CLI Reference

This section documents the CloudOS CLI commands and options.

cloudos

CloudOS CLI python package: a package for interacting with Lifebit Platform.

Usage

cloudos [OPTIONS] COMMAND [ARGS]...

Options

--debug

Show detailed error information and tracebacks

--version

Show the version and exit.

bash

Lifebit Platform bash-specific job functionality.

Usage

cloudos bash [OPTIONS] COMMAND [ARGS]...

Options

--debug

Show detailed error information and tracebacks

array-job

Run a bash array job in Lifebit Platform.

Usage

cloudos bash array-job [OPTIONS]

Options

-k, --apikey <apikey>

Required Your Lifebit Platform API key

--command <command>

The command to run in the bash job.

-c, --cloudos-url <cloudos_url>

Required The Lifebit Platform url you are trying to access to. Default=https://cloudos.lifebit.ai.

--workspace-id <workspace_id>

Required The specific Lifebit Platform workspace id.

--project-name <project_name>

Required The name of a Lifebit Platform project.

--workflow-name <workflow_name>

Required The name of a Lifebit Platform workflow or pipeline.

--last

When the workflows are duplicated, use the latest imported workflow (by date).

-p, --parameter <parameter>

A single parameter to pass to the job call. It should be in the following form: parameter_name=parameter_value. E.g.: -p –test=value or -p -test=value or -p test=value. You can use this option as many times as parameters you want to include. For parameters pointing to a file, the format expected is parameter_name=<project>/Data/parameter_value. The parameter value must be a file located in the Data subfolder. If no <project> is specified, it defaults to the project specified by the profile or –project-name parameter. E.g.: -p “–file=Data/file.txt” or “–file=<project>/Data/folder/file.txt”

--job-name <job_name>

The name of the job. Default=new_job.

--do-not-save-logs

Avoids process log saving. If you select this option, your job process logs will not be stored.

--job-queue <job_queue>

Name of the job queue to use with a batch job.

--instance-type <instance_type>

The type of compute instance to use as master node. Default=c5.xlarge(aws)|Standard_D4as_v4(azure).

--instance-disk <instance_disk>

The disk space of the master node instance, in GB. Default=500.

--cpus <cpus>

The number of CPUs to use for the task’s master node. Default=1.

--memory <memory>

The amount of memory, in GB, to use for the task’s master node. Default=4.

--wait-completion

Whether to wait to job completion and report final job status.

--wait-time <wait_time>

Max time to wait (in seconds) to job completion. Default=3600.

--repository-platform <repository_platform>

Name of the repository platform of the workflow. Default=github.

Options:

github | gitlab | bitbucketServer

--execution-platform <execution_platform>

Name of the execution platform implemented in your Lifebit Platform. Default=aws.

Options:

aws | azure | hpc

--cost-limit <cost_limit>

Add a cost limit to your job. Default=30.0 (For no cost limit please use -1).

--accelerate-saving-results

Enables saving results directly to cloud storage bypassing the master node.

--request-interval <request_interval>

Time interval to request (in seconds) the job status. For large jobs is important to use a high number to make fewer requests so that is not considered spamming by the API. Default=30.

--disable-ssl-verification

Disable SSL certificate verification. Please, remember that this option is not generally recommended for security reasons.

--ssl-cert <ssl_cert>

Path to your SSL certificate file.

--profile <profile>

Profile to use from the config file

--array-file <array_file>

Required Path to a file containing an array of commands to run in the bash job.

--separator <separator>

Required Separator to use in the array file. Default=”,”.

Options:

, | ; | tab | space | |

--list-columns

List columns present in the array file. This option will not run any job.

--array-file-project <array_file_project>

Name of the project in which the array file is placed, if different from –project-name.

--disable-column-check

Disable the check for the columns in the array file. This option is only used when –array-file is provided.

-a, --array-parameter <array_parameter>

Required A single parameter to pass to the job call only for specifying array columns. It should be in the following form: parameter_name=array_file_column_name. E.g.: -a –test=value or -a -test=value or -a test=value or -a =value (for no prefix). You can use this option as many times as parameters you want to include.

--custom-script-path <custom_script_path>

Path of a custom script to run in the bash array job instead of a command.

--debug

Show detailed error information and tracebacks

--custom-script-project <custom_script_project>

Name of the project to use when running the custom command script, if different than –project-name.

job

Run a bash job in Lifebit Platform.

Usage

cloudos bash job [OPTIONS]

Options

-k, --apikey <apikey>

Required Your Lifebit Platform API key

--command <command>

Required The command to run in the bash job.

-c, --cloudos-url <cloudos_url>

Required The Lifebit Platform url you are trying to access to. Default=https://cloudos.lifebit.ai.

--workspace-id <workspace_id>

Required The specific Lifebit Platform workspace id.

--project-name <project_name>

Required The name of a Lifebit Platform project.

--workflow-name <workflow_name>

Required The name of a Lifebit Platform workflow or pipeline.

--last

When the workflows are duplicated, use the latest imported workflow (by date).

-p, --parameter <parameter>

A single parameter to pass to the job call. It should be in the following form: parameter_name=parameter_value. E.g.: -p –test=value or -p -test=value or -p test=value. You can use this option as many times as parameters you want to include.

--job-name <job_name>

The name of the job. Default=new_job.

--do-not-save-logs

Avoids process log saving. If you select this option, your job process logs will not be stored.

--job-queue <job_queue>

Name of the job queue to use with a batch job.

--instance-type <instance_type>

The type of compute instance to use as master node. Default=c5.xlarge(aws)|Standard_D4as_v4(azure).

--instance-disk <instance_disk>

The disk space of the master node instance, in GB. Default=500.

--cpus <cpus>

The number of CPUs to use for the task’s master node. Default=1.

--memory <memory>

The amount of memory, in GB, to use for the task’s master node. Default=4.

--wait-completion

Whether to wait to job completion and report final job status.

--wait-time <wait_time>

Max time to wait (in seconds) to job completion. Default=3600.

--repository-platform <repository_platform>

Name of the repository platform of the workflow. Default=github.

Options:

github | gitlab | bitbucketServer

--execution-platform <execution_platform>

Name of the execution platform implemented in your Lifebit Platform. Default=aws.

--cost-limit <cost_limit>

Add a cost limit to your job. Default=30.0 (For no cost limit please use -1).

--accelerate-saving-results

Enables saving results directly to cloud storage bypassing the master node.

--request-interval <request_interval>

Time interval to request (in seconds) the job status. For large jobs is important to use a high number to make fewer requests so that is not considered spamming by the API. Default=30.

--disable-ssl-verification

Disable SSL certificate verification. Please, remember that this option is not generally recommended for security reasons.

--ssl-cert <ssl_cert>

Path to your SSL certificate file.

--debug

Show detailed error information and tracebacks

--profile <profile>

Profile to use from the config file

configure

Lifebit Platform configuration.

Usage

cloudos configure [OPTIONS] [COMMAND] [ARGS]...

Options

--profile <profile>

Profile to use from the config file

--debug

Show detailed error information and tracebacks

--make-default

Make the profile the default one.

list-profiles

List all available configuration profiles.

Usage

cloudos configure list-profiles [OPTIONS]

Options

--debug

Show detailed error information and tracebacks

remove-profile

Remove a configuration profile.

