Command Index

icav2

Command line interface for the Illumina Connected Analytics, a genomics platform-as-a-service

Usage:
  icav2 [command]

Available Commands:
  analysisstorages      Analysis storages commands
  completion            generate the autocompletion script for the specified shell
  config                Config actions
  dataformats           Data format commands
  help                  Help about any command
  metadatamodels        Metadata model commands
  pipelines             Pipeline commands
  projectanalyses       Project analyses commands
  projectdata           Project Data commands
  projectpipelines      Project pipeline commands
  projects              Project commands
  projectsamples        Project samples commands
  regions               Region commands
  storagebundles        Storage bundle commands
  storageconfigurations Storage configurations commands
  tokens                Tokens commands
  version               The version of this application

Flags:
  -t, --access-token string    JWT used to call rest service
  -h, --help                   help for icav2
  -o, --output-format string   output format (default "table")
  -s, --server-url string      server url to direct commands
  -v, --version                version for icav2
  -k, --x-api-key string       api key used to call rest service

Use "icav2 [command] --help" for more information about a command.

icav2 analysisstorages

This is the root command for actions that act on analysis storages

Usage:
  icav2 analysisstorages [command]

Available Commands:
  list        list of storage id's

Flags:
  -h, --help   help for analysisstorages

Global Flags:
  -t, --access-token string    JWT used to call rest service
  -o, --output-format string   output format (default "table")
  -s, --server-url string      server url to direct commands
  -k, --x-api-key string       api key used to call rest service

Use "icav2 analysisstorages [command] --help" for more information about a command.

icav2 analysisstorages list

This command lists all the analysis storage id's

Usage:
  icav2 analysisstorages list [flags]

Flags:
  -h, --help   help for list

Global Flags:
  -t, --access-token string    JWT used to call rest service
  -o, --output-format string   output format (default "table")
  -s, --server-url string      server url to direct commands
  -k, --x-api-key string       api key used to call rest service

icav2 completion

This command generates custom completion functions for icav2 tool. These functions facilitate the generation of context-aware suggestions based on the user's input and specific directives provided by the icav2 tool. For example, for ZSH shell the completion function _icav2() is generated. It could provide suggestions for available commands, flags, and arguments depending on the context, making it easier for the user to interact with the tool without having to constantly refer to documentation.

To enable this custom completion function, you would typically include it in your Zsh configuration (e.g., in .zshrc or a separate completion script) and then use the compdef command to associate the function with the icav2 command:

compdef _icav2 icav2

This way, when the user types icav2 followed by a space and presses the TAB key, Zsh will call the _icav2 function to provide context-aware suggestions based on the user's input and the icav2 tool's directives.


Generate the autocompletion script for icav2 for the specified shell.
See each sub-command's help for details on how to use the generated script.

Usage:
  icav2 completion [command]

Available Commands:
  bash        generate the autocompletion script for bash
  fish        generate the autocompletion script for fish
  powershell  generate the autocompletion script for powershell
  zsh         generate the autocompletion script for zsh

Flags:
  -h, --help   help for completion

Global Flags:
  -t, --access-token string    JWT used to call rest service
  -o, --output-format string   output format (default "table")
  -s, --server-url string      server url to direct commands
  -k, --x-api-key string       api key used to call rest service

Use "icav2 completion [command] --help" for more information about a command.

icav2 completion bash


Generate the autocompletion script for the bash shell.

This script depends on the 'bash-completion' package.
If it is not installed already, you can install it via your OS's package manager.

To load completions in your current shell session:
$ source <(icav2 completion bash)

To load completions for every new session, execute once:
Linux:
  $ icav2 completion bash > /etc/bash_completion.d/icav2
MacOS:
  $ icav2 completion bash > /usr/local/etc/bash_completion.d/icav2

You will need to start a new shell for this setup to take effect.

Usage:
  icav2 completion bash

Flags:
  -h, --help              help for bash
      --no-descriptions   disable completion descriptions

Global Flags:
  -t, --access-token string    JWT used to call rest service
  -o, --output-format string   output format (default "table")
  -s, --server-url string      server url to direct commands
  -k, --x-api-key string       api key used to call rest service

icav2 completion fish


Generate the autocompletion script for the fish shell.

