Command Index
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.
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.
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
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.
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
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
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
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
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.
Get configuration information.
Usage:
icav2 config get [flags]
Flags:
-h, --help help for get
Remove configuration information.
Usage:
icav2 config reset [flags]
Flags:
-h, --help help for reset
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
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.
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
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
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.
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
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.
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
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
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.
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
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
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
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
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
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.
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
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
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
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
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
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;
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
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
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
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
icav2 projectdata list --project-id <project_id> --parent-folder /SOURCE/
icav2 projectdata list --project-id <project_id> --parent-folder /SOURCE/ --data-type FOLDER
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
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
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
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
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]
Flags:
--add-tech-tag stringArray Tech tag to add. Add flag multiple times for multiple values.
--add-user-tag stringArray User tag to add. Add flag multiple times for multiple values.
--format-code string Format to assign to the data. Only available for files.
-h, --help help for update
--project-id string project ID to set current project context
--remove-tech-tag stringArray Tech tag to remove. Add flag multiple times for multiple values.
--remove-user-tag stringArray User tag to remove. Add flag multiple times for multiple values.
--will-be-archived-at string Time when data will be archived. Format is YYYY-MM-DD. Time is set to 00:00:00UTC time. Only available for files.
--will-be-deleted-at string Time when data will be deleted. Format is YYYY-MM-DD. Time is set to 00:00:00UTC time. Only available for files.
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
Upload a file/folder. For files : if the target path does not already exist, it will be created automatically. For folders : overwrite will need to be acknowledged. Argument "icapath" is optional.
Usage:
icav2 projectdata upload [local path] [icapath] [flags]
Flags:
--existing-sample Link to existing sample
-h, --help help for upload
--new-sample Create and link to new sample
--num-workers int number of workers to parallelize. Default calculated based on CPUs available.
--project-id string project ID to set current project context
--sample-description string Set Sample Description for new sample
--sample-id string Set Sample id of existing sample
--sample-name string Set Sample name for new sample or from existing sample
--sample-technical-tag stringArray Set Sample Technical tag for new sample
--sample-user-tag stringArray Set Sample User tag for new sample
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
In this example all the fastq.gz files from source will be uploaded to target using xargs utility.
find $source -name '*.fastq.gz' | xargs -n 1 -P 10 -I {} icav2 projectdata upload {} /$target/
In this example we upload multiple bam files specified with the corresponding path in the file bam_files.csv. The files will be renamed. We are using screen in detached mode (this creates a new session but not attaching to it):
while IFS=, read -r current_bam_file_name bam_path new_bam_file_name
do
screen -d -m icav2 projectdata upload ${bam_path}/${current_bam_file} /bam_files/${new_bam_file_name} --project-id $projectID
done <./bam_files.csv 2>./log.txt
This is the root command for actions that act on projects pipeline
Usage:
icav2 projectpipelines [command]
Available Commands:
create Create a pipeline
input Retrieve input parameters of pipeline
link Link pipeline to a project
list List of pipelines for a project
start Start a pipeline
unlink Unlink pipeline from a project
Flags:
-h, --help help for projectpipelines
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 projectpipelines [command] --help" for more information about a command.
This command creates a pipeline in the current project
Usage:
icav2 projectpipelines create [command]
Available Commands:
cwl Create a cwl pipeline
nextflow Create a nextflow pipeline
Flags:
-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")