G4Hunter [1][2] is a powerful and widely used tool for G4 prediction which takes into account G-richness and G-skewness of a DNA or RNA sequence and provides a quadruplex propensity score. G4Hunter is written in R programming language. The source code is available at https://github.com/LacroixLaurent/G4HunterPaperGit.
Running G4Hunter requires installation of a specific version of R, and specific versions of several R packages as depenecies. These steps take some time and are different for different operating systems. In this project, we Dockerize G4Hunter to avoid repeating these configuration steps everytime a user wants to run G4Hunter. A text file called a Dockerfile is used to specify all the configuration steps. A Docker engine creates a Docker image from the Dockerfile. Docker engine runs containers created off of the docker image. Container technologies such as Docker also offer other benefits such as portability, performance, agility, isolation, and scalability [3].
In order to run the Dockerized version of G4Hunter, you need to have the Docker engine installed on your box. Please refer to instructions at https://docs.docker.com/engine/install/. You also need the G4Hunter Docker image. You can either get the G4Hunter Docker image from Docker Hub, or you can build the image locally. If you are getting the image from the Docker Hub (preferred), you can skip the instructions for building/pushing the image, and go to the instructions for running G4Hunter Docker container.
To pull the G4Hunter Docker image from the Docker Hub repository:
docker pull kxk302/g4hunter:1.0.0
To view the pulled image:
docker images -f "reference=kxk302/g4hunter:1.0.0"
All the commands are run in the same directory, say, /Users/kxk302/workspace/
Clone G4Hunter_Docker repository (This creates a folder called G4Hunter_Docker):
Change your directory to G4Hunter_Docker folder:
cd ./G4Hunter_Docker
To create a Docker image:
docker build --progress=plain -t kxk302/g4hunter:1.0.0 .
To view the created image:
docker images -f "reference=kxk302/g4hunter:1.0.0"
To push the created image to your Docker Hub repository (You need to be regsitered at https://hub.docker.com/):
docker login
docker push kxk302/g4hunter:1.0.0
You can run G4Hunter on any genome specified in BSgenome package (https://bioconductor.org/packages/release/bioc/html/BSgenome.html). To get a list available genomes, run the following command in an R environment:
install.packages('BiocManager')
BiocManager::install('BSgenome')
BSgenome::available.genomes()
In case the genome is not specified in BSgenome package, you have 2 options: Either use the Python version of G4Hunter (https://github.com/kxk302/G4Hunter_Python), or you can create your own BSgenome package by following the instructions here: http://bioconductor.org/packages/release/bioc/vignettes/BSgenome/inst/doc/BSgenomeForge.pdf. The outcome of this step is a tar file that you must pass to G4Hunter. For example, suppose you created a BSgenome package for chimpanzee and the tar file is located at '/Users/kxk302/workspace/G4Hunter_Docker/genomes/BSgenome.Ptroglodytes.NCBI.T2TXYv11.tar'.
Suppose you want G4Hunter to save the output file at '/Users/kxk302/workspace/G4Hunter_Docker/output/g4_out.txt'. The output file name is 'g4_out.txt', the output file folder is '/Users/kxk302/workspace/G4Hunter_Docker/output/', and absolute path to output file name is '/Users/kxk302/workspace/G4Hunter_Docker/output/g4_out.txt'.
Besides genome and output file, g4hunter accepts window size, chromosome number, and the threshold as input parameters.
On Unix/Mac OS, to run the containerized version of G4Hunter, run the following command:
./scripts/run_g4hunter.sh Genome OutputFileAbsolutePath WindowSize ChromosomeNumber Threshold
For example:
./scripts/run_g4hunter.sh BSgenome.Hsapiens.UCSC.hg19 /Users/kxk302/workspace/G4Hunter_Docker/output/g4_out.txt 25 1 1.5
On Windows, to run the containerized version of G4Hunter, run the following command:
docker run -v OutputFileFolder:/output kxk302/g4hunter:1.0.0 Genome /output/OutputFileName WindowSize ChromosomeNumber Threshold
Below is an actual invocation of Dockerzed G4Hunter:
docker run -v /Users/kxk302/workspace/G4Hunter_Docker/output:/output kxk302/g4hunter:1.0.0 BSgenome.Hsapiens.UCSC.hg19 /output/g4_out.txt 25 1 1.5
The -v flag simply mounts a folder on your host machine to the container, to make your local files accessible to the container.
If you were to run G4Hunter for a genome NOT specified in BSgenome package, you need to pass your BSgenome's tar file as the second argument to G4Hunter.
On Unix/Mac OS, to run the containerized version of G4Hunter for a genome NOT specified in BSgenome package, run the following command:
./scripts/run_g4hunter.sh BSgenomeTarFileAbsolutePath OutputFileAbsolutePath WindowSize ChromosomeNumber Threshold
For example:
./scripts/run_g4hunter.sh /Users/kxk302/workspace/G4Hunter_Docker/genomes/BSgenome.Ptroglodytes.NCBI.T2TXYv11.tar /Users/kxk302/workspace/G4Hunter_Docker/output/g4_out.txt 25 1 1.5
On Windows, to run the containerized version of G4Hunter for a genome NOT specified in BSgenome package, run the following command:
docker run -v OutputFileFolder:/output -v GenomeTarFilePath:/GenomeTarFileName kxk302/g4hunter:1.0.0 GenomeTarFileName /output/OutputFileName WindowSize ChromosomeNumber Threshold
Below is an actual invocation of Dockerzed G4Hunter:
docker run -v /Users/kxk302/workspace/G4Hunter_Docker/output:/output -v /Users/kxk302/workspace/G4Hunter_Docker/genomes/BSgenome.Ptroglodytes.NCBI.T2TXYv11.tar:/BSgenome.Ptroglodytes.NCBI.T2TXYv11.tar kxk302/g4hunter:1.0.0 BSgenome.Ptroglodytes.NCBI.T2TXYv11.tar /output/g4_out.txt 25 1 1.5
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Amina Bedrat, Laurent Lacroix, Jean-Louis Mergny, Re-evaluation of G-quadruplex propensity with G4Hunter, Nucleic Acids Research, Volume 44, Issue 4, 29 February 2016, Pages 1746–1759, https://doi.org/10.1093/nar/gkw006