permedcoe 0.0.12

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).