Usage

cloudos configure remove-profile [OPTIONS]

Options

--debug

Show detailed error information and tracebacks

--profile <profile>

Required Name of the profile. Not using this option will lead to profile named “deafults” being generated

cromwell

Lifebit Platform Cromwell server functionality.

Usage

cloudos cromwell [OPTIONS] COMMAND [ARGS]...

Options

--debug

Show detailed error information and tracebacks

start

Restart Cromwell server in Lifebit Platform.

Usage

cloudos cromwell start [OPTIONS]

Options

--version

Show the version and exit.

-k, --apikey <apikey>

Your Lifebit Platform API key.

-t, --cromwell-token <cromwell_token>

Specific Cromwell server authentication token. You can use it instead of the apikey.

-c, --cloudos-url <cloudos_url>

Required The Lifebit Platform url you are trying to access to. Default=https://cloudos.lifebit.ai.

--workspace-id <workspace_id>

Required The specific Lifebit Platform workspace id.

--wait-time <wait_time>

Max time to wait (in seconds) to Cromwell restart. Default=300.

--verbose

Whether to print information messages or not.

--disable-ssl-verification

Disable SSL certificate verification. Please, remember that this option is not generally recommended for security reasons.

--ssl-cert <ssl_cert>

Path to your SSL certificate file.

--debug

Show detailed error information and tracebacks

--profile <profile>

Profile to use from the config file

status

Check Cromwell server status in Lifebit Platform.

Usage

cloudos cromwell status [OPTIONS]

Options

--version

Show the version and exit.

-k, --apikey <apikey>

Your Lifebit Platform API key.

-t, --cromwell-token <cromwell_token>

Specific Cromwell server authentication token. You can use it instead of the apikey.

-c, --cloudos-url <cloudos_url>

Required The Lifebit Platform url you are trying to access to. Default=https://cloudos.lifebit.ai.

--workspace-id <workspace_id>

Required The specific Lifebit Platform workspace id.

--verbose

Whether to print information messages or not.

--disable-ssl-verification

Disable SSL certificate verification. Please, remember that this option is not generally recommended for security reasons.

--ssl-cert <ssl_cert>

Path to your SSL certificate file.

--debug

Show detailed error information and tracebacks

--profile <profile>

Profile to use from the config file

stop

Stop Cromwell server in Lifebit Platform.

Usage

cloudos cromwell stop [OPTIONS]

Options

--version

Show the version and exit.

-k, --apikey <apikey>

Your Lifebit Platform API key.

-t, --cromwell-token <cromwell_token>

Specific Cromwell server authentication token. You can use it instead of the apikey.

-c, --cloudos-url <cloudos_url>

Required The Lifebit Platform url you are trying to access to. Default=https://cloudos.lifebit.ai.

--workspace-id <workspace_id>

Required The specific Lifebit Platform workspace id.

--verbose

Whether to print information messages or not.

--disable-ssl-verification

Disable SSL certificate verification. Please, remember that this option is not generally recommended for security reasons.

--ssl-cert <ssl_cert>

Path to your SSL certificate file.

--debug

Show detailed error information and tracebacks

--profile <profile>

Profile to use from the config file

datasets

Lifebit Platform datasets functionality.

Usage

cloudos datasets [OPTIONS] COMMAND [ARGS]...

Options

--debug

Show detailed error information and tracebacks

cp

Copy a file or folder (S3 or virtual) from SOURCE_PATH to DESTINATION_PATH.

SOURCE_PATH [path]: the full path to the file or folder to copy.

E.g.: AnalysesResults/my_analysis/results/my_plot.png

DESTINATION_PATH [path]: the full path to the destination folder. It must be a ‘Data’ folder path.

E.g.: Data/plots

Usage

cloudos datasets cp [OPTIONS] SOURCE_PATH DESTINATION_PATH

Options

-k, --apikey <apikey>

Required Your Lifebit Platform API key.

-c, --cloudos-url <cloudos_url>

Required The Lifebit Platform URL.

--workspace-id <workspace_id>

Required The Lifebit Platform workspace ID.

--project-name <project_name>

Required The source project name.

--destination-project-name <destination_project_name>

The destination project name. Defaults to the source project.

--disable-ssl-verification

Disable SSL certificate verification.

--ssl-cert <ssl_cert>

Path to your SSL certificate file.

--debug

Show detailed error information and tracebacks

--profile <profile>

Profile to use from the config file.

Arguments

SOURCE_PATH

Required argument

DESTINATION_PATH

Required argument

ls

List contents of a path within a Lifebit Platform workspace dataset.

Usage

cloudos datasets ls [OPTIONS] [PATH]

Options

-k, --apikey <apikey>

Required Your Lifebit Platform API key.

-c, --cloudos-url <cloudos_url>

Required The Lifebit Platform url you are trying to access to. Default=https://cloudos.lifebit.ai.

--workspace-id <workspace_id>

Required The specific Lifebit Platform workspace id.

--disable-ssl-verification

Disable SSL certificate verification. Please, remember that this option is not generally recommended for security reasons.

--ssl-cert <ssl_cert>

Path to your SSL certificate file.

--project-name <project_name>

Required The name of a Lifebit Platform project.

--profile <profile>

Profile to use from the config file

--details

When selected, it prints the details of the listed files. Details contains “Type”, “Owner”, “Size”, “Last Updated”, “Virtual Name”, “Storage Path”.

--output-format <output_format>

The desired display for the output, either directly in standard output or saved as file. Default=stdout.

Options:

stdout | csv

--debug

Show detailed error information and tracebacks

--output-basename <output_basename>

Output file base name to save jobs details. Default=datasets_ls

Arguments

PATH

Optional argument

mkdir

Create a virtual folder in a Lifebit Platform project.

NEW_FOLDER_PATH [path]: Full path to the new folder including its name. Must start with ‘Data’.

Usage

cloudos datasets mkdir [OPTIONS] NEW_FOLDER_PATH

Options

-k, --apikey <apikey>

Required Your Lifebit Platform API key.

-c, --cloudos-url <cloudos_url>

Required The Lifebit Platform URL.

--workspace-id <workspace_id>

Required The Lifebit Platform workspace ID.

--project-name <project_name>

Required The project name.

--disable-ssl-verification

Disable SSL certificate verification.

--ssl-cert <ssl_cert>

Path to your SSL certificate file.

--debug

Show detailed error information and tracebacks

--profile <profile>

Profile to use from the config file.

Arguments

NEW_FOLDER_PATH

Required argument

mv

Move a file or folder from a source path to a destination path within or across Lifebit Platform projects.

SOURCE_PATH [path]: the full path to the file or folder to move. It must be a ‘Data’ folder path.

E.g.: ‘Data/folderA/file.txt’

DESTINATION_PATH [path]: the full path to the destination folder. It must be a ‘Data’ folder path.

E.g.: ‘Data/folderB’

Usage

cloudos datasets mv [OPTIONS] SOURCE_PATH DESTINATION_PATH

Options

-k, --apikey <apikey>

Required Your Lifebit Platform API key.

-c, --cloudos-url <cloudos_url>

Required The Lifebit Platform URL.

--workspace-id <workspace_id>

Required The Lifebit Platform workspace ID.

