CATS-rf

Installation

Running CATS-rf via Docker

Starting from version 1.0.2, CATS-rf can be run using Docker:

Build the Docker image with:

docker pull bodulic/cats-rf

Run the container with:

docker run --rm -v "$PWD":/data -w /data bodulic/cats-rf CATS_rf

docker run --rm -v "$PWD":/data -w /data bodulic/cats-rf CATS_rf_compare

Running CATS-rf via Singularity

Build the Singularity image with:

singularity build cats_rf.sif docker://bodulic/cats-rf:latest

Run the container with:

singularity run cats_rf.sif CATS_rf

singularity run cats_rf.sif CATS_rf_compare

Installing CATS-rf via conda

CATS-rf and its dependencies can be directly installed via Bioconda:

conda install -c bioconda cats-rf

In case of dependency conflicts, please see the Troubleshooting section.

Installing CATS-rf from source

CATS-rf consists of Bash and R scripts located in the scripts directory of this repository. After cloning the repository, all CATS-rf scripts must be included in the PATH environment variable. The following dependencies are required:

Dependency	Tested Version	Homepage	Conda Installation
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`
Bowtie2	2.5.4	https://github.com/BenLangmead/bowtie2	`conda install -c bioconda bowtie2`
Samtools	1.21	https://www.htslib.org	`conda install -c bioconda samtools`
kallisto	0.50.1	https://github.com/pachterlab/kallisto	`conda install -c bioconda kallisto`
GNU Parallel	20220922	https://www.gnu.org/software/parallel	`conda install conda-forge::parallel`
bedtools (bamToBed)	2.31.1	https://github.com/arq5x/bedtools2	`conda install -c bioconda bedtools`
python	3.6-3.12	https://github.com/arq5x/bedtools2	`conda install -c bioconda bedtools`
pysamstats	1.1.2	https://github.com/alimanfoo/pysamstats	`conda install -c bioconda pysamstats`

R, Bowtie2, Samtools, kallisto, GNU Parallel, bedtools (bamToBed), and pysamstats executables must be included in PATH. R package data.table can be installed via conda or directly in R with install.packages("data.table")

MacOS

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-rf uses GNU versions of core utilities:

Install Bash ≥ 4.0 via Homebrew:

brew install bash

Install GNU utilities:

brew install coreutils gnu-sed gawk

Add Bash and GNU utilities to your 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"

Run CATS-rf using the installed Bash version:

bash CATS_rf

The stated changes can be made permanent by modifying the appropriate .rc file.

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