homer-docker-singularity

Build Docker container for Homer and (optionally) convert to Apptainer/Singularity.

HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and next-gen sequencing analysis. It is a collection of command line programs for UNIX-style operating systems written in Perl and C++. HOMER was primarily written as a de novo motif discovery algorithm and is well suited for finding 8-20 bp motifs in large scale genomics data. HOMER contains many useful tools for analyzing ChIP-Seq, GRO-Seq, RNA-Seq, DNase-Seq, Hi-C and numerous other types of functional genomics sequencing data sets.
http://homer.ucsd.edu/homer/

Requirements:

gcc g++ make perl zip/unzip gzip/gunzip wget samtools (optional) R (optional)

Build docker container:

1. For homer installation instructions:

http://homer.ucsd.edu/homer/introduction/install.html
http://homer.ucsd.edu/homer/download.html

2. Build the Docker Image

# Assumes current working directory is the top-level tophat2-docker-singularity directory
docker build -t homer:4.11.1 . # tag should match software version (configureHomer.pl can specify version version)

• Can do this on Google shell

To test this tool from the command line:

Mount and use your current directory and call the tool now encapsulated within the container

docker run --rm -it homer:4.11.1 homer
docker run --rm -it homer:4.11.1 perl /opt/homer/configureHomer.pl -list | grep homer
docker run --rm -it homer:4.11.1 perl /opt/homer/configureHomer.pl -check

3. Download and mount homer data

Due to space limitations, especially on Google Cloud Shell, need to link/mount Homer annotation data from outside containers

mkdir homer_data && cd homer_data
wget http://homer.ucsd.edu/homer/configureHomer.pl
perl ./configureHomer.pl -install hg38 # this will download "hg38" and "human" annotation packages

# Optional: archive and compress for transfer to eg HPC without internet access
cd .. && tar -czvf homer_data.tar.gz homer_data
# Transfer to final location and extract
tar -xzvf homer_data.tar.gz

Check if homer can see mounted reference and annotation data

# first set up path to homer_data
HOMER_DATA=path/to/homer_data
# Mount homer data in container at /opt/homerdata (see symlinks created in Dockerfile)
docker run --rm -it -v $HOMER_DATA:/opt/homerdata homer:4.11.1 /usr/bin/perl /opt/homer/configureHomer.pl -list
# output should indicate that correct genome packages are installed

Optional: Conversion of Docker image to Singularity

4. Build a Docker image to run Singularity

(skip if this image is already on your system)
https://github.com/mattgalbraith/singularity-docker

5. Save Docker image as tar and convert to sif (using singularity run from Docker container)

docker images
docker save <Image_ID> -o homer4.11.1-docker.tar && gzip homer4.11.1-docker.tar # = IMAGE_ID of tophat image
docker run -v "$PWD":/data --rm -it singularity:1.1.5 bash -c "singularity build /data/homer4.11.1.sif docker-archive:///data/homer4.11.1-docker.tar.gz"

NB: On Apple M1/M2 machines ensure Singularity image is built with x86_64 architecture or sif may get built with arm64

Next, transfer the homer.sif file to the system on which you want to run Homer from the Singularity container

6. Test singularity container with mounted homer data on (HPC) system with Singularity/Apptainer available

# set up path to the homer Singularity container
HOMER_SIF=path/to/homer4.11.1.sif
# set up path to homer_data
HOMER_DATA=path/to/homer_data

# Test that Homer can run from Singularity container
singularity run $HOMER_SIF homer # depending on system/version, singularity is now apptainer

# Mount homer data in container at /opt/homerdata (see symlinks created in Dockerfile)
singularity run --bind $HOMER_DATA:/opt/homerdata $HOMER_SIF bash # depending on system/version, singularity is now apptainer
ls -lah /opt/homer/ # should show symlinks to homerdata
ls -lah /opt/homerdata/ # should see data and config.txt
perl /opt/homer/configureHomer.pl -list # output should indicate that correct genome packages are installed