To load completions in your current shell session:
$ icav2 completion fish | source

To load completions for every new session, execute once:
$ icav2 completion fish > ~/.config/fish/completions/icav2.fish

You will need to start a new shell for this setup to take effect.

Usage:
  icav2 completion fish [flags]

Flags:
  -h, --help              help for fish
      --no-descriptions   disable completion descriptions

Global Flags:
  -t, --access-token string    JWT used to call rest service
  -o, --output-format string   output format (default "table")
  -s, --server-url string      server url to direct commands
  -k, --x-api-key string       api key used to call rest service

icav2 completion powershell


Generate the autocompletion script for powershell.

To load completions in your current shell session:
PS C:\> icav2 completion powershell | Out-String | Invoke-Expression

To load completions for every new session, add the output of the above command
to your powershell profile.

Usage:
  icav2 completion powershell [flags]

Flags:
  -h, --help              help for powershell
      --no-descriptions   disable completion descriptions

Global Flags:
  -t, --access-token string    JWT used to call rest service
  -o, --output-format string   output format (default "table")
  -s, --server-url string      server url to direct commands
  -k, --x-api-key string       api key used to call rest service

icav2 completion zsh


Generate the autocompletion script for the zsh shell.

If shell completion is not already enabled in your environment you will need
to enable it.  You can execute the following once:

$ echo "autoload -U compinit; compinit" >> ~/.zshrc

To load completions for every new session, execute once:
# Linux:
$ icav2 completion zsh > "${fpath[1]}/ icav2"
# macOS:
$ icav2 completion zsh > /usr/local/share/zsh/site-functions/ icav2

You will need to start a new shell for this setup to take effect.

Usage:
  icav2 completion zsh [flags]

Flags:
  -h, --help              help for zsh
      --no-descriptions   disable completion descriptions

Global Flags:
  -t, --access-token string    JWT used to call rest service
  -o, --output-format string   output format (default "table")
  -s, --server-url string      server url to direct commands
  -k, --x-api-key string       api key used to call rest service

icav2 config

Config command provides functions for CLI configuration management.

Usage:
  icav2 config [command]

Available Commands:
  get         Get configuration information
  reset       Remove the configuration information
  set         Set configuration information

Flags:
  -h, --help   help for config

Global Flags:
  -t, --access-token string    JWT used to call rest service
  -o, --output-format string   output format (default "table")
  -s, --server-url string      server url to direct commands
  -k, --x-api-key string       api key used to call rest service

Use "icav2 config [command] --help" for more information about a command.

icav2 config get

Get configuration information.

Usage:
  icav2 config get [flags]

Flags:
  -h, --help   help for get

icav2 config reset

Remove configuration information.

Usage:
  icav2 config reset [flags]

Flags:
  -h, --help   help for reset

icav2 config set

Set configuration information. Following information is asked when starting the command : 

 - server-url : used to form the url for the rest api's. 
 - x-api-key : api key used to fetch the JWT used to authenticate to the API server. 
 - colormode : set depending on your background color of your terminal. Input's and errors are colored. Default is 'none', meaning that no colors will be used in the output.
 - table-format : Output layout, defaults to a table, other allowed values are json and yaml

Usage:
  icav2 config set [flags]

Flags:
  -h, --help   help for set

icav2 dataformats

This is the root command for actions that act on Data formats

Usage:
  icav2 dataformats [command]

Available Commands:
  list        List data formats

Flags:
  -h, --help   help for dataformats

Global Flags:
  -t, --access-token string    JWT used to call rest service
  -o, --output-format string   output format (default "table")
  -s, --server-url string      server url to direct commands
  -k, --x-api-key string       api key used to call rest service

Use "icav2 dataformats [command] --help" for more information about a command.

icav2 dataformats list

This command lists the data formats you can use inside of a project

Usage:
  icav2 dataformats list [flags]

Flags:
  -h, --help   help for list

Global Flags:
  -t, --access-token string    JWT used to call rest service
  -o, --output-format string   output format (default "table")
  -s, --server-url string      server url to direct commands
  -k, --x-api-key string       api key used to call rest service

icav2 help

Help provides help for any command in the application.
Simply type icav2 help [path to command] for full details.

