kallisto
Download : docker pull ghcr.io/autamus/kallisto
Compressed Size : 27MB
Description
kallisto is a program for quantifying abundances of transcripts from RNA-Seq data.
Usage
Pull (Download)
To download the latest version of kallisto run,
docker pull ghcr.io/autamus/kallisto:latest
or to download a specific version of kallisto run,
docker pull ghcr.io/autamus/kallisto:0.46.2
Run
To run the container as an application run,
docker run --rm ghcr.io/autamus