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.

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
  • 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
• 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
• 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