HPC/Exascale Centre of Excellence in Personalised Medicine

Base Building Block

This package provides the base for all Building Blocks (BBs) developed in the HPC/Exascale Centre of Excellence in Personalised Medicine (PerMedCoE) project.

Table of Contents

• HPC/Exascale Centre of Excellence in Personalised Medicine
  • Base Building Block
  • Table of Contents
  • User instructions
    • Requirements
    • Installation
    • Command line
      • Option execute:
      • Option template:
      • Option deploy:
    • Public API
    • Uninstall
  • Developer instructions
    • Building block
  • License
  • Contact

User instructions

Requirements

• Python >= 3.6
• Singularity

Installation

There are two ways to install this package (from Pypi and manually):

• From Pypi:

  This package is publicly available in Pypi:

  pip install permedcoe
  

  or more specifically:

  python3 -m pip install permedcoe
  

• From source code:

  This package provides an automatic installation script:

  ./install.sh
  

Command line

This package provides the permedcoe command:

$ permedcoe -h
usage: permedcoe [-h] [-d] [-l {debug,info,warning,error,critical}]
               {execute,x,template,t,deploy,d} ...

positional arguments:
  {execute,x,template,t,deploy,d}
    execute (x)         Execute a building block.
    template (t)        Shows an example of the requested template.
    deploy (d)          Download and deploy the requested workflow or building block.

options:
  -h, --help            show this help message and exit
  -d, --debug           Enable debug mode. Overrides log_level (default: False)
  -l {debug,info,warning,error,critical}, --log_level {debug,info,warning,error,critical}
                        Set logging level. (default: error)

Option execute:

• It enables to execute single building blocks or applications:

  $ permedcoe execute -h
  usage: permedcoe execute [-h] {building_block,bb,application,app} ...
  
  positional arguments:
    {building_block,bb,application,app}
      building_block (bb)
                          Execute a building block.
      application (app)   Execute an application.
  
  optional arguments:
    -h, --help            show this help message and exit
  

  • In particular for building blocks:

    $ permedcoe execute building_block -h
    usage: permedcoe execute building_block [-h] name [parameters ...]
    
    positional arguments:
      name        Building Block to execute
      parameters  Building Block parameters (default: None)
    
    options:
      -h, --help  show this help message and exit
    

    Specifying the particular building block to execute (must be installed), provides more detailed information:

    $ permedcoe execute building_block MaBoSS_BB -h
    usage: permedcoe [-h] [-c CONFIG] [-d] [-l {debug,info,warning,error,critical}] [--tmpdir TMPDIR]
                 [--processes PROCESSES] [--gpus GPUS] [--memory MEMORY] [--mount_points MOUNT_POINTS]
                 {default,sensitivity} ...
    
      This building block uses MaBoSS to screen all the possible knockouts of a given Boolean model. It
      produces a candidate gene list formatted as a text file (single gene per row). More information on
      MaBoSS can be found in [Stoll G. et al. (2017)](https://academic.oup.com/bioinformatics/article-
      lookup/doi/10.1093/bioinformatics/btx123) and in the [MaBoSS GitHub
      repository](https://github.com/maboss-bkmc/MaBoSS-env-2.0).
    
      positional arguments:
        {default,sensitivity}
    
      options:
        -h, --help            show this help message and exit
        -c CONFIG, --config CONFIG
                              (CONFIG) Configuration file path
        -d, --debug           Enable Building Block debug mode. Overrides log_level
        -l {debug,info,warning,error,critical}, --log_level {debug,info,warning,error,critical}
                              Set logging level
        --tmpdir TMPDIR       Temp directory to be mounted in the container
        --processes PROCESSES
                              Number of processes for MPI executions
        --gpus GPUS           Requirements for GPU jobs
        --memory MEMORY       Memory requirement
        --mount_points MOUNT_POINTS
                              Comma separated alias:folder to be mounted in the container
    

  • In particular for building blocks:

    $ permedcoe execute application -h
    usage: permedcoe execute application [-h] [-w {none,pycompss,nextflow,snakemake}]
                                        [-f FLAGS [FLAGS ...]]
                                        name [parameters [parameters ...]]
    
    positional arguments:
      name                  Application to execute
      parameters            Application parameters (default: None)
    
    optional arguments:
      -h, --help            show this help message and exit
      -w {none,pycompss,nextflow,snakemake}, --workflow_manager {none,pycompss,nextflow,snakemake}
                            Workflow manager to use (default: none)
      -f FLAGS [FLAGS ...], --flags FLAGS [FLAGS ...]
                            Workflow manager flags (default: None)
    

Option template:

• It available to create a skeleton of a building block or an application:

  $ permedcoe template -h
  usage: permedcoe template [-h] [-t {all,pycompss,nextflow,snakemake}]
                            {bb,building_block,app,application} name
  
  positional arguments:
    {bb,building_block,app,application}
                          Creates a Building Block or Application template.
    name                  Building Block or Application name.
  
  optional arguments:
    -h, --help            show this help message and exit
    -t {all,pycompss,nextflow,snakemake}, --type {all,pycompss,nextflow,snakemake}
                          Application type. (default: all)
  

Option deploy:

• It available to deploy an existing Building Block or Workflow in a local machine (e.g. laptop):

  $ permedcoe deploy -h
  usage: permedcoe deploy [-h] {building_block,bb,workflow,wf} ...
  
  positional arguments:
    {building_block,bb,workflow,wf}
      building_block (bb)
                          A specific building block.
      workflow (wf)       A specific workflow.
  
  options:
    -h, --help            show this help message and exit
  

For the deployment in supercomputers, please contact PerMedCoE: https://permedcoe.eu/contact/.

Public API

The permedcoe package provides a set of public decorators, parameter type definition and functions to be used in the Building Block implementation.

• Public decorators:

  from permedcoe import container
  from permedcoe import constraint
  from permedcoe import binary
  from permedcoe import mpi
  from permedcoe import task
  

• Parameter type definition:

  from permedcoe import Type
  from permedcoe import FILE_IN
  from permedcoe import FILE_OUT
  from permedcoe import FILE_INOUT
  from permedcoe import DIRECTORY_IN
  from permedcoe import DIRECTORY_OUT
  from permedcoe import DIRECTORY_INOUT
  from permedcoe import StdIOStream
  from permedcoe import STDIN
  from permedcoe import STDOUT
  from permedcoe import STDERR
  

• Functions:

  from permedcoe import get_environment
  from permedcoe import set_debug
  from permedcoe import invoker
  

• Classes:

  from permedcoe import Arguments
  

Uninstall

Uninstall can be done as usual pip packages:

There are two ways to uninstall this package, that depends on the way that it was installed (from Pypi or using install.sh):

• From Pypi:

  pip uninstall permedcoe
  

  or more specifically:

  python3 -m pip uninstall permedcoe
  

• From manual installation (using install.sh):

  ./uninstall.sh
  

  And then the folder can be cleaned as well using the clean.sh script.

  ./clean.sh
  

Developer instructions

Building block

If you are willing to implement your Building Block (BB), check the following repositories, where you will find documentation, tutorials, and BB/application samples:

• Documentation
• Tutorial
• basic_application
• Lysozyme_in_water

License

Apache 2.0

Contact

https://permedcoe.eu/contact/

This software has been developed for the PerMedCoE project, funded by the European Commission (EU H2020 951773).