BioBB Global Properties

Overview

The BioBBGlobalProperties class provides a centralized way to manage global configuration properties that are shared across all BiobbObject instances in your workflow. This eliminates the need to pass the same properties repeatedly to each building block.

Features

Global Configuration: Set properties once and use them across all BioBB objects
Priority System: Local properties override global properties when conflicts arise
Dictionary Interface: Behaves like a standard Python dictionary
Shallow Copy Support: Safe property sharing without unintended modifications

Usage

Basic Usage

The global properties instance is automatically created and available for import:

from biobb_common import biobb_global_properties

# Set global properties
biobb_global_properties.update({
    'container_path': '/usr/bin/singularity',
    'container_image': 'biocontainers/gromacs:latest',
    'remove_tmp': True,
    'restart': False
})

Setting Properties

You can set properties using dictionary-style operations:

# Set individual properties
biobb_global_properties['binary_path'] = '/usr/local/bin/gmx'
biobb_global_properties['timeout'] = 3600

# Set multiple properties at once
biobb_global_properties.update({
    'container_volume_path': '/data',
    'container_working_dir': '/tmp',
    'disable_logs': False
})

Using with BioBB Objects

When creating BioBB objects, global properties are automatically merged with local properties:

from biobb_gromacs.gromacs.mdrun import mdrun
from biobb_common import biobb_global_properties

# Set global properties once
biobb_global_properties.update({
    'container_path': '/usr/bin/singularity',
    'container_image': 'biocontainers/gromacs:latest',
    'remove_tmp': True
})

# Create BioBB object - global properties are automatically applied
mdrun_obj = mdrun(
    input_tpr_path='input.tpr',
    output_trr_path='output.trr',
    output_gro_path='output.gro',
    output_edr_path='output.edr',
    output_log_path='output.log',
    properties={
        'mpi_bin': 'mpirun',  # This local property is added
        'timeout': 7200       # This overrides global timeout if set
    }
)

Property Priority

Local properties always take precedence over global properties:

# Global setting
biobb_global_properties['timeout'] = 3600

# Local setting overrides global
my_object = SomeBioBBClass(
    properties={
        'timeout': 7200  # This value will be used, not 3600
    }
)

Common Use Cases

Container Configuration

Set container settings once for all building blocks:

biobb_global_properties.update({
    'container_path': '/usr/bin/singularity',
    'container_image': 'biocontainers/gromacs:2021.1--h_fbb9dd7_1',
    'container_volume_path': '/data',
    'container_working_dir': '/tmp'
})

Workflow-wide Settings

Configure common workflow properties:

biobb_global_properties.update({
    'remove_tmp': True,
    'restart': False,
    'sandbox_path': './workflow_sandbox',
    'disable_logs': False
})

Environment Variables

Set environment variables for all containers:

biobb_global_properties['env_vars_dict'] = {
    'OMP_NUM_THREADS': '4',
    'CUDA_VISIBLE_DEVICES': '0',
    'GMX_MAXBACKUP': '-1'
}

Best Practices

Set Early: Configure global properties at the beginning of your workflow
Use for Common Settings: Apply to properties shared across multiple building blocks
Override When Needed: Use local properties for block-specific configurations
Clear Documentation: Document which properties are set globally in your workflow

Example Workflow

from biobb_common import biobb_global_properties
from biobb_gromacs.gromacs.editconf import editconf
from biobb_gromacs.gromacs.solvate import solvate
from biobb_gromacs.gromacs.mdrun import mdrun

# Configure global properties once
biobb_global_properties.update({
    'container_path': '/usr/bin/singularity',
    'container_image': 'biocontainers/gromacs:latest',
    'remove_tmp': True,
    'restart': False,
    'env_vars_dict': {
        'OMP_NUM_THREADS': '8'
    }
})

# All building blocks will inherit these properties
editconf_step = editconf(
    input_gro_path='input.gro',
    output_gro_path='editconf.gro'
)

solvate_step = solvate(
    input_solute_gro_path='editconf.gro',
    output_gro_path='solvated.gro',
    properties={
        'shell': 1.0  # Local property specific to solvate
    }
)

mdrun_step = mdrun(
    input_tpr_path='input.tpr',
    output_trr_path='output.trr',
    properties={
        'timeout': 7200  # Override global timeout for this step
    }
)

API Reference

class biobb_common.BioBBGlobalProperties[source]

Bases: dict

Global properties container for all BiobbObject instances.

dict()[source]: Create a shallow copy of the global properties.

biobb_common.biobb_global_properties = BioBBGlobalProperties()

Global properties container for all BiobbObject instances.

Global instance of BioBBGlobalProperties available for immediate use.