Usage:
  icav2 help [command] [flags]

Flags:
  -h, --help   help for help

Global Flags:
  -t, --access-token string    JWT used to call rest service
  -o, --output-format string   output format (default "table")
  -s, --server-url string      server url to direct commands
  -k, --x-api-key string       api key used to call rest service

icav2 metadatamodels

This is the root command for actions that act on metadata models

Usage:
  icav2 metadatamodels [command]

Available Commands:
  list        list of metadata models

Flags:
  -h, --help   help for metadatamodels

Global Flags:
  -t, --access-token string    JWT used to call rest service
  -o, --output-format string   output format (default "table")
  -s, --server-url string      server url to direct commands
  -k, --x-api-key string       api key used to call rest service

Use "icav2 metadatamodels [command] --help" for more information about a command.

icav2 metadatamodels list

This command lists all the metadata models

Usage:
  icav2 metadatamodels list [flags]

Flags:
  -h, --help   help for list

Global Flags:
  -t, --access-token string    JWT used to call rest service
  -o, --output-format string   output format (default "table")
  -s, --server-url string      server url to direct commands
  -k, --x-api-key string       api key used to call rest service

icav2 pipelines

This is the root command for actions that act on pipelines

Usage:
  icav2 pipelines [command]

Available Commands:
  get         Get details of a pipeline
  list        List pipelines

Flags:
  -h, --help   help for pipelines

Global Flags:
  -t, --access-token string    JWT used to call rest service
  -o, --output-format string   output format (default "table")
  -s, --server-url string      server url to direct commands
  -k, --x-api-key string       api key used to call rest service

Use "icav2 pipelines [command] --help" for more information about a command.

icav2 pipelines get

This command fetches the details of a pipeline without a project context

Usage:
  icav2 pipelines get [pipeline id] [flags]

Flags:
  -h, --help   help for get

Global Flags:
  -t, --access-token string    JWT used to call rest service
  -o, --output-format string   output format (default "table")
  -s, --server-url string      server url to direct commands
  -k, --x-api-key string       api key used to call rest service

icav2 pipelines list

This command lists the pipelines without the context of a project

Usage:
  icav2 pipelines list [flags]

Flags:
  -h, --help   help for list

Global Flags:
  -t, --access-token string    JWT used to call rest service
  -o, --output-format string   output format (default "table")
  -s, --server-url string      server url to direct commands
  -k, --x-api-key string       api key used to call rest service

icav2 projectanalyses

This is the root command for actions that act on projects analysis

Usage:
  icav2 projectanalyses [command]

Available Commands:
  get         Get the details of an analysis 
  input       Retrieve input of analyses commands
  list        List of analyses for a project 
  output      Retrieve output of analyses commands
  update      Update tags of analyses

Flags:
  -h, --help   help for projectanalyses

Global Flags:
  -t, --access-token string    JWT used to call rest service
  -o, --output-format string   output format (default "table")
  -s, --server-url string      server url to direct commands
  -k, --x-api-key string       api key used to call rest service

Use "icav2 projectanalyses [command] --help" for more information about a command.

icav2 projectanalyses get

This command returns all the details of a analysis.

Usage:
  icav2 projectanalyses get [analysis id] [flags]

Flags:
  -h, --help                help for get
      --project-id string   project ID to set current project context

Global Flags:
  -t, --access-token string    JWT used to call rest service
  -o, --output-format string   output format (default "table")
  -s, --server-url string      server url to direct commands
  -k, --x-api-key string       api key used to call rest service

icav2 projectanalyses input

Retrieve input of analyses commands

Usage:
  icav2 projectanalyses input [analysisId] [flags]

Flags:
  -h, --help                help for input
      --project-id string   project ID to set current project context

Global Flags:
  -t, --access-token string    JWT used to call rest service
  -o, --output-format string   output format (default "table")
  -s, --server-url string      server url to direct commands
  -k, --x-api-key string       api key used to call rest service

icav2 projectanalyses list

This command lists the analyses for a given project. Sorting can be done on 
- reference
- userReference
- pipeline
- status
- startDate
- endDate
- summary