--project-name <project_name>

Required The source project name.

--destination-project-name <destination_project_name>

The destination project name. Defaults to the source project.

--disable-ssl-verification

Disable SSL certificate verification.

--ssl-cert <ssl_cert>

Path to your SSL certificate file.

--debug

Show detailed error information and tracebacks

--profile <profile>

Profile to use from the config file.

Arguments

SOURCE_PATH

Required argument

DESTINATION_PATH

Required argument

rename

Rename a file or folder in a Lifebit Platform project.

SOURCE_PATH [path]: the full path to the file or folder to rename. It must be a ‘Data’ folder path.

E.g.: ‘Data/folderA/old_name.txt’

NEW_NAME [name]: the new name to assign to the file or folder. E.g.: ‘new_name.txt’

Usage

cloudos datasets rename [OPTIONS] SOURCE_PATH NEW_NAME

Options

-k, --apikey <apikey>

Required Your Lifebit Platform API key.

-c, --cloudos-url <cloudos_url>

Required The Lifebit Platform URL.

--workspace-id <workspace_id>

Required The Lifebit Platform workspace ID.

--project-name <project_name>

Required The project name.

--disable-ssl-verification

Disable SSL certificate verification.

--ssl-cert <ssl_cert>

Path to your SSL certificate file.

--debug

Show detailed error information and tracebacks

--profile <profile>

Profile to use from the config file.

Arguments

SOURCE_PATH

Required argument

NEW_NAME

Required argument

rm

Delete a file or folder in a Lifebit Platform project.

TARGET_PATH [path]: the full path to the file or folder to delete. Must start with ‘Data’.

E.g.: ‘Data/folderA/file.txt’ or ‘Data/my_analysis/results/folderB’

Usage

cloudos datasets rm [OPTIONS] TARGET_PATH

Options

-k, --apikey <apikey>

Required Your Lifebit Platform API key.

-c, --cloudos-url <cloudos_url>

Required The Lifebit Platform URL.

--workspace-id <workspace_id>

Required The Lifebit Platform workspace ID.

--project-name <project_name>

Required The project name.

--disable-ssl-verification

Disable SSL certificate verification.

--ssl-cert <ssl_cert>

Path to your SSL certificate file.

--profile <profile>

Profile to use from the config file.

--debug

Show detailed error information and tracebacks

--force

Force delete files. Required when deleting user uploaded files. This may also delete the file from the cloud provider storage.

Arguments

TARGET_PATH

Required argument

interactive-session

Lifebit Platform interactive session functionality: list and manage interactive sessions.

Usage

cloudos interactive-session [OPTIONS] COMMAND [ARGS]...

Options

--debug

Show detailed error information and tracebacks

create

Create a new interactive session.

Usage

cloudos interactive-session create [OPTIONS]

Options

-k, --apikey <apikey>

Your Lifebit Platform API key

-c, --cloudos-url <cloudos_url>

The Lifebit Platform url you are trying to access to. Default=https://cloudos.lifebit.ai.

--workspace-id <workspace_id>

The specific Lifebit Platform workspace id.

--project-name <project_name>

Required The project name. Will be resolved to project ID automatically.

--name <name>

Required Name for the interactive session (1-100 characters).

--session-type <session_type>

Required Type of interactive session.

Options:

jupyter | vscode | spark | rstudio

--instance <instance>

Instance type (e.g., c5.xlarge for AWS, Standard_F1s for Azure). Default depends on execution platform.

--storage <storage>

Storage in GB (100-5000). Default=500.

--spot

Use spot instances.

--shared

Make session shared (accessible to workspace).

--cost-limit <cost_limit>

Cost limit in USD. Default=-1 (unlimited).

--shutdown-in <shutdown_in>

Auto-shutdown duration (e.g., 8h, 2d). Default=12h.

Link a file or folder into the session for read access. Supports S3 files/folders (s3://bucket/path/) and File Explorer files/folders. File Explorer paths can be given in two forms: (1) include the project name explicitly (e.g. my-project/Data/results) or (2) start with a known root folder (Data/, AnalysesResults/, Cohorts/, etc.) and –project-name or a profile project will be used to resolve the project. Both S3 and File Explorer types can be combined. Provide multiple paths as comma-separated values or use –link multiple times. Use –copy to copy data into the session instead. Examples: –link s3://bucket/data/,my-project/Data/results OR –link s3://bucket1/path/ –link Data/results

--copy

Copy data into the session instead of linking for read access. When specified, the paths provided by –link are copied into the session’s data volume. Supports Lifebit Platform datasets (project_name/Data/file.csv) and S3 files (s3://bucket/path/to/file).

--r-version <r_version>

R version for RStudio. Options: 4.5.2 (default), 4.4.2.

Options:

4.5.2 | 4.4.2

--spark-master <spark_master>

Master instance type for Spark. Default=c5.2xlarge.

--spark-core <spark_core>

Core instance type for Spark. Default=c5.xlarge.

--spark-workers <spark_workers>

Initial worker count for Spark. Default=1.

--execution-platform <execution_platform>

Cloud execution platform (aws or azure). Default is obtained from profile.

Options:

aws | azure

--disable-ssl-verification

Disable SSL certificate verification. Please, remember that this option is not generally recommended for security reasons.

--ssl-cert <ssl_cert>

Path to your SSL certificate file.

--profile <profile>

Profile to use from the config file

--debug

Show detailed error information and tracebacks

--verbose

Whether to print information messages or not.

list

List interactive sessions for a Lifebit Platform team.

Usage

cloudos interactive-session list [OPTIONS]

Options

-k, --apikey <apikey>

Required Your Lifebit Platform API key

-c, --cloudos-url <cloudos_url>

Required The Lifebit Platform url you are trying to access to. Default=https://cloudos.lifebit.ai.

--workspace-id <workspace_id>

Required The specific Lifebit Platform workspace id.

--filter-status <filter_status>

Filter sessions by status. Can be specified multiple times to filter by multiple statuses. (Supports both initialising and initializing spellings)

Options:

setup | initialising | initializing | running | scheduled | paused

--limit <limit>

Number of results per page. Default=10, max=100.

--page <page>

Page number to retrieve. Default=1.

--filter-only-mine

Show only the current user’s sessions.

--archived

When this flag is used, only archived sessions list is collected.

--output-format <output_format>

Output format for session list.

Options:

stdout | csv | json

--output-basename <output_basename>

Output file base name to save sessions list. Default=interactive_sessions_list

--table-columns <table_columns>

Comma-separated list of columns to display in the table. Only applicable when –output-format=stdout. Available columns: backend, cost, cost_limit, created_at, id, instance, name, owner, project, resources, runtime, saved_at, spot, status, time_left, type, version. Default: responsive (auto-selects columns based on terminal width)

--all-fields

Whether to collect all available fields from sessions or just the preconfigured selected fields. Only applicable when –output-format=csv.

--verbose

Whether to print information messages or not.

--disable-ssl-verification

Disable SSL certificate verification. Please, remember that this option is not generally recommended for security reasons.

--ssl-cert <ssl_cert>

Path to your SSL certificate file.

--debug

Show detailed error information and tracebacks

--profile <profile>

Profile to use from the config file

pause

Pause a running interactive session.

