CLI Reference

This section documents the CloudOS CLI commands and options.

cloudos

CloudOS python package: a package for interacting with CloudOS.

Usage

cloudos [OPTIONS] COMMAND [ARGS]...

Options

--debug

Show detailed error information and tracebacks

--version

Show the version and exit.

bash

CloudOS bash functionality.

Usage

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

Options

--debug

Show detailed error information and tracebacks

array-job

Run a bash array job in CloudOS.

Usage

cloudos bash array-job [OPTIONS]

Options

-k, --apikey <apikey>

Required Your CloudOS API key

--command <command>

The command to run in the bash job.

-c, --cloudos-url <cloudos_url>

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

--workspace-id <workspace_id>

Required The specific CloudOS workspace id.

--project-name <project_name>

Required The name of a CloudOS project.

--workflow-name <workflow_name>

Required The name of a CloudOS 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.

--storage-mode <storage_mode>

Either ‘lustre’ or ‘regular’. Indicates if the user wants to select regular or lustre storage. Default=regular.

--lustre-size <lustre_size>

The lustre storage to be used when –storage-mode=lustre, in GB. It should be 1200 or a multiple of it. Default=1200.

--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 CloudOS. 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>

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 CloudOS.

Usage

cloudos bash job [OPTIONS]

Options

-k, --apikey <apikey>

Required Your CloudOS API key

--command <command>

Required The command to run in the bash job.

-c, --cloudos-url <cloudos_url>

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

--workspace-id <workspace_id>

Required The specific CloudOS workspace id.

--project-name <project_name>

Required The name of a CloudOS project.

--workflow-name <workflow_name>

Required The name of a CloudOS 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.

--storage-mode <storage_mode>

Either ‘lustre’ or ‘regular’. Indicates if the user wants to select regular or lustre storage. Default=regular.

--lustre-size <lustre_size>

The lustre storage to be used when –storage-mode=lustre, in GB. It should be 1200 or a multiple of it. Default=1200.

--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 CloudOS. 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

CloudOS 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

Usage

cloudos configure list-profiles [OPTIONS]

Options

--debug

Show detailed error information and tracebacks

remove-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

Cromwell server functionality: check status, start and stop.

Usage

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

Options

--debug

Show detailed error information and tracebacks

start

Restart Cromwell server in CloudOS.

Usage

cloudos cromwell start [OPTIONS]

Options

--version

Show the version and exit.

-k, --apikey <apikey>

Your CloudOS 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 CloudOS url you are trying to access to. Default=https://cloudos.lifebit.ai.

--workspace-id <workspace_id>

Required The specific CloudOS 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 CloudOS.

Usage

cloudos cromwell status [OPTIONS]

Options

--version

Show the version and exit.

-k, --apikey <apikey>

Your CloudOS 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 CloudOS url you are trying to access to. Default=https://cloudos.lifebit.ai.

--workspace-id <workspace_id>

Required The specific CloudOS 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 CloudOS.

Usage

cloudos cromwell stop [OPTIONS]

Options

--version

Show the version and exit.

-k, --apikey <apikey>

Your CloudOS 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 CloudOS url you are trying to access to. Default=https://cloudos.lifebit.ai.

--workspace-id <workspace_id>

Required The specific CloudOS 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

CloudOS 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 CloudOS API key.

-c, --cloudos-url <cloudos_url>

Required The CloudOS URL.

--workspace-id <workspace_id>

Required The CloudOS 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 CloudOS workspace dataset.

Usage

cloudos datasets ls [OPTIONS] [PATH]

Options

-k, --apikey <apikey>

Required Your CloudOS API key.

-c, --cloudos-url <cloudos_url>

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

--workspace-id <workspace_id>

Required The specific CloudOS 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>

The name of a CloudOS 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 CloudOS 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 CloudOS API key.

-c, --cloudos-url <cloudos_url>

Required The CloudOS URL.

--workspace-id <workspace_id>

Required The CloudOS 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 CloudOS 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 CloudOS API key.

-c, --cloudos-url <cloudos_url>

Required The CloudOS URL.

--workspace-id <workspace_id>

Required The CloudOS 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 CloudOS 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 CloudOS API key.

-c, --cloudos-url <cloudos_url>

Required The CloudOS URL.

--workspace-id <workspace_id>

Required The CloudOS 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 CloudOS 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 CloudOS API key.

