Skip to content

Latest commit

 

History

History

export_solver_hdf5

README.md

Export Solver HDF5 Building Block

This package provides the Export Solver HDF5 Building Block (BB).

Table of Contents

Description

Exports input data required by the vanilla version of CARNIVAL (sif file, measurements and perturbations) into a HDF5 file required by the optimised version of CARNIVAL with the parallel ACO C++ solver.

User instructions

Requirements

  • Python >= 3.6
  • Singularity
  • permedcoe base package: python3 -m pip install permedcoe

In addition to the dependencies, it is necessary to generate the associated singularity image (toolset.singularity), located in the Resources folder of this repository.

They MUST be available and exported respectively in the following environment variable before its usage:

export PERMEDCOE_IMAGES="/path/to/images/"

Installation

This package provides an automatic installation script:

./install.sh

Usage

The export_solver_hdf5_BB 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:

export_solver_hdf5_BB -d \
    --tmpdir <working_directory> \
    --sif <sif> \
    --measurements <measurements> \
    --inputs <inputs> \
    --verbose <verbose> \
    --output_file <output_file>

Where the parameters are:

Flag Parameter Type Description
--tmpdir <working_directory> Folder Working directory (temporary files)
Input --sif <sif> File The sif csv file containing the signaling network
Input --measurements <measurements> String The measurements csv with the TFs and weights
Input --inputs <inputs> File The csv file with the input protein targets
Input --verbose <verbose> String Verbose output (TRUE/FALSE)
Output --output_file <output_file> File The final HDF5 file.

An example with toy data from here https://github.com/saezlab/permedcoe/tree/master/containers/toolset/scripts/examples/export would be:

export_solver_hdf5_BB \
    --sif sif.csv \
    --measurements measurements.csv \
    --inputs inputs.csv \
    --verbose TRUE \
    --output_file file.h5

Uninstall

Uninstall can be achieved by executing the following scripts:

./uninstall.sh
./clean.sh

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).