Usage

cloudos interactive-session pause [OPTIONS]

Options

--session-id <session_id>

Required The session ID to pause (24-character hex string).

-k, --apikey <apikey>

Your Lifebit Platform API key

-c, --cloudos-url <cloudos_url>

The Lifebit Platform url you are trying to access to. Default=https://cloudos.lifebit.ai.

--workspace-id <workspace_id>

The specific Lifebit Platform workspace id.

--no-upload

Don’t save session data before pausing (use with caution).

--force

Force immediate termination and skip confirmation prompt.

--wait

Wait for session to fully pause.

-y, --yes

Skip confirmation prompt.

--verbose

Whether to print information messages or not.

--disable-ssl-verification

Disable SSL certificate verification. Please, remember that this option is not generally recommended for security reasons.

--ssl-cert <ssl_cert>

Path to your SSL certificate file.

--debug

Show detailed error information and tracebacks

--profile <profile>

Profile to use from the config file

resume

Resume a paused interactive session with optional configuration updates.

Usage

cloudos interactive-session resume [OPTIONS]

Options

--session-id <session_id>

Required Session ID to resume.

-k, --apikey <apikey>

Your Lifebit Platform API key

-c, --cloudos-url <cloudos_url>

The Lifebit Platform url you are trying to access to. Default=https://cloudos.lifebit.ai.

--workspace-id <workspace_id>

The specific Lifebit Platform workspace id.

--instance <instance>

Change instance type when resuming.

--storage <storage>

Update storage size in GB (100-5000).

--cost-limit <cost_limit>

Update compute cost limit in USD. Default=-1 (unlimited).

--shutdown-in <shutdown_in>

Update auto-shutdown duration (e.g., 8h, 2d).

--verbose

Whether to print information messages or not.

--disable-ssl-verification

Disable SSL certificate verification. Please, remember that this option is not generally recommended for security reasons.

--ssl-cert <ssl_cert>

Path to your SSL certificate file.

--debug

Show detailed error information and tracebacks

--profile <profile>

Profile to use from the config file

status

Get status of an interactive session.

Usage

cloudos interactive-session status [OPTIONS]

Options

-k, --apikey <apikey>

Your Lifebit Platform API key

-c, --cloudos-url <cloudos_url>

The Lifebit Platform url you are trying to access to. Default=https://cloudos.lifebit.ai.

--session-id <session_id>

Required The session ID to retrieve status for (24-character hex string).

--workspace-id <workspace_id>

The specific Lifebit Platform workspace id.

--output-format <output_format>

Output format for session status.

Options:

stdout | csv | json

--output-basename <output_basename>

Output file base name to save session status. Default=interactive_session_status

--watch

Continuously poll status until session reaches running state (only for pre-running statuses).

--watch-interval <watch_interval>

Poll interval in seconds when using –watch. Default=30.

--max-wait-time <max_wait_time>

Maximum time to wait for session in watch mode. Accepts formats: 30s, 5m, 2h, 1d. Default=30m (30 minutes).

--verbose

Whether to print information messages or not.

--disable-ssl-verification

Disable SSL certificate verification. Please, remember that this option is not generally recommended for security reasons.

--ssl-cert <ssl_cert>

Path to your SSL certificate file.

--debug

Show detailed error information and tracebacks

--profile <profile>

Profile to use from the config file

job

Lifebit Platform job functionality: run, clone, resume, check and abort jobs in Lifebit Platform.

Usage

cloudos job [OPTIONS] COMMAND [ARGS]...

Options

--debug

Show detailed error information and tracebacks

abort

Abort all specified jobs from a Lifebit Platform workspace.

Usage

cloudos job abort [OPTIONS]

Options

-k, --apikey <apikey>

Required Your Lifebit Platform API key

-c, --cloudos-url <cloudos_url>

Required The Lifebit Platform url you are trying to access to. Default=https://cloudos.lifebit.ai.

--workspace-id <workspace_id>

Required The specific Lifebit Platform workspace id.

--job-ids <job_ids>

Required One or more job ids to abort. If more than one is provided, they must be provided as a comma separated list of ids. E.g. id1,id2,id3

--verbose

Whether to print information messages or not.

--disable-ssl-verification

Disable SSL certificate verification. Please, remember that this option is not generally recommended for security reasons.

--ssl-cert <ssl_cert>

Path to your SSL certificate file.

--profile <profile>

Profile to use from the config file

--debug

Show detailed error information and tracebacks

--force

Force abort the job even if it is not in a running or initializing state.

archive-unarchive-jobs

Archive specified jobs in a Lifebit Platform workspace.

Usage

cloudos job archive-unarchive-jobs [OPTIONS]

Options

-k, --apikey <apikey>

Required Your Lifebit Platform API key

-c, --cloudos-url <cloudos_url>

Required The Lifebit Platform url you are trying to access to. Default=https://cloudos.lifebit.ai.

--workspace-id <workspace_id>

Required The specific Lifebit Platform workspace id.

--job-ids <job_ids>

Required One or more job ids to archive/unarchive. If more than one is provided, they must be provided as a comma separated list of ids. E.g. id1,id2,id3

--verbose

Whether to print information messages or not.

--disable-ssl-verification

Disable SSL certificate verification. Please, remember that this option is not generally recommended for security reasons.

--ssl-cert <ssl_cert>

Path to your SSL certificate file.

--debug

Show detailed error information and tracebacks

--profile <profile>

Profile to use from the config file

archive-unarchive-jobs

Unarchive specified jobs in a Lifebit Platform workspace.

Usage

cloudos job archive-unarchive-jobs [OPTIONS]

Options

-k, --apikey <apikey>

Required Your Lifebit Platform API key

-c, --cloudos-url <cloudos_url>

Required The Lifebit Platform url you are trying to access to. Default=https://cloudos.lifebit.ai.

--workspace-id <workspace_id>

Required The specific Lifebit Platform workspace id.

--job-ids <job_ids>

Required One or more job ids to archive/unarchive. If more than one is provided, they must be provided as a comma separated list of ids. E.g. id1,id2,id3

--verbose

Whether to print information messages or not.

--disable-ssl-verification

Disable SSL certificate verification. Please, remember that this option is not generally recommended for security reasons.

--ssl-cert <ssl_cert>

Path to your SSL certificate file.

--debug

Show detailed error information and tracebacks

--profile <profile>

Profile to use from the config file

clone-resume

Clone a job with modified parameters

Usage

cloudos job clone-resume [OPTIONS]

Options

-k, --apikey <apikey>

Required Your Lifebit Platform API key

-c, --cloudos-url <cloudos_url>

Required The Lifebit Platform url you are trying to access to. Default=https://cloudos.lifebit.ai.

--workspace-id <workspace_id>

Required The specific Lifebit Platform workspace id.

--project-name <project_name>

The name of a Lifebit Platform project.

-p, --parameter <parameter>

A single parameter to pass to the job call. It should be in the following form: parameter_name=parameter_value. E.g.: -p input=s3://path_to_my_file. You can use this option as many times as parameters you want to include.

--nextflow-profile <nextflow_profile>

A comma separated string indicating the nextflow profile/s to use with your job.

--nextflow-version <nextflow_version>

Nextflow version to use when executing the workflow in Lifebit Platform.