-c, --cloudos-url <cloudos_url>

Required The CloudOS URL.

--workspace-id <workspace_id>

Required The CloudOS 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

job

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

Usage

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

Options

--debug

Show detailed error information and tracebacks

abort

Abort all specified jobs from a CloudOS workspace.

Usage

cloudos job abort [OPTIONS]

Options

-k, --apikey <apikey>

Required Your CloudOS API key

-c, --cloudos-url <cloudos_url>

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

--workspace-id <workspace_id>

Required The specific CloudOS 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.

--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 CloudOS API key

-c, --cloudos-url <cloudos_url>

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

--workspace-id <workspace_id>

Required The specific CloudOS workspace id.

--project-name <project_name>

The name of a CloudOS 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 CloudOS. Default=22.10.8.

Options:

22.10.8 | 24.04.4 | 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 CloudOS 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.

--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 CloudOS API key

-c, --cloudos-url <cloudos_url>

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

--workspace-id <workspace_id>

Required The specific CloudOS workspace id.

--project-name <project_name>

The name of a CloudOS 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 CloudOS. Default=22.10.8.

Options:

22.10.8 | 24.04.4 | 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 CloudOS 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.

--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 CloudOS.

Usage

cloudos job cost [OPTIONS]

Options

-k, --apikey <apikey>

Required Your CloudOS API key

-c, --cloudos-url <cloudos_url>

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

--workspace-id <workspace_id>

Required The specific CloudOS workspace id.

--job-id <job_id>

Required The job id in CloudOS 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 CloudOS.

Usage

cloudos job details [OPTIONS]

Options

-k, --apikey <apikey>

Required Your CloudOS API key

-c, --cloudos-url <cloudos_url>

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

--workspace-id <workspace_id>

Required The specific CloudOS workspace id.

--job-id <job_id>

Required The job id in CloudOS 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 CloudOS workspace.

Usage

cloudos job list [OPTIONS]

Options

-k, --apikey <apikey>

Required Your CloudOS API key

-c, --cloudos-url <cloudos_url>

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

--workspace-id <workspace_id>

Required The specific CloudOS 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 CloudOS API key

-c, --cloudos-url <cloudos_url>

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

--workspace-id <workspace_id>

Required The specific CloudOS workspace id.

--job-id <job_id>

Required The job id in CloudOS to search for.

Link the logs directories to an interactive session.

--session-id <session_id>

The specific CloudOS 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 CloudOS API key

-c, --cloudos-url <cloudos_url>

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

--workspace-id <workspace_id>

Required The specific CloudOS workspace id.

--job-id <job_id>

Required The job id in CloudOS to search for.

Link the results directories to an interactive session.

--delete

Delete the results directory of a CloudOS job.

-y, --yes

Skip confirmation prompt when deleting results.

--session-id <session_id>

The specific CloudOS 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

Submit a job to CloudOS.

Usage

cloudos job run [OPTIONS]

Options

-k, --apikey <apikey>

Required Your CloudOS API key

-c, --cloudos-url <cloudos_url>

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

--workspace-id <workspace_id>

Required The specific CloudOS workspace id.

--project-name <project_name>

Required The name of a CloudOS project.

--workflow-name <workflow_name>

Required The name of a CloudOS 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.

-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 CloudOS. Default=22.10.8.

Options:

22.10.8 | 24.04.4 | 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.

--storage-mode <storage_mode>

Either ‘lustre’ or ‘regular’. Indicates if the user wants to select regular or lustre storage. Default=regular.

--lustre-size <lustre_size>

The lustre storage to be used when –storage-mode=lustre, in GB. It should be 1200 or a multiple of it. Default=1200.

--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 CloudOS. 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 CloudOS.

--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

Check job status in CloudOS.

Usage

cloudos job status [OPTIONS]

Options

-k, --apikey <apikey>

Required Your CloudOS API key

-c, --cloudos-url <cloudos_url>

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

--workspace-id <workspace_id>

Required The specific CloudOS workspace id.

--job-id <job_id>

Required The job id in CloudOS 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 CloudOS API key

-c, --cloudos-url <cloudos_url>

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

--workspace-id <workspace_id>

Required The specific CloudOS workspace id.

--job-id <job_id>

Required The job id in CloudOS to search for.

Link the working directory to an interactive session.

--delete

Delete the results directory of a CloudOS job.

-y, --yes

Skip confirmation prompt when deleting results.

