Starting from version 1.0.2, CATS-rb can be run using Docker:
Build the Docker image with:
docker pull bodulic/cats-rb
Run the container with:
docker run --rm -v "$PWD":/data -w /data bodulic/cats-rb CATS_rb_index
docker run --rm -v "$PWD":/data -w /data bodulic/cats-rb CATS_rb_map
docker run --rm -v "$PWD":/data -w /data bodulic/cats-rb CATS_rb_compare
Build the Singularity image with:
singularity build cats_rb.sif docker://bodulic/cats-rb:latest
Run the container with:
singularity run cats_rb.sif CATS_rb_index
singularity run cats_rb.sif CATS_rb_map
singularity run cats_rb.sif CATS_rb_compare
CATS-rb and its dependencies can be directly installed via Bioconda:
conda install -c bioconda cats-rb
In case of dependency conflicts, please see the Troubleshooting section.
CATS-rb consists of Bash and R scripts located in the scripts directory of this repository. After cloning the repository, all CATS-rb scripts must be included in the PATH environment variable.
The following dependencies are required:
| Dependency | Tested Version | Homepage | Conda Installation | R installation |
|---|---|---|---|---|
| spaln | 3.0.1 | https://github.com/ogotoh/spaln | conda install -c bioconda spaln |
/ |
| R | 4.3.0.-4.4.3 | https://www.r-project.org | conda install conda-forge::r-base |
/ |
| data.table (R) | 1.16.4 | https://cran.r-project.org/package=data.table | conda install conda-forge::r-data.table |
install.packages("data.table") |
| pandoc | 2.19.2 | https://pandoc.org/ | conda install conda-forge::pandoc |
/ |
| rmarkdown (R) | 2.29 | https://cran.r-project.org/package=rmarkdown | conda install conda-forge::r-rmarkdown |
install.packages("rnarkdown) |
| ggplot2 (R) | 3.5.1 | https://cran.r-project.org/web/packages/ggplot2 | conda install conda-forge::r-ggplot2 |
install.packages("ggplot2") |
| ggdist (R) | 3.3.2 | https://cran.r-project.org/web/packages/ggdist | conda install conda-forge::r-ggdist |
install.packages("ggdist") |
| GenomicRanges (R) | 1.56.2 | https://www.bioconductor.org/packages/devel/bioc/html/GenomicRanges.html | conda install -c bioconda bioconductor-genomicranges |
BiocManager::install("GenomicRanges") |
| Matrix (R) | 1.7.1 | https://cran.r-project.org/web/packages/Matrix | conda install conda-forge::r-matrix |
install.packages("Matrix") |
| igraph (R) | 4.4.2 | https://cran.r-project.org/web/packages/igraph | conda install conda-forge::igraph |
install.packages("igraph") |
| UpSetR (R) | 2.1.3 | https://cran.r-project.org/web/packages/UpSetR | conda install conda-forge::r-upsetr |
install.packages("UpSetR") |
| ggVennDiagram (R) | 1.5.2 | https://cran.r-project.org/web/packages/ggVennDiagram | / | install.packages("ggVennDiagram") |
| egg (R) | 0.4.5 | https://cran.r-project.org/web/packages/egg/index.html | conda install conda-forge::r-egg |
install.packages("egg") |
| ComplexHeatmap (R) | 2.20.0 | https://www.bioconductor.org/packages/devel/bioc/html/ComplexHeatmap.html | conda install -c bioconda bioconductor-complexheatmap |
BiocManager::install("ComplexHeatmap") |
| GenomeInfoDb (R) | 1.40.1 | https://www.bioconductor.org/packages/devel/bioc/html/GenomeInfoDb.html | conda install -c bioconda bioconductor-genomeinfodb |
BiocManager::install("GenomeInfoDb") |
| GenomicDistributions (R) | 1.12.0 | https://www.bioconductor.org/packages/devel/bioc/html/GenomicDistributions.html | conda install -c bioconda bioconductor-genomicdistributions |
BiocManager::install("GenomicDistributions") |
R (Rscript), Spaln, and pandoc executables must be included in PATH. Tools denoted with (R) correspond to R packages and can be installed via conda or directly in R with the supplied commands. R package BiocManager is required when installing Bioconductor packages (GenomicRanges, ComplexHeatmap, GenomeInfoDb, and GenomicDistributions) in R.
If you are using MacOS, Bash (version >= 4.0) and GNU versions of core utilities are required. In this case, PATH should be adjusted so that CATS-rb uses GNU versions of core utilities:
brew install bash
brew install coreutils gnu-sed gawk
PATH (adjust path depending on your architecture):For Apple Silicon:
export PATH="/opt/homebrew/bin:$PATH"
export PATH="/opt/homebrew/opt/coreutils/libexec/gnubin:$PATH"
export PATH="/opt/homebrew/opt/gnu-sed/libexec/gnubin:$PATH"
For Intel-based configurations
export PATH="/usr/local/bin:$PATH"
export PATH="/usr/local/opt/coreutils/libexec/gnubin:$PATH"
export PATH="/usr/local/opt/gnu-sed/libexec/gnubin:$PATH"
bash CATS_rb
The stated changes can be made permanent by modifying the appropriate .rc file.