Options:

22.10.8 | 24.04.4 | 25.04.8 | 25.10.4 | 22.11.1-edge | latest

--git-branch <git_branch>

The branch to run for the selected pipeline. If not specified it defaults to the last commit of the default branch.

--repository-platform <repository_platform>

Name of the repository platform of the workflow. Default=github.

Options:

github | gitlab | bitbucketServer

--job-name <job_name>

The name of the job. If not set, will take the name of the cloned job.

--do-not-save-logs

Avoids process log saving. If you select this option, your job process logs will not be stored.

--job-queue <job_queue>

Name of the job queue to use with a batch job. In Azure workspaces, this option is ignored.

--instance-type <instance_type>

The type of compute instance to use as master node. Default=c5.xlarge(aws)|Standard_D4as_v4(azure).

--cost-limit <cost_limit>

Add a cost limit to your job. Default=30.0 (For no cost limit please use -1).

--job-id <job_id>

Required The Lifebit Platform job id of the job to be cloned.

--accelerate-file-staging

Enables AWS S3 mountpoint for quicker file staging.

--accelerate-saving-results

Enables saving results directly to cloud storage bypassing the master node.

--resumable

Whether to make the job able to be resumed or not.

--wait-completion

Whether to wait to job completion and report final job status.

--wait-time <wait_time>

Max time to wait (in seconds) to job completion. Default=3600.

--request-interval <request_interval>

Time interval to request (in seconds) the job status. For large jobs is important to use a high number to make fewer requests so that is not considered spamming by the API. Default=30.

--verbose

Whether to print information messages or not.

--disable-ssl-verification

Disable SSL certificate verification. Please, remember that this option is not generally recommended for security reasons.

--ssl-cert <ssl_cert>

Path to your SSL certificate file.

--debug

Show detailed error information and tracebacks

--profile <profile>

Profile to use from the config file

clone-resume

Resume a job with modified parameters

Usage

cloudos job clone-resume [OPTIONS]

Options

-k, --apikey <apikey>

Required Your Lifebit Platform API key

-c, --cloudos-url <cloudos_url>

Required The Lifebit Platform url you are trying to access to. Default=https://cloudos.lifebit.ai.

--workspace-id <workspace_id>

Required The specific Lifebit Platform workspace id.

--project-name <project_name>

The name of a Lifebit Platform project.

-p, --parameter <parameter>

A single parameter to pass to the job call. It should be in the following form: parameter_name=parameter_value. E.g.: -p input=s3://path_to_my_file. You can use this option as many times as parameters you want to include.

--nextflow-profile <nextflow_profile>

A comma separated string indicating the nextflow profile/s to use with your job.

--nextflow-version <nextflow_version>

Nextflow version to use when executing the workflow in Lifebit Platform.

Options:

22.10.8 | 24.04.4 | 25.04.8 | 25.10.4 | 22.11.1-edge | latest

--git-branch <git_branch>

The branch to run for the selected pipeline. If not specified it defaults to the last commit of the default branch.

--repository-platform <repository_platform>

Name of the repository platform of the workflow. Default=github.

Options:

github | gitlab | bitbucketServer

--job-name <job_name>

The name of the job. If not set, will take the name of the cloned job.

--do-not-save-logs

Avoids process log saving. If you select this option, your job process logs will not be stored.

--job-queue <job_queue>

Name of the job queue to use with a batch job. In Azure workspaces, this option is ignored.

--instance-type <instance_type>

The type of compute instance to use as master node. Default=c5.xlarge(aws)|Standard_D4as_v4(azure).

--cost-limit <cost_limit>

Add a cost limit to your job. Default=30.0 (For no cost limit please use -1).

--job-id <job_id>

Required The Lifebit Platform job id of the job to be cloned.

--accelerate-file-staging

Enables AWS S3 mountpoint for quicker file staging.

--accelerate-saving-results

Enables saving results directly to cloud storage bypassing the master node.

--resumable

Whether to make the job able to be resumed or not.

--wait-completion

Whether to wait to job completion and report final job status.

--wait-time <wait_time>

Max time to wait (in seconds) to job completion. Default=3600.

--request-interval <request_interval>

Time interval to request (in seconds) the job status. For large jobs is important to use a high number to make fewer requests so that is not considered spamming by the API. Default=30.

--verbose

Whether to print information messages or not.

--disable-ssl-verification

Disable SSL certificate verification. Please, remember that this option is not generally recommended for security reasons.

--ssl-cert <ssl_cert>

Path to your SSL certificate file.

--debug

Show detailed error information and tracebacks

--profile <profile>

Profile to use from the config file

cost

Retrieve job cost information in Lifebit Platform.

Usage

cloudos job cost [OPTIONS]

Options

-k, --apikey <apikey>

Required Your Lifebit Platform API key

-c, --cloudos-url <cloudos_url>

Required The Lifebit Platform url you are trying to access to. Default=https://cloudos.lifebit.ai.

--workspace-id <workspace_id>

Required The specific Lifebit Platform workspace id.

--job-id <job_id>

Required The job id in Lifebit Platform to get costs for.

--output-format <output_format>

The desired file format (file extension) for the output. For json option –all-fields will be automatically set to True. Default=csv.

Options:

stdout | csv | json

--verbose

Whether to print information messages or not.

--disable-ssl-verification

Disable SSL certificate verification. Please, remember that this option is not generally recommended for security reasons.

--ssl-cert <ssl_cert>

Path to your SSL certificate file.

--debug

Show detailed error information and tracebacks

--profile <profile>

Profile to use from the config file

details

Retrieve job details in Lifebit Platform.

Usage

cloudos job details [OPTIONS]

Options

-k, --apikey <apikey>

Required Your Lifebit Platform API key

-c, --cloudos-url <cloudos_url>

Required The Lifebit Platform url you are trying to access to. Default=https://cloudos.lifebit.ai.

--workspace-id <workspace_id>

Required The specific Lifebit Platform workspace id.

--job-id <job_id>

Required The job id in Lifebit Platform to search for.

--output-format <output_format>

The desired display for the output, either directly in standard output or saved as file. Default=stdout.

Options:

stdout | csv | json

--output-basename <output_basename>

Output file base name to save jobs details. Default={job_id}_details

--parameters

Whether to generate a “.config” file that can be used as input for –job-config parameter. It will have the same basename as defined in “–output-basename”.

--verbose

Whether to print information messages or not.

--disable-ssl-verification

Disable SSL certificate verification. Please, remember that this option is not generally recommended for security reasons.

--ssl-cert <ssl_cert>

Path to your SSL certificate file.

--debug

Show detailed error information and tracebacks

--profile <profile>

Profile to use from the config file

list

Collect and display workspace jobs from a Lifebit Platform workspace.

Usage

cloudos job list [OPTIONS]

Options

-k, --apikey <apikey>

Required Your Lifebit Platform API key

-c, --cloudos-url <cloudos_url>

Required The Lifebit Platform url you are trying to access to. Default=https://cloudos.lifebit.ai.

--workspace-id <workspace_id>

Required The specific Lifebit Platform workspace id.

--output-basename <output_basename>

Output file base name to save jobs list. Default=joblist

--output-format <output_format>

The desired output format. For json option –all-fields will be automatically set to True. Default=stdout.

