This package provides the base for all Building Blocks (BBs) developed in the HPC/Exascale Centre of Excellence in Personalised Medicine (PerMedCoE) project.
- Python >= 3.6
- Singularity
There are two ways to install this package (from Pypi and manually):
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From Pypi:
This package is publicly available in Pypi:
pip install permedcoe
or more specifically:
python3 -m pip install permedcoe
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From source code:
This package provides an automatic installation script:
./install.sh
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)-
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)
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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)
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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/.
The permedcoe package provides a set of public decorators, parameter type definition and functions to be used in the Building Block implementation.
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Public decorators:
from permedcoe import container from permedcoe import constraint from permedcoe import binary from permedcoe import mpi from permedcoe import task
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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
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Functions:
from permedcoe import get_environment from permedcoe import set_debug from permedcoe import invoker
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Classes:
from permedcoe import Arguments
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):
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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.shscript../clean.sh
If you are willing to implement your Building Block (BB), check the following repositories, where you will find documentation, tutorials, and BB/application samples:
This software has been developed for the PerMedCoE project, funded by the European Commission (EU H2020 951773).