--session-id <session_id>

The specific CloudOS 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

CloudOS procurement functionality.

Usage

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

Options

--debug

Show detailed error information and tracebacks

images

CloudOS procurement images functionality.

Usage

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

Options

--debug

Show detailed error information and tracebacks

ls

List images associated with organisations of a given procurement.

Usage

cloudos procurement images ls [OPTIONS]

Options

-k, --apikey <apikey>

Required Your CloudOS API key.

-c, --cloudos-url <cloudos_url>

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

--procurement-id <procurement_id>

Required The specific CloudOS 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.

--debug

Show detailed error information and tracebacks

--profile <profile>

Profile to use from the config file

reset

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

Usage

cloudos procurement images reset [OPTIONS]

Options

-k, --apikey <apikey>

Required Your CloudOS API key.

-c, --cloudos-url <cloudos_url>

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

--procurement-id <procurement_id>

Required The specific CloudOS procurement id.

--organisation-id <organisation_id>

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

--image-type <image_type>

Required The CloudOS resource image type.

Options:

RegularInteractiveSessions | SparkInteractiveSessions | RStudioInteractiveSessions | JupyterInteractiveSessions | JobDefault | NextflowBatchComputeEnvironment

--provider <provider>

Required The cloud provider. Only aws is supported.

Options:

aws

--region <region>

Required The cloud region. Only aws 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.

--debug

Show detailed error information and tracebacks

--profile <profile>

Profile to use from the config file

set

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

Usage

cloudos procurement images set [OPTIONS]

Options

-k, --apikey <apikey>

Required Your CloudOS API key.

-c, --cloudos-url <cloudos_url>

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

--procurement-id <procurement_id>

Required The specific CloudOS procurement id.

--organisation-id <organisation_id>

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

--image-type <image_type>

Required The CloudOS resource image type.

Options:

RegularInteractiveSessions | SparkInteractiveSessions | RStudioInteractiveSessions | JupyterInteractiveSessions | JobDefault | NextflowBatchComputeEnvironment

--provider <provider>

Required The cloud provider. Only aws is supported.

Options:

aws

--region <region>

Required The cloud region. Only aws regions are supported.

--image-id <image_id>

Required The new image id value.

--image-name <image_name>

The new image name 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.

--debug

Show detailed error information and tracebacks

--profile <profile>

Profile to use from the config file

project

CloudOS project functionality: list and create projects in CloudOS.

Usage

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

Options

--debug

Show detailed error information and tracebacks

create

Create a new project in CloudOS.

Usage

cloudos project create [OPTIONS]

Options

-k, --apikey <apikey>

Required Your CloudOS API key

-c, --cloudos-url <cloudos_url>

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

--workspace-id <workspace_id>

Required The specific CloudOS 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 all projects from a CloudOS workspace in CSV format.

Usage

cloudos project list [OPTIONS]

Options

-k, --apikey <apikey>

Required Your CloudOS API key

-c, --cloudos-url <cloudos_url>

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

--workspace-id <workspace_id>

Required The specific CloudOS workspace id.

--output-basename <output_basename>

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

--output-format <output_format>

The desired file format (file extension) for the output. Default=csv.

Options:

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

CloudOS job queue functionality.

Usage

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

Options

--debug

Show detailed error information and tracebacks

list

Collect all available job queues from a CloudOS workspace.

Usage

cloudos queue list [OPTIONS]

Options

-k, --apikey <apikey>

Required Your CloudOS API key

-c, --cloudos-url <cloudos_url>

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

--workspace-id <workspace_id>

Required The specific CloudOS workspace id.

--output-basename <output_basename>

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

--output-format <output_format>

The desired file format (file extension) for the output. Default=csv.

Options:

csv | json

--all-fields

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

--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

CloudOS 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 CloudOS API key

-c, --cloudos-url <cloudos_url>

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

--workspace-id <workspace_id>

Required The specific CloudOS 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 CloudOS.

-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 all workflows from a CloudOS workspace in CSV format.

Usage

cloudos workflow list [OPTIONS]

Options

-k, --apikey <apikey>

Required Your CloudOS API key

-c, --cloudos-url <cloudos_url>

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

--workspace-id <workspace_id>

Required The specific CloudOS workspace id.

--output-basename <output_basename>

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

--output-format <output_format>

The desired file format (file extension) for the output. Default=csv.

Options:

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