Options:

stdout | csv | json

--table-columns <table_columns>

Comma-separated list of columns to display in the table. Only applicable when –output-format=stdout. Available columns: status,name,project,owner,pipeline,id,submit_time,end_time,run_time,commit,cost,resources,storage_type. Default: responsive (auto-selects columns based on terminal width)

--all-fields

Whether to collect all available fields from jobs or just the preconfigured selected fields. Only applicable when –output-format=csv. Automatically enabled for json output.

--last-n-jobs <last_n_jobs>

The number of last workspace jobs to retrieve. You can use ‘all’ to retrieve all workspace jobs. When adding this option, options ‘–page’ and ‘–page-size’ are ignored.

--page <page>

Page number to fetch from the API. Used with –page-size to control jobs per page (e.g. –page=4 –page-size=20). Default=1.

--page-size <page_size>

Page size to retrieve from API, corresponds to the number of jobs per page. Maximum allowed integer is 100. Default=10.

--archived

When this flag is used, only archived jobs list is collected.

--filter-status <filter_status>

Filter jobs by status (e.g., completed, running, failed, aborted).

--filter-job-name <filter_job_name>

Filter jobs by job name ( case insensitive ).

--filter-project <filter_project>

Filter jobs by project name.

--filter-workflow <filter_workflow>

Filter jobs by workflow/pipeline name.

--last

When workflows are duplicated, use the latest imported workflow (by date).

--filter-job-id <filter_job_id>

Filter jobs by specific job ID.

--filter-only-mine

Filter to show only jobs belonging to the current user.

--filter-queue <filter_queue>

Filter jobs by queue name. Only applies to jobs running in batch environment. Non-batch jobs are preserved in results.

--filter-owner <filter_owner>

Filter jobs by owner username.

--verbose

Whether to print information messages or not.

--disable-ssl-verification

Disable SSL certificate verification. Please, remember that this option is not generally recommended for security reasons.

--ssl-cert <ssl_cert>

Path to your SSL certificate file.

--debug

Show detailed error information and tracebacks

--profile <profile>

Profile to use from the config file

logs

Get the path to the logs of a specified job.

Usage

cloudos job logs [OPTIONS]

Options

-k, --apikey <apikey>

Required Your Lifebit Platform API key

-c, --cloudos-url <cloudos_url>

Required The Lifebit Platform url you are trying to access to. Default=https://cloudos.lifebit.ai.

--workspace-id <workspace_id>

Required The specific Lifebit Platform workspace id.

--job-id <job_id>

Required The job id in Lifebit Platform to search for.

Link the logs directories to an interactive session.

--session-id <session_id>

The specific Lifebit Platform interactive session id. Required when using –link flag.

--verbose

Whether to print information messages or not.

--disable-ssl-verification

Disable SSL certificate verification. Please, remember that this option is not generally recommended for security reasons.

--ssl-cert <ssl_cert>

Path to your SSL certificate file.

--debug

Show detailed error information and tracebacks

--profile <profile>

Profile to use from the config file

results

Get the path to the results of a specified job or check deletion status.

Usage

cloudos job results [OPTIONS]

Options

-k, --apikey <apikey>

Required Your Lifebit Platform API key

-c, --cloudos-url <cloudos_url>

Required The Lifebit Platform url you are trying to access to. Default=https://cloudos.lifebit.ai.

--workspace-id <workspace_id>

Required The specific Lifebit Platform workspace id.

--job-id <job_id>

Required The job id in Lifebit Platform to search for.

Link the results directories to an interactive session.

--delete

Delete the results directory of a Lifebit Platform job.

-y, --yes

Skip confirmation prompt when deleting results.

--session-id <session_id>

The specific Lifebit Platform interactive session id. Required when using –link flag.

--status

Check the deletion status of the job results.

--verbose

Whether to print information messages or not.

--disable-ssl-verification

Disable SSL certificate verification. Please, remember that this option is not generally recommended for security reasons.

--ssl-cert <ssl_cert>

Path to your SSL certificate file.

--debug

Show detailed error information and tracebacks

--profile <profile>

Profile to use from the config file

run

Run a Lifebit Platform workflow.

Usage

cloudos job run [OPTIONS]

Options

-k, --apikey <apikey>

Required Your Lifebit Platform API key

-c, --cloudos-url <cloudos_url>

Required The Lifebit Platform url you are trying to access to. Default=https://cloudos.lifebit.ai.

--workspace-id <workspace_id>

Required The specific Lifebit Platform workspace id.

--project-name <project_name>

Required The name of a Lifebit Platform project.

--workflow-name <workflow_name>

Required The name of a Lifebit Platform workflow or pipeline.

--last

When the workflows are duplicated, use the latest imported workflow (by date).

--job-config <job_config>

A config file similar to a nextflow.config file, but only with the parameters to use with your job.

--params-file <params_file>

A file containing the parameters to pass to the job call. It should be a .json or .yaml file with a dictionary structure where keys are parameter names and values are parameter values. This expects an S3 URI, Azure Blob URI (az://<account>.blob.core.windows.net/<container>/<blob>) or a File Explorer relative path (e.g., Data/params_file.json) and does not work with local files.

-p, --parameter <parameter>

A single parameter to pass to the job call. It should be in the following form: parameter_name=parameter_value. E.g.: -p input=s3://path_to_my_file. You can use this option as many times as parameters you want to include.

--nextflow-profile <nextflow_profile>

A comma separated string indicating the nextflow profile/s to use with your job.

--nextflow-version <nextflow_version>

Nextflow version to use when executing the workflow in Lifebit Platform. Defaults to 22.10.8 for Platform Workflows or 24.04.4 for user-imported Workflows.

Options:

22.10.8 | 24.04.4 | 25.04.8 | 25.10.4 | 22.11.1-edge | latest

--git-commit <git_commit>

The git commit hash to run for the selected pipeline. If not specified it defaults to the last commit of the default branch.

--git-tag <git_tag>

The tag to run for the selected pipeline. If not specified it defaults to the last commit of the default branch.

--git-branch <git_branch>

The branch to run for the selected pipeline. If not specified it defaults to the last commit of the default branch.

--job-name <job_name>

The name of the job. Default=new_job.

--resumable

Whether to make the job able to be resumed or not.

--do-not-save-logs

Avoids process log saving. If you select this option, your job process logs will not be stored.

--job-queue <job_queue>

Name of the job queue to use with a batch job.

--instance-type <instance_type>

The type of compute instance to use as master node. Default=c5.xlarge(aws)|Standard_D4as_v4(azure).

--instance-disk <instance_disk>

The disk space of the master node instance, in GB. Default=500.

--wait-completion

Whether to wait to job completion and report final job status.

--wait-time <wait_time>

Max time to wait (in seconds) to job completion. Default=3600.

--wdl-mainfile <wdl_mainfile>

For WDL workflows, which mainFile (.wdl) is configured to use.

--wdl-importsfile <wdl_importsfile>

For WDL workflows, which importsFile (.zip) is configured to use.

-t, --cromwell-token <cromwell_token>

Specific Cromwell server authentication token. Currently, not necessary as apikey can be used instead, but maintained for backwards compatibility.

--repository-platform <repository_platform>

Name of the repository platform of the workflow. Default=github.

