Welcome to BIOMERO’s documentation!
For publication references and guidance on which BIOMERO paper to cite, see Citing BIOMERO.
BIOMERO - Get Started
BIOMERO — BioImage Analysis in OMERO- BIOMERO 2.0
- BIOMERO Python library (BIOMERO.analyzer)
- Quickstart
- Prerequisites & Getting Started with BIOMERO
- BIOMERO.scripts
- BIOMERO Web Interface
- (Docker) containers
- See the tutorials
- Developer: Eventsourcing and Views
- SSH
- SlurmClient class
- slurm-config.ini
- How to add an existing workflow
- How to add your new custom workflow
- Slurm jobs
- Batching
- Using the GPU on Slurm
- Transfering data
- Testing the Python code
- Logging
- Citing BIOMERO
Tutorials
- Cellprofiler tutorial
- 0. Prerequisite: OMERO, Slurm and
biomero. - 1. Grab the data and pipeline
- 2. Try the pipeline locally
- 3. Upload the data to OMERO
- 4. Package the cellprofiler in a FAIR package
- 5. Add this workflow to the OMERO Slurm Client
- 6. Add a OMERO script to run this from the Web UI
- Extra: How to add workflow parameters to cellprofiler?
- Extra 2: We should add a LICENSE
- 0. Prerequisite: OMERO, Slurm and
- CellExpansion tutorial
- Local Slurm tutorial
- Google Cloud Slurm tutorial
- Microsoft Azure Slurm tutorial
- Extra thoughts
Configuration
Package
- biomero
- biomero package
- biomero.slurm_client module
SlurmClientSlurmClient.slurm_data_pathSlurmClient.slurm_images_pathSlurmClient.slurm_converters_pathSlurmClient.slurm_model_pathsSlurmClient.slurm_model_reposSlurmClient.slurm_model_imagesSlurmClient.slurm_script_pathSlurmClient.slurm_script_repoSlurmClient.bring_listener_uptodate()SlurmClient.check_job_status()SlurmClient.cleanup_tmp_files()SlurmClient.convert_param_type_to_omtype()SlurmClient.convert_url()SlurmClient.copy_zip_locally()SlurmClient.extract_data_location_from_log()SlurmClient.extract_job_id()SlurmClient.extract_parts_from_url()SlurmClient.from_config()SlurmClient.generate_slurm_job_for_workflow()SlurmClient.generic_descriptor_from_github()SlurmClient.get_active_job_progress()SlurmClient.get_all_image_versions_and_data_files()SlurmClient.get_authoritative_config_path()SlurmClient.get_cellpose_command()SlurmClient.get_config_paths()SlurmClient.get_config_write_path()SlurmClient.get_conversion_command()SlurmClient.get_conversion_logfile_from_slurm()SlurmClient.get_file_attachment_params()SlurmClient.get_image_versions_and_data_files()SlurmClient.get_job_status_command()SlurmClient.get_jobs_info_command()SlurmClient.get_listeners()SlurmClient.get_logfile_from_slurm()SlurmClient.get_or_create_github_session()SlurmClient.get_recent_log_command()SlurmClient.get_unzip_command()SlurmClient.get_update_slurm_scripts_command()SlurmClient.get_workflow_command()SlurmClient.get_workflow_parameters()SlurmClient.get_zip_command()SlurmClient.init_workflows()SlurmClient.initialize_analytics_system()SlurmClient.list_active_jobs()SlurmClient.list_all_jobs()SlurmClient.list_available_converter_versions()SlurmClient.list_completed_jobs()SlurmClient.load_config()SlurmClient.parse_docker_image_version()SlurmClient.run_commands()SlurmClient.run_commands_split_out()SlurmClient.run_conversion_workflow_job()SlurmClient.run_workflow()SlurmClient.run_workflow_job()SlurmClient.setup_container_images()SlurmClient.setup_converters()SlurmClient.setup_directories()SlurmClient.setup_job_scripts()SlurmClient.setup_listeners()SlurmClient.setup_slurm()SlurmClient.str_to_class()SlurmClient.transfer_data()SlurmClient.unpack_data()SlurmClient.update_slurm_scripts()SlurmClient.validate()SlurmClient.workflow_bilayers_folder_params_to_subs()SlurmClient.workflow_params_to_envvars()SlurmClient.workflow_params_to_subs()SlurmClient.workflow_template_subs()SlurmClient.zip_data_on_slurm_server()
SlurmJob
- biomero.eventsourcing module
NoOpWorkflowTrackerResultDictTaskTask.workflow_idTask.task_nameTask.task_versionTask.input_dataTask.paramsTask.job_idsTask.resultsTask.result_messageTask.statusTask.CreatedTask.EventTask.INITIAL_VERSIONTask.JobIdAddedTask.ProgressUpdatedTask.ResultAddedTask.StatusUpdatedTask.TaskCompletedTask.TaskCreatedTask.TaskFailedTask.TaskStartedTask.add_job_idTask.add_result()Task.complete_taskTask.fail_taskTask.start_taskTask.update_task_progressTask.update_task_status
WorkflowRunWorkflowRun.nameWorkflowRun.descriptionWorkflowRun.userWorkflowRun.groupWorkflowRun.tasksWorkflowRun.CreatedWorkflowRun.EventWorkflowRun.INITIAL_VERSIONWorkflowRun.TaskAddedWorkflowRun.WorkflowCompletedWorkflowRun.WorkflowFailedWorkflowRun.WorkflowInitiatedWorkflowRun.WorkflowStartedWorkflowRun.add_taskWorkflowRun.complete_workflowWorkflowRun.fail_workflowWorkflowRun.start_workflow
WorkflowTrackerWorkflowTracker.initiate_workflow()WorkflowTracker.add_task_to_workflow()WorkflowTracker.start_workflow()WorkflowTracker.complete_workflow()WorkflowTracker.fail_workflow()WorkflowTracker.start_task()WorkflowTracker.complete_task()WorkflowTracker.fail_task()WorkflowTracker.add_job_id()WorkflowTracker.add_result()WorkflowTracker.update_task_status()WorkflowTracker.update_task_progress()WorkflowTracker.add_job_id()WorkflowTracker.add_result()WorkflowTracker.add_task_to_workflow()WorkflowTracker.complete_task()WorkflowTracker.complete_workflow()WorkflowTracker.fail_task()WorkflowTracker.fail_workflow()WorkflowTracker.initiate_workflow()WorkflowTracker.nameWorkflowTracker.start_task()WorkflowTracker.start_workflow()WorkflowTracker.update_task_progress()WorkflowTracker.update_task_status()
- biomero.views module
- biomero.slurm_client module
- biomero package