqs-queue string URL for the AWS SQS queue
--description string Optional description for the subscription
--filter-expression string JSON-structured filter expression for events matching the subscription
-h, --help help for create
--name string Name of the subscription
--type string Event type which will be subscribed to
--workflow-id string ID of the workflow to launch
--workflow-run-input string Input for the workflow run
--workflow-run-name string Name for the workflow run
--workflow-version string Version of the workflow to launch
subscriptions delete
Get subscription info
Usage:
ica subscriptions get [subscription id] [flags]
Flags:
-h, --help help for get
subscriptions get
Get subscription info
Usage:
ica subscriptions get [subscription id] [flags]
Flags:
-h, --help help for get
subscriptions list
Get a list of subscriptions to which you have access.
Usage:
ica subscriptions list [flags]
Flags:
--event-type string filter by event type
-h, --help help for list
--max-items int maximum number of items to return, use 0 for no limit (default 50)
--page-size int32 optimizes listing operations by limiting the number of items retrieved with each API call (default 1000)
--page-token string page token used for retrieving paged list results
--sort-by string specifies the order to list items (default "timeCreated Desc")
tasks
The root command for commands that act on tasks in TES
Usage:
ica tasks [flags]
ica tasks [command]
Available Commands:
create Create a task
get Get task info
list Get list of tasks
runs Task Run actions
update Update a task
versions Task Version actions
Flags:
-h, --help help for tasks
tasks create
Create a task in TES
Usage:
ica tasks create [optional path to createTaskRequest] [flags]
Flags:
--description string description of the task
-h, --help help for create
--name string name of the task
tasks get
Get task info
Usage:
ica tasks get [task id] [flags]
Flags:
-h, --help help for get
tasks list
Get a list of tasks to which you have access.
Usage:
ica tasks list [flags]
Flags:
-h, --help help for list
--max-items int maximum number of items to return, use 0 for no limit (default 50)
--page-size int32 optimizes listing operations by limiting the number of items retrieved with each API call (default 1000)
--page-token string page token used for retrieving paged list results
--sort-by string specifies the order to list items (default "timeCreated Desc")
tasks runs
The root command for actions that act on task runs in TES
Usage:
ica tasks runs [flags]
ica tasks runs [command]
Available Commands:
abort Abort a task run
create Create and launch a single instance of a task run
get Get information for a specific task run
list Get list of task runs
list Get list of task runs
logs Download log files generated by a task run
output List output directories for a specific task run
Flags:
-h, --help help for runs
tasks runs abort
Abort a task run
Usage:
ica tasks runs abort [task run id] [flags]
Flags:
-h, --help help for abort
tasks runs create
Create and launch a single instance of a task run
Usage:
ica tasks runs create [path to json CreateTaskRunRequest or pipe json to command] [flags]
Flags:
--description string description of the task run
--execution string path to the execution details of the task run
-h, --help help for create
--name string name of the task run
tasks runs get
Get information for a specific task run
Usage:
ica tasks runs get [task run id] [flags]
Flags:
-h, --help help for get
tasks runs list
Get list of task runs
Usage:
ica tasks runs list [flags]
Flags:
-h, --help help for list
--max-items int maximum number of items to return, use 0 for no limit (default 50)
--page-size int32 optimizes listing operations by limiting the number of items retrieved with each API call (default 1000)
--page-token string page token used for retrieving paged list results
--sort-by string specifies the order to list items (default "timeCreated Desc")
--status string filter by status
tasks runs logs
Download log files generated by a task run to the destination folder
Usage:
ica tasks runs logs [task run id] [dest path] [flags]
Flags:
-h, --help help for logs
tasks runs output
List output directories for a specific task run
Usage:
ica tasks runs output [task run id] [flags]
Flags:
-h, --help help for output
tasks update
Update a task in TES
Usage:
ica tasks update [task id] [optional path to updateTaskRequest] [flags]
Flags:
--description string description of the task
-h, --help help for update
--name string name of the task
tasks versions
The root command for actions that act on task version in TES
Usage:
ica tasks versions [flags]
ica tasks versions [command]
Available Commands:
create Create a new version for a specified task
get Get information for a specific task and version
launch Launches a specific task version with the specified arguments
list Get list of versions for a given task
update Update a version for a specified task
Flags:
-h, --help help for versions
tasks versions create
Create a new version for a specified task
Usage:
ica tasks versions create [task id] [optional path to createTaskVersionRequest] [flags]
Flags:
--description string description of the task version
--execution string path to execution details of the task version
-h, --help help for create
--version string version name of the task version
tasks versions get
Get information for a specific task and version
Usage:
ica tasks versions get [task id] [version id] [flags]
Flags: