This package provides the cll_run_boolean_model Building Block (BB) using the HPC/Exascale Centre of Excellence in Personalised Medicine (PerMedCoE) base Building Block.
This building block evaluates a single patient or group-specific model using MaBoSS.
- Python >= 3.6
- Singularity
permedcoebase package:python3 -m pip install permedcoe
In addition to the dependencies, it is necessary to generate the associated
singularity image (cll_run_boolean_model.singularity),
located in the Resources folder of this repository.
They MUST be available and exported in the following environment variable before its usage:
export PERMEDCOE_IMAGES="/path/to/images/"This package provides an automatic installation script:
./install.shThe cll_run_boolean_model package provides a clear interface that allows
it to be used with multiple workflow managers (e.g. PyCOMPSs, NextFlow and
Snakemake).
It can be imported from python and invoked directly from a PyCOMPSs application, or through the command line for other workflow managers (e.g. Snakemake and NextFlow).
The command line is:
cll_run_boolean_model_BB -d \
--tmpdir <working_directory> \
--sif <sif> \
--bnd <bnd> \
--cfg <cfg> \
--id <id> \
--outdir <outdir>Where the parameters are:
| Flag | Parameter | Type | Description | |
|---|---|---|---|---|
| --tmpdir | <working_directory> | Folder | Working directory (temporary files) | |
| Input | --sif | <sif> | File | Inferred network (in sif format) |
| Input | --bnd | <bnd> | File | BND boolean model file |
| Input | --cfg | <cfg> | File | CFG file describing group of patient personalised rates |
| Input | --id | <id> | String | Selected group/patient id |
| Output | --outdir | <outdir> | Folder | Output folder |
Uninstall can be achieved by executing the following scripts:
./uninstall.sh
./clean.shThis software has been developed for the PerMedCoE project, funded by the European Commission (EU H2020 951773).