Usage:
  icav2 projectanalyses list [flags]

Flags:
  -h, --help                help for list
      --max-items int       maximum number of items to return, use 0 for no limit
      --page-offset int     Page offset, only used in combination with sort-by. Offset-based pagination has a result limit of 200K rows and does not guarantee unique results across pages (default -1)
      --page-size int32     Page size, only used in combination with sort-by. The amount of rows to return. Use in combination with the offset or cursor parameter to get subsequent results. Default and max value of pagesize=1000 (default 1000)
      --page-token string   Page token used for retrieving paged list results. Cursor-based pagination guarantees complete and unique results across all pages.
      --project-id string   project ID to set current project context
      --sort-by string      specifies the order to list items

Global Flags:
  -t, --access-token string    JWT used to call rest service
  -o, --output-format string   output format (default "table")
  -s, --server-url string      server url to direct commands
  -k, --x-api-key string       api key used to call rest service

icav2 projectanalyses output

Retrieve output of analyses commands

Usage:
  icav2 projectanalyses output [analysisId] [flags]

Flags:
  -h, --help                help for output
      --project-id string   project ID to set current project context
      --raw-output          Add this flag if output should be in raw format. Applies only for Cwl pipelines ! This flag needs no value, adding it sets the value to true.

Global Flags:
  -t, --access-token string    JWT used to call rest service
  -o, --output-format string   output format (default "table")
  -s, --server-url string      server url to direct commands
  -k, --x-api-key string       api key used to call rest service

icav2 projectanalyses update

Updates the user and technical tags of an analysis

Usage:
  icav2 projectanalyses update [analysisId] [flags]

Flags:
      --add-tech-tag stringArray      Tech tag to add to analysis. Add flag multiple times for multiple values.
      --add-user-tag stringArray      User tag to add to analysis. Add flag multiple times for multiple values.
  -h, --help                          help for update
      --project-id string             project ID to set current project context
      --remove-tech-tag stringArray   Tech tag to remove from analysis. Add flag multiple times for multiple values.
      --remove-user-tag stringArray   User tag to remove from analysis. Add flag multiple times for multiple values.

Global Flags:
  -t, --access-token string    JWT used to call rest service
  -o, --output-format string   output format (default "table")
  -s, --server-url string      server url to direct commands
  -k, --x-api-key string       api key used to call rest service

icav2 projectdata

This is the root command for actions that act on projects data

Usage:
  icav2 projectdata [command]

Available Commands:
  archive              archive data 
  create               Create data id for a project
  delete               delete data 
  download             Download a file/folder
  downloadurl          get download url 
  folderuploadsession  Get details of a folder upload
  get                  Get details of a data
  link                 Link data to a project
  list                 List data 
  mount                Mount project data 
  temporarycredentials fetch temporal credentials for data
  unarchive            unarchive data 
  unlink               Unlink data to a project
  unmount              Unmount project data 
  update               Updates the details of a data
  upload               Upload a file/folder

Flags:
  -h, --help   help for projectdata

Global Flags:
  -t, --access-token string    JWT used to call rest service
  -o, --output-format string   output format (default "table")
  -s, --server-url string      server url to direct commands
  -k, --x-api-key string       api key used to call rest service

Use "icav2 projectdata [command] --help" for more information about a command.

icav2 projectdata archive

This command archives data for a given project

Usage:
  icav2 projectdata archive [path or data Id] [flags]

Flags:
  -h, --help                help for archive
      --project-id string   project ID to set current project context

Global Flags:
  -t, --access-token string    JWT used to call rest service
  -o, --output-format string   output format (default "table")
  -s, --server-url string      server url to direct commands
  -k, --x-api-key string       api key used to call rest service

icav2 projectdata create

This command creates a data on a project. It takes name of file/folder as an argument

Usage:
  icav2 projectdata create [name] [flags]

Flags:
      --data-type string     (*) Data type : FILE or FOLDER
      --folder-id string     Id of the folder
      --folder-path string   Folder path under which the new project data will be created.
      --format string        Only allowed for file, sets the format of the file.
  -h, --help                 help for create
      --project-id string    project ID to set current project context

