CLI Reference¶
This section documents the CloudOS CLI commands and options.
cloudos¶
CloudOS python package: a package for interacting with CloudOS.
cloudos [OPTIONS] COMMAND [ARGS]...
Options
- --debug¶
Show detailed error information and tracebacks
- --version¶
Show the version and exit.
bash¶
CloudOS bash functionality.
cloudos bash [OPTIONS] COMMAND [ARGS]...
array-job¶
Run a bash array job in CloudOS.
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).
- --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 parameter. It should be in the following form: parameter_name=parameter_value. E.g.: -a –test=value or -a -test=value or -a test=value. 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.
- --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.
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).
- --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
configure¶
CloudOS configuration.
cloudos configure [OPTIONS] COMMAND [ARGS]...
Options
- --profile <profile>¶
Profile to use from the config file
- --make-default¶
Make the profile the default one.
list-profiles¶
cloudos configure list-profiles [OPTIONS]
remove-profile¶
cloudos configure remove-profile [OPTIONS]
Options
- --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.
cloudos cromwell [OPTIONS] COMMAND [ARGS]...
start¶
Restart Cromwell server in CloudOS.
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.
- --profile <profile>¶
Profile to use from the config file
status¶
Check Cromwell server status in CloudOS.
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.
- --profile <profile>¶
Profile to use from the config file
stop¶
Stop Cromwell server in CloudOS.
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.
- --profile <profile>¶
Profile to use from the config file
datasets¶
CloudOS datasets functionality.
cloudos datasets [OPTIONS] COMMAND [ARGS]...
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
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.
- --profile <profile>¶
Profile to use from the config file.
Arguments
- SOURCE_PATH¶
Required argument
- DESTINATION_PATH¶
Required argument
link¶
Link a folder (S3 or File Explorer) to an active interactive analysis.
PATH [path]: the full path to the S3 folder to link or relative to File Explorer. E.g.: ‘s3://bucket-name/folder/subfolder’, ‘Data/Downloads’ or ‘Data’.
cloudos datasets link [OPTIONS] PATH
Options
- -k, --apikey <apikey>¶
Required Your CloudOS API key
- -c, --cloudos-url <cloudos_url>¶
The CloudOS url you are trying to access to. Default=https://cloudos.lifebit.ai.
- --project-name <project_name>¶
The name of a CloudOS project.
- --workspace-id <workspace_id>¶
Required The specific CloudOS workspace id.
- --session-id <session_id>¶
Required The specific CloudOS interactive session id.
- --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
Arguments
- PATH¶
Required argument
ls¶
List contents of a path within a CloudOS workspace dataset.
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”.
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’.
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.
- --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’
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.
- --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’
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.
- --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’
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.
- --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.
cloudos job [OPTIONS] COMMAND [ARGS]...
abort¶
Abort all specified jobs from a CloudOS workspace.
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.
- --profile <profile>¶
Profile to use from the config file
clone-resume¶
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.
- --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.
- --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.
- --profile <profile>¶
Profile to use from the config file
clone-resume¶
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.
- --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.
- --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.
- --profile <profile>¶
Profile to use from the config file
details¶
Retrieve job details in CloudOS.
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.
- --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 | json
- --output-basename <output_basename>¶
Output file base name to save jobs details. Default=job_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.
- --profile <profile>¶
Profile to use from the config file
list¶
Collect workspace jobs from a CloudOS workspace in CSV or JSON format.
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 file format (file extension) for the output. For json option –all-fields will be automatically set to True. Default=csv.
- Options:
csv | json
- --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. Default=30.
- --page <page>¶
Response page to retrieve. If –last-n-jobs is set, then –page value corresponds to the first page to retrieve. Default=1.
- --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.
- --profile <profile>¶
Profile to use from the config file
logs¶
Get the path to the logs of a specified job.
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.
- --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
results¶
Get the path to the results of a specified job.
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.
- --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
run¶
Submit a job to CloudOS.
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.
- --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.
- --profile <profile>¶
Profile to use from the config file
status¶
Check job status in CloudOS.
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.
- --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.
- --profile <profile>¶
Profile to use from the config file
workdir¶
Get the path to the working directory of a specified job.
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.
- --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
procurement¶
CloudOS procurement functionality.
cloudos procurement [OPTIONS] COMMAND [ARGS]...
images¶
CloudOS procurement images functionality.
cloudos procurement images [OPTIONS] COMMAND [ARGS]...
ls¶
List images associated with organisations of a given procurement.
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.
- --profile <profile>¶
Profile to use from the config file
reset¶
Reset image associated with an organisations of a given procurement to CloudOS defaults.
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.
- --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.
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.
- --profile <profile>¶
Profile to use from the config file
project¶
CloudOS project functionality: list and create projects in CloudOS.
cloudos project [OPTIONS] COMMAND [ARGS]...
create¶
Create a new project in CloudOS.
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.
- --profile <profile>¶
Profile to use from the config file
list¶
Collect all projects from a CloudOS workspace in CSV format.
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.
- --profile <profile>¶
Profile to use from the config file
queue¶
CloudOS job queue functionality.
cloudos queue [OPTIONS] COMMAND [ARGS]...
list¶
Collect all available job queues from a CloudOS workspace.
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.
- --profile <profile>¶
Profile to use from the config file
workflow¶
CloudOS workflow functionality: list and import workflows.
cloudos workflow [OPTIONS] COMMAND [ARGS]...
import¶
Import workflows from supported repository providers.
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.
- --profile <profile>¶
Profile to use from the config file
list¶
Collect all workflows from a CloudOS workspace in CSV format.
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.
- --profile <profile>¶
Profile to use from the config file