Options:

github | gitlab | bitbucketServer

--execution-platform <execution_platform>

Name of the execution platform implemented in your Lifebit Platform. Default=aws.

Options:

aws | azure | hpc

--hpc-id <hpc_id>

ID of your HPC, only applicable when –execution-platform=hpc. Default=660fae20f93358ad61e0104b

--azure-worker-instance-type <azure_worker_instance_type>

The worker node instance type to be used in azure. Default=Standard_D4as_v4

--azure-worker-instance-disk <azure_worker_instance_disk>

The disk size in GB for the worker node to be used in azure. Default=100

--azure-worker-instance-spot

Whether the azure worker nodes have to be spot instances or not.

--cost-limit <cost_limit>

Add a cost limit to your job. Default=30.0 (For no cost limit please use -1).

--accelerate-file-staging

Enables AWS S3 mountpoint for quicker file staging.

--accelerate-saving-results

Enables saving results directly to cloud storage bypassing the master node.

--use-private-docker-repository

Allows to use private docker repository for running jobs. The Docker user account has to be already linked to Lifebit Platform.

--verbose

Whether to print information messages or not.

--request-interval <request_interval>

Time interval to request (in seconds) the job status. For large jobs is important to use a high number to make fewer requests so that is not considered spamming by the API. Default=30.

--disable-ssl-verification

Disable SSL certificate verification. Please, remember that this option is not generally recommended for security reasons.

--ssl-cert <ssl_cert>

Path to your SSL certificate file.

--debug

Show detailed error information and tracebacks

--profile <profile>

Profile to use from the config file

status

Get the status of a Lifebit Platform job.

Usage

cloudos job status [OPTIONS]

Options

-k, --apikey <apikey>

Required Your Lifebit Platform API key

-c, --cloudos-url <cloudos_url>

Required The Lifebit Platform url you are trying to access to. Default=https://cloudos.lifebit.ai.

--workspace-id <workspace_id>

Required The specific Lifebit Platform workspace id.

--job-id <job_id>

Required The job id in Lifebit Platform to search for.

--verbose

Whether to print information messages or not.

--disable-ssl-verification

Disable SSL certificate verification. Please, remember that this option is not generally recommended for security reasons.

--ssl-cert <ssl_cert>

Path to your SSL certificate file.

--debug

Show detailed error information and tracebacks

--profile <profile>

Profile to use from the config file

workdir

Get the path to the working directory of a specified job or check deletion status.

Usage

cloudos job workdir [OPTIONS]

Options

-k, --apikey <apikey>

Required Your Lifebit Platform API key

-c, --cloudos-url <cloudos_url>

Required The Lifebit Platform url you are trying to access to. Default=https://cloudos.lifebit.ai.

--workspace-id <workspace_id>

Required The specific Lifebit Platform workspace id.

--job-id <job_id>

Required The job id in Lifebit Platform to search for.

Link the working directory to an interactive session.

--delete

Delete the results directory of a Lifebit Platform job.

-y, --yes

Skip confirmation prompt when deleting results.

--session-id <session_id>

The specific Lifebit Platform interactive session id. Required when using –link flag.

--status

Check the deletion status of the working directory.

--verbose

Whether to print information messages or not.

--disable-ssl-verification

Disable SSL certificate verification. Please, remember that this option is not generally recommended for security reasons.

--ssl-cert <ssl_cert>

Path to your SSL certificate file.

--debug

Show detailed error information and tracebacks

--profile <profile>

Profile to use from the config file

procurement

Lifebit Platform procurement functionality.

Usage

cloudos procurement [OPTIONS] COMMAND [ARGS]...

Options

--debug

Show detailed error information and tracebacks

images

Lifebit Platform procurement images functionality.

Usage

cloudos procurement images [OPTIONS] COMMAND [ARGS]...
ls

List images associated with organisations of a given procurement.

Usage

cloudos procurement images ls [OPTIONS]

Options

-k, --apikey <apikey>

Required Your Lifebit Platform API key.

-c, --cloudos-url <cloudos_url>

Required The Lifebit Platform url you are trying to access to. Default=https://cloudos.lifebit.ai.

--procurement-id <procurement_id>

Required The specific Lifebit Platform procurement id.

--page <page>

The response page. Defaults to 1.

--limit <limit>

The page size limit. Defaults to 10

--disable-ssl-verification

Disable SSL certificate verification. Please, remember that this option is not generally recommended for security reasons.

--ssl-cert <ssl_cert>

Path to your SSL certificate file.

--profile <profile>

Profile to use from the config file

reset

Reset image associated with an organisations of a given procurement to Lifebit Platform defaults.

Usage

cloudos procurement images reset [OPTIONS]

Options

-k, --apikey <apikey>

Required Your Lifebit Platform API key.

-c, --cloudos-url <cloudos_url>

Required The Lifebit Platform url you are trying to access to. Default=https://cloudos.lifebit.ai.

--procurement-id <procurement_id>

Required The specific Lifebit Platform procurement id.

--organisation-id <organisation_id>

Required The Organisation Id where the change is going to be applied.

--image-type <image_type>

Required The Lifebit Platform resource image type.

Options:

RegularInteractiveSessions | SparkInteractiveSessions | JobDefault | NextflowBatchComputeEnvironment

--provider <provider>

Required The cloud provider. Only aws and azure are supported.

Options:

aws | azure

--region <region>

Required The cloud region. Only aws and azure regions are supported.

--disable-ssl-verification

Disable SSL certificate verification. Please, remember that this option is not generally recommended for security reasons.

--ssl-cert <ssl_cert>

Path to your SSL certificate file.

--profile <profile>

Profile to use from the config file

set

Set a new image id, name, or version to image associated with an organisations of a given procurement.

Usage

cloudos procurement images set [OPTIONS]

Options

-k, --apikey <apikey>

Required Your Lifebit Platform API key.

-c, --cloudos-url <cloudos_url>

Required The Lifebit Platform url you are trying to access to. Default=https://cloudos.lifebit.ai.

--procurement-id <procurement_id>

Required The specific Lifebit Platform procurement id.

--organisation-id <organisation_id>

Required The Organisation Id where the change is going to be applied.

--image-type <image_type>

Required The Lifebit Platform resource image type.

Options:

RegularInteractiveSessions | SparkInteractiveSessions | JobDefault | NextflowBatchComputeEnvironment

--provider <provider>

Required The cloud provider. Only aws and azure are supported.

Options:

aws | azure

--region <region>

Required The cloud region. Only aws and azure regions are supported.

--image-id <image_id>

Required The new image id value.

--image-name <image_name>

The new image name value.

--image-version <image_version>

Required The new image version value.

--disable-ssl-verification

Disable SSL certificate verification. Please, remember that this option is not generally recommended for security reasons.

--ssl-cert <ssl_cert>

Path to your SSL certificate file.

--profile <profile>

Profile to use from the config file

project

Lifebit Platform project functionality.

Usage

cloudos project [OPTIONS] COMMAND [ARGS]...

Options

--debug

Show detailed error information and tracebacks

create

Create a new project in Lifebit Platform.

Usage

cloudos project create [OPTIONS]

Options

-k, --apikey <apikey>

Required Your Lifebit Platform API key

-c, --cloudos-url <cloudos_url>

Required The Lifebit Platform url you are trying to access to. Default=https://cloudos.lifebit.ai.

--workspace-id <workspace_id>

Required The specific Lifebit Platform workspace id.

--new-project <new_project>

Required The name for the new project.

--verbose

Whether to print information messages or not.

--disable-ssl-verification

Disable SSL certificate verification. Please, remember that this option is not generally recommended for security reasons.

--ssl-cert <ssl_cert>

Path to your SSL certificate file.

--debug

Show detailed error information and tracebacks

--profile <profile>

Profile to use from the config file

list

Collect and display all projects from a Lifebit Platform workspace.

Usage

cloudos project list [OPTIONS]

Options

-k, --apikey <apikey>

Required Your Lifebit Platform API key

-c, --cloudos-url <cloudos_url>

Required The Lifebit Platform url you are trying to access to. Default=https://cloudos.lifebit.ai.

--workspace-id <workspace_id>

Required The specific Lifebit Platform workspace id.

--output-basename <output_basename>

Output file base name to save project list. Default=project_list

--output-format <output_format>

Output format for project list. Options: stdout (display as interactive table in terminal), csv (save as comma-separated values file), json (save as JSON file with full API response). Default=stdout.

Options:

stdout | csv | json

--all-fields

Whether to collect all available fields from projects or just the preconfigured selected fields. Only applicable when –output-format=csv

--page <page>

Response page to retrieve. Default=1.

--verbose

Whether to print information messages or not.

--disable-ssl-verification

Disable SSL certificate verification. Please, remember that this option is not generally recommended for security reasons.

--ssl-cert <ssl_cert>

Path to your SSL certificate file.

--debug

Show detailed error information and tracebacks

--profile <profile>

Profile to use from the config file

queue

Lifebit Platform job queue functionality.

Usage

cloudos queue [OPTIONS] COMMAND [ARGS]...

Options

--debug

Show detailed error information and tracebacks

create

Create a new job queue in a Lifebit Platform workspace.

A preset template is used to create the queue.

Usage

cloudos queue create [OPTIONS]

Options

-k, --apikey <apikey>

Required Your Lifebit Platform API key

-c, --cloudos-url <cloudos_url>

Required The Lifebit Platform url you are trying to access to. Default=https://cloudos.lifebit.ai.

--workspace-id <workspace_id>

Required The specific Lifebit Platform workspace id.

--label <label>

Name (label) for the new job queue.

--description <description>

Short description of the new job queue.

--preset <preset>

Preset template to use. Choices: standard-stable, standard-cost-saving, read-write-optimised, standard-gpu. Default=standard-stable.

Default:

'standard-stable'

Options:

standard-stable | standard-cost-saving | read-write-optimised | standard-gpu

--executor <executor>

Workflow executor for the queue. Default=nextflow.

Default:

'nextflow'

Options:

nextflow | cromwell

-y, --yes

Skip the confirmation prompt and proceed immediately.

--set-default

Set the new job queue as the workspace default. Default=False.

--execution-platform <execution_platform>

Name of the execution platform implemented in your Lifebit Platform. Default=aws.

Options:

aws | azure | hpc

--disable-ssl-verification

Disable SSL certificate verification. Please, remember that this option is not generally recommended for security reasons.

--ssl-cert <ssl_cert>

Path to your SSL certificate file.

--debug

Show detailed error information and tracebacks

--profile <profile>

Profile to use from the config file

list

Collect and display all available job queues from a Lifebit Platform workspace.

Usage

cloudos queue list [OPTIONS]

Options

-k, --apikey <apikey>

Required Your Lifebit Platform API key

-c, --cloudos-url <cloudos_url>

Required The Lifebit Platform url you are trying to access to. Default=https://cloudos.lifebit.ai.

--workspace-id <workspace_id>

Required The specific Lifebit Platform workspace id.

--output-basename <output_basename>

Output file base name to save job queue list. Default=job_queue_list

--output-format <output_format>

Output format for queue list. Options: stdout (display as interactive table in terminal), csv (save as comma-separated values file), json (save as JSON file with full API response). Default=stdout.

Options:

stdout | csv | json

--all-fields

Whether to collect all available fields from queues or just the preconfigured selected fields. Only applicable when –output-format=csv

--exclude-system-queues

Exclude system job queues from the list.

--execution-platform <execution_platform>

Name of the execution platform implemented in your Lifebit Platform. Default=aws.

Options:

aws | azure | hpc

--disable-ssl-verification

Disable SSL certificate verification. Please, remember that this option is not generally recommended for security reasons.

--ssl-cert <ssl_cert>

Path to your SSL certificate file.

--debug

Show detailed error information and tracebacks

--profile <profile>

Profile to use from the config file

workflow

Lifebit Platform workflow functionality: list and import workflows.

Usage

cloudos workflow [OPTIONS] COMMAND [ARGS]...

Options

--debug

Show detailed error information and tracebacks

import

Import workflows from supported repository providers.

Usage

cloudos workflow import [OPTIONS]

Options

-k, --apikey <apikey>

Required Your Lifebit Platform API key

-c, --cloudos-url <cloudos_url>

Required The Lifebit Platform url you are trying to access to. Default=https://cloudos.lifebit.ai.

--workspace-id <workspace_id>

Required The specific Lifebit Platform workspace id.

--repository-platform <repository_platform>

Name of the repository platform of the workflow. Default=github.

Options:

github | gitlab | bitbucketServer

--workflow-name <workflow_name>

Required The name that the workflow will have in Lifebit Platform.

-w, --workflow-url <workflow_url>

Required URL of the workflow repository.

-d, --workflow-docs-link <workflow_docs_link>

URL to the documentation of the workflow.

--cost-limit <cost_limit>

Cost limit for the workflow. Default: $30 USD.

--workflow-description <workflow_description>

Workflow description

--disable-ssl-verification

Disable SSL certificate verification. Please, remember that this option is not generally recommended for security reasons.

--ssl-cert <ssl_cert>

Path to your SSL certificate file.

--debug

Show detailed error information and tracebacks

--profile <profile>

Profile to use from the config file

list

Collect and display workflows from a Lifebit Platform workspace.

Usage

cloudos workflow list [OPTIONS]

Options

-k, --apikey <apikey>

Required Your Lifebit Platform API key

-c, --cloudos-url <cloudos_url>

Required The Lifebit Platform url you are trying to access to. Default=https://cloudos.lifebit.ai.

--workspace-id <workspace_id>

Required The specific Lifebit Platform workspace id.

--output-basename <output_basename>

Output file base name to save workflow list. Default=workflow_list

--output-format <output_format>

Output format for workflow list. Options: stdout (display as interactive table in terminal), csv (save as comma-separated values file), json (save as JSON file with full API response). Default=stdout.

Options:

stdout | csv | json

--all-fields

Whether to collect all available fields from workflows or just the preconfigured selected fields. Only applicable when –output-format=csv

--verbose

Whether to print information messages or not.

--disable-ssl-verification

Disable SSL certificate verification. Please, remember that this option is not generally recommended for security reasons.

--ssl-cert <ssl_cert>

Path to your SSL certificate file.

--debug

Show detailed error information and tracebacks

--profile <profile>

Profile to use from the config file