Description:

permedcoe 0.0.12

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).

License

For personal and professional use. You cannot resell or redistribute these repositories in their original state.

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