Nucleosome Dynamics Server

This repository wrapps Nucleosome Dynamics CLI as a tool to make it accessible at the MuGVRE platform (http://multiscalegenomics.eu).

Nucleosome Dynamics

Nucleosome Dynamics is a suite of programs for defining nucleosome architecture and dynamics from MNase-seq and ATAC-seq experiments. They are implemented as a set of R libraries ([nucleR] (http://mmb.pcb.ub.es/gitlab/NuclDynamics/nucleR) and nucDyn) and programs (Nucleosome Dynamics CLI) on top of which several implementations have been created in order to improve accessibility and usability. These include:

1. MuGVRE platform: the domain-specific virtual research environment for 3D/4D genomics - http://multiscalegenomics.eu
2. Galaxy platform {GIT}: the popular analysis platform - https://dev.usegalaxy.es
3. Docker container {GIT}: find the image here
4. Singularity container {GIT}: find the image here

MuGVRE platform

MuG Virtual Research Environment (MuGVRE) is the virtual research environment specifically developed for the Multiscale complex Genomics (MuG) group, a research community focused on the 3D/4D genomics field. MuGVRE is a cloud-based e-infrastructure that integrates in a single framework rellevant data, tools and visualizers for the community in order to build a one-stop research platform.

Learn more and access MuGVRE : http://multiscalegenomics.eu

'Nucleosome Dynamics' is one of the tools offered at the platform (check the complete catalog).

Requirements

• Nucleosome Dynamics:
  • Nucleosome Dynamics CLI
    • NucDyn
    • nucleR
• Python Modules:
  • mg-tool-api logger

Nucleosome Dynamics CLI

Follow the instructions detailed at the Nucleosome Dynamics CLI repository on how to install the set of R scripts and dependencies.

mg-tool-api

The present Nucleosome Dynamics wrapping makes use of some MuG-developed utilities like mg-tool-api logger, already included in this repository. It is a python logging falicity to report execution progress, exceptions, etc

Nucleosome Dynamics Server

This repository contains the python wrappers and the configuration files necessary to register and integrate 'Nucleosome Dynamics CLI' into MuGVRE server:

• nucleosome_dynamics.py : MuGVRE tool. Interface for MuGVRE backend that receives web-user input files and calls 'Nucleosome Dynamics CLI' with them.
• nucleosome_dynamics.json: Tool definition. MuGVRE registry entry that defines 'Nucleosome Dynamics' tool with its input and output files, parameter definitions, resources, metadatam, etc.
• test/: Files for reproducing a 'Nucleosome Dynamics' run.

MuGVRE documentation includes a detailed explanation on the number of steps necessary to integrate a new tool into the platform.

Running 'Nucleosome Dynamics' tool

'Nucleosome Dynamics' tool is mean to be executed though the MuGVRE web interface. Yet, for checking this code integrity, the 'test/' folder contains a simple bash script and the required sample data that emulates how MuGVRE server deals with a tool execution.

MUGVRE platform interacts with a tool through a main wrapper, here nucleosome_dynamics.py. It always take as inputs a set of configuration JSON files that contains the rellevant information gathered from the web-user (input files and arguments) for a particular run. Also includes the data for the expected output files. For nucleosome dynamics, the script sequencially runs 'Nucleosome Dynamics CLI' according the given configuration files to end up executing a tailored Nucleosome Dynamics workflow based on the web-user indications.

Arguments

• config: JSON file containing the run parameters, working directory, analyses to be performed, and their specific arguments
• in_metadata: JSON file containing MuG metadata attached to each of the web-user input files
• out_metadata: Filename for the JSON that will contain output file metadata
• log_file: Filename for the log file

The following bash script runs the MuGVRE tool (nucleosome_dynamics.py) with the the configuration files set to read the MNase-seq sample data found at test/data.

cd test/test
bash test_0_AnalyseMNaseseqdata.sh

The test/test content has been automatically created by MuGVRE during the tool integration procedure (http://multiscalegenomics.eu/MuGVRE/instructions/) in order to check that VRE prepares the right configuration files based on the given tool definition. In this way, tool developers can easily check whether the MUGVRE tool (here nucleosome_dynamics.py) correctly fits the MuGVRE job processing.