Docker and Singularity containers

Container image recipe repository for Docker and Singularity

About

This repository serves as a resource for building and maintaining Docker and Singularity images for different projects.

For more information on using and building individual recipies, see the README for each recipe. Each recipe also explains how to download the image from dockerhub and how to convert the docker image to a singularity/apptainer image if you desire.

Most images are also on dockerhub with individual links below.

Current recipes

• RNA seq
  • general_docker - Includes a recipe to build the container to run RNA seq analysis, including STAR, featureCounts, cutadapt, samtools, and fastqc
    • built image
  • R docker - Includes a recipe to build the container to run R scripts associated with RNA seq analysis. Includes packages like DESeq2. Check the R_dependencies.R file for a full list of installed packages
    • built image
• ATAC seq
  • general docker - Includes a recipe to build the container to run RNA seq analysis, including bowtie2, Macs2, hmmratac, cutadapt, samtools, and fastqc
  • Picard docker - Includes a recipe to build a docker container to run picard tools
  • R docker - Includes a recipe to build the container to run R scripts associated with RNA seq analysis. Includes packages like DiffBind. Check the R_dependencies.R file for a full list of installed packages
    • built image
• Cut and Run
  • general docker - Includes a recipe to build the container to run RNA seq analysis, including bowtie2, Macs2, cutadapt, samtools, and fastqc
  • Picard docker - Includes a recipe to build a docker container to run picard tools
  • R docker - Includes a recipe to build the container to run R scripts associated with RNA seq analysis. Includes packages like DiffBind. Check the R_dependencies.R file for a full list of installed packages
  • Sussel R docker - Includes a recipe to build the container to run R scripts associated with RNA seq analysis. Includes packages like DiffBind. Check the R_dependencies.R file for a full list of installed packages
• Long read scRNA seq
  • R docker - Includes a recipe to build the container to run R scripts associated with RNA seq analysis. Includes packages like Seurat and scAnalysisR. Check the R_dependencies.R file for a full list of installed packages
  • Dorado - Includes a recipe to build a container for dorado
  • Sockeye - Includes a recipe to build a container for sockeye
• scRNA seq
  • R docker - Includes a recipe to build the container to run R scripts associated with RNA seq analysis. Includes packages like Seurat and scAnalysisR. Check the R_dependencies.R file for a full list of installed packages
  • Smith R docker - Includes a recipe to build the container to run R scripts associated with RNA seq analysis. Includes packages like Seurat and scAnalysisR. Check the R_dependencies.R file for a full list of installed packages. Versions are slightly different than R docker
  • Friedman R docker - Includes a recipe to build the container to run R scripts associated with RNA seq analysis. Includes packages like Seurat and scAnalysisR. Check the R_dependencies.R file for a full list of installed packages. Versions are slightly different than R docker
  • Immcantation - Includes a recipe to build a container with immcantation
  • Dropkick - Includes a recipe to build a continer with dropkick

R vulenerabilities

We are aware of the R vulenerabilities and I am working on updating all of these images to use R 4.4 or higher.

Images recipies that have been updated with R 4.4:

• RNA_seq/r_docker
• cut_and_run/r_docker
• atac_seq/sussel_r_docker
• mixcr/r_docker

For those using my pre-built images, the following images are R 4.4 or higher:

• RNA_seq/r_docker/rnaseq_r_v1.tar and RNA_seq/r_docker/rnaseq_r_v1.sif
• cut_and_run/r_docker/cut_and_run_v1.tar and cut_and_run/r_docker/cut_and_run_v1.sif
• atac_seq/sussel_r_docker/atac_r.tar and atac_seq/sussel_r_docker/atac_r.sif
• mixcr/r_docker/mixcr_r_v1.tar and mixcr/r_docker/mixcr_r_v1.tar