Global Flags:
  -t, --access-token string    JWT used to call rest service
  -o, --output-format string   output format (default "table")
  -s, --server-url string      server url to direct commands
  -k, --x-api-key string       api key used to call rest service

icav2 projectdata delete

This command deletes data for a given project

Usage:
  icav2 projectdata delete [path or dataId] [flags]

Flags:
  -h, --help                help for delete
      --project-id string   project ID to set current project context

Global Flags:
  -t, --access-token string    JWT used to call rest service
  -o, --output-format string   output format (default "table")
  -s, --server-url string      server url to direct commands
  -k, --x-api-key string       api key used to call rest service

icav2 projectdata download

Download a file/folder.  Source path can be a data id or a path. Source path for download of a folder should end with '*'. For files : Target defines either local folder into which the download will occur, or a path with a new name for the file. If the  file already exists locally, it is overwritten. For folders : If folder does not exist locally, it will be created automatically. Overwrite of an existing folder will need to be acknowledged.

Usage:
  icav2 projectdata download [source path] [target path] [flags]

Flags:
      --exclude string      Regex filter for file names to exclude from download
  -h, --help                help for download
      --project-id string   project ID to set current project context
      --exclude-source-path used to not include the parent folder structure when downloading the data, only the data and subfolder structure will be included

Global Flags:
  -t, --access-token string    JWT used to call rest service
  -o, --output-format string   output format (default "table")
  -s, --server-url string      server url to direct commands
  -k, --x-api-key string       api key used to call rest service

Example

Using this command all the files starting with VariantCaller- will be downloaded (prerequisite: a tool jq is installed on the machine):

icav2 projectdata list --data-type FILE --file-name VariantCaller- --match-mode FUZZY -o json | jq -r '.items[].id' > filelist.txt; for item in $(cat filelist.txt); do echo "--- $item ---"; icav2 projectdata download $item . ; done;

icav2 projectdata downloadurl

This command returns the data download url for a given project

Usage:
  icav2 projectdata downloadurl [path or data Id] [flags]

Flags:
  -h, --help                help for downloadurl
      --project-id string   project ID to set current project context

Global Flags:
  -t, --access-token string    JWT used to call rest service
  -o, --output-format string   output format (default "table")
  -s, --server-url string      server url to direct commands
  -k, --x-api-key string       api key used to call rest service

icav2 projectdata folderuploadsession

This command fetches the details a folder upload

Usage:
  icav2 projectdata folderuploadsession [project id] [data id] [folder upload session id] [flags]

Flags:
  -h, --help                help for folderuploadsession
      --project-id string   project ID to set current project context

Global Flags:
  -t, --access-token string    JWT used to call rest service
  -o, --output-format string   output format (default "table")
  -s, --server-url string      server url to direct commands
  -k, --x-api-key string       api key used to call rest service

icav2 projectdata get

This command fetches the details a data

Usage:
  icav2 projectdata get [data id] or [path] [flags]

Flags:
  -h, --help                help for get
      --project-id string   project ID to set current project context

Global Flags:
  -t, --access-token string    JWT used to call rest service
  -o, --output-format string   output format (default "table")
  -s, --server-url string      server url to direct commands
  -k, --x-api-key string       api key used to call rest service
This links data to a project. Use data id or the path + the source project flag identifiy the data.

Usage:
  icav2 projectdata link [data id] or [path] [flags]

Flags:
  -h, --help                       help for link
      --project-id string          project ID to set current project context
      --source-project-id string   project ID from where the data needs to be linked

Global Flags:
  -t, --access-token string    JWT used to call rest service
  -o, --output-format string   output format (default "table")
  -s, --server-url string      server url to direct commands
  -k, --x-api-key string       api key used to call rest service

icav2 projectdata list

This command lists the data for a given project

Usage:
  icav2 projectdata list [path] [flags]

