Nucleosome Dynamics - docker implementation

Nucleosome Dynamics docker image is a containerized implementation of 'Nucleosome Dynamics suite' particularly developed for use with the Galaxy platform.

Nucleosome Dynamics

Nucleosome Dynamics is a suite of R programs for nucleosome-related analyses based on MNase-seq experimental data. The toolkit includes the following analyses:

• nucleR: define and classify the location of nucleosomes from MNase-seq data.
• Nucleosome Dynamics: compares different MNase-seq experiments identifying variations in nucleosomes location.
• NFR: locate nucleosome-free regions
• Periodicity: predicts nucleosome phasing at gene level
• TSS: classify transcription start sites based on the surrounding nucleosomes
• Stiffness: computes nucleosome stiffness derived from a Gaussian function fitting

Container software

This docker image extends and distributes the following rellevant software:

• R libraries:
  • NucleR R library: https://github.com/nucleosome-dynamics/nucleR
  • Nucleosome Dynamics R library: https://github.com/nucleosome-dynamics/NucDyn
• R programs:
  • Nucleosome Dynamics analyses: https://github.com/nucleosome-dynamics/nucleosome_dynamics

Build the image

The docker image for Nucleosome Dynamics can be found in the docker hub as mmbirb/nucleosome-dynamics. However, this repository contains the data to manually rebuild it by running docker build.

docker build -t nucleosome-dynamics .

Note that the current working directory must contain the Dockerfile file.

Running nucleosome-dynamics container

You can either run the container manually, or via the web-based Galaxy platform. In both cases, individual nucleosome-related analyses are offered as:

• individual analyses
• workflow

Install docker for your system, if not previously done.

Running an individual analysis

You can run manually your containers using the following command:

docker run -v /path/to/data_dir/:/path/to/data_dir mmbirb/nucleosome-dynamics  [analysis] [analysis_options]

In case you do not have the container stored locally, docker will download it for you. Once the execution is finished, the container will exit.

A short description of the parameters would be:

• docker run will run the container for you.
• -v /path/to/data_dir/:/path/to/data_dir will make the data_dir where input files are stored available to the container
• mmbirb/nucleosome-dynamics is the image name, which can be found in the docker hub.
• [analysis] [analysis_options] correspond to the analysis type you want to run and its paremeters.

Available analysis are:

[analysis]	Description
readBAM	Read Aligned MSase-seq BAM into a RData structure (required for further process)
nucleR	Determine the positions of the nucleosomes across the genome
NFR	Short regions depleted of nucleosomes
txstart	Classify Transciption start accordint to the properties of surrounding nucleosomes
periodicity	Periodic properties of nucleosomes inside gene bodies
stiffness	Aparent stiffness constant foreach nucleosome obtained by fitting the coverage to a gaussian distribution
nucleR_stats	Nucleosome call statistics
nucDyn	Comparison of two diferent MNase-seq experiments to nucleosome architecture local changes
NFR_stats	Nucleosome Free Regions statistics
txstart_stats	TSS and TTS statistics
periodicity_stats	Statistics on Nucleosome periodicity
stiffness_stats	Statistics on stiffness
nucDyn_stats	Statistics on Nucleosome Dynamics analysis

Each analysis has its own input files and arguments. docker run mmbirb/nucleosome-dynamics [analysis] --help will display such information in detail. Yet, a full usage description can be found at the Nucleosome Dynamics repository.

Example

Here is an example on how to load a MNase-seq reads file using readBAM. It takes as input a BAM file and convert it into an RData file ready to be feed to other analyses ('nucleR', 'NFR', etc.).

docker run -v $PWD/test/data/:$PWD/test/data mmbirb/nucleosome-dynamics readBAM --input $PWD/test/data/cellcycleG2_chrII.bam --output $PWD/test/data/cellcycleG2_chrII.RData --type paired

Running a workflow script

You can combine different analysis tools to build your own workflow, you can do it at Galaxy platform or you can run it manually following this command:

docker run -v /path/to/data_dir/:/path/to/data_dir mmbirb/nucleosome-dynamics  run  [WF_file_path]

Where:

• WF_file_path: is a bash file containing the Rscript calls to different analyses.

Example

Here is an example on how to run the test workflow file test/scripts/wf-test.sh, a bash file sequencially calling all 'Nucleosome Dynamics' analyses.

docker run -v /path/to/data_dir/:/path/to/data_dir mmbirb/nucleosome-dynamics  run /path/to/data_dir/test/scripts/wf-test.sh