Flags:
      --data-type string        Data type. Available values : FILE or FOLDER
      --eligible-link           Add this flag if output should contain only the data that is eligible for linking on the current project. This flag needs no value, adding it sets the value to true.
      --file-name stringArray   The filenames to filter on. The filenameMatchMode-parameter determines how the filtering is done. Add flag multiple times for multiple values.
  -h, --help                    help for list
      --match-mode string       Match mode for the file name. Available values : EXACT (default), EXCLUDE, FUZZY.
      --max-items int           maximum number of items to return, use 0 for no limit
      --page-offset int         Offset-based pagination has a result limit of 200K rows and does not guarantee unique results across pages (default -1)
      --page-size int32         The amount of rows to return. Use in combination with the offset or cursor parameter to get subsequent results. Default and max value of pagesize=1000 (default 1000)
      --parent-folder           Indicates that the given argument is path of the parent folder. All children are selected for list, not the folder itself. This flag needs no value, adding it sets the value to true.
      --project-id string       project ID to set current project context
      --sort-by string          specifies the order to list items (default "timeCreated Desc")
      --status stringArray      Add the status of the data. Available values : PARTIAL, AVAILABLE, ARCHIVING, ARCHIVED, UNARCHIVING, DELETING. Add flag multiple times for multiple values.

Global Flags:
  -t, --access-token string    JWT used to call rest service
  -o, --output-format string   output format (default "table")
  -s, --server-url string      server url to direct commands
  -k, --x-api-key string       api key used to call rest service

Example to list files in the folder SOURCE

icav2 projectdata list --project-id <project_id> --parent-folder /SOURCE/

Example to list only subfolders in the folder SOURCE

icav2 projectdata list --project-id <project_id> --parent-folder /SOURCE/ --data-type FOLDER

icav2 projectdata mount

This command mounts the project data as a file system directory for a given project

Usage:
  icav2 projectdata mount [mount directory path] [flags]

Flags:
  -h, --help                help for mount
      --list                List currently mounted projects
      --project-id string   project ID to set current project context

Global Flags:
  -t, --access-token string    JWT used to call rest service
  -o, --output-format string   output format (default "table")
  -s, --server-url string      server url to direct commands
  -k, --x-api-key string       api key used to call rest service

icav2 projectdata temporarycredentials

This command fetches  temporal AWS and Rclone credentials for a given project-data. If path is given, project id from the flag --project-id is used. If flag not present project is taken from the context

Usage:
  icav2 projectdata temporarycredentials [path or data Id] [flags]

Flags:
  -h, --help                help for temporarycredentials
      --project-id string   project ID to set current project context

Global Flags:
  -t, --access-token string    JWT used to call rest service
  -o, --output-format string   output format (default "table")
  -s, --server-url string      server url to direct commands
  -k, --x-api-key string       api key used to call rest service

icav2 projectdata unarchive

This command unarchives data for a given project

Usage:
  icav2 projectdata unarchive [path or dataId] [flags]

Flags:
  -h, --help                help for unarchive
      --project-id string   project ID to set current project context

Global Flags:
  -t, --access-token string    JWT used to call rest service
  -o, --output-format string   output format (default "table")
  -s, --server-url string      server url to direct commands
  -k, --x-api-key string       api key used to call rest service
This unlinks data from a project. Use path or id to identifiy the data.

Usage:
  icav2 projectdata unlink [data id] or [path] [flags]

Flags:
  -h, --help                help for unlink
      --project-id string   project ID to set current project context

Global Flags:
  -t, --access-token string    JWT used to call rest service
  -o, --output-format string   output format (default "table")
  -s, --server-url string      server url to direct commands
  -k, --x-api-key string       api key used to call rest service

icav2 projectdata unmount

This command unmounts previously mounted project data

Usage:
  icav2 projectdata unmount [flags]

Flags:
      --directory-path string   Set path to unmount
  -h, --help                    help for unmount
      --project-id string       project ID to set current project context

Global Flags:
  -t, --access-token string    JWT used to call rest service
  -o, --output-format string   output format (default "table")
  -s, --server-url string      server url to direct commands
  -k, --x-api-key string       api key used to call rest service

icav2 projectdata update

This command updates some details of a data. Only user/tech tags, format and dates of will be archived/delete can be updated.

Usage:
  icav2 projectdata update [data id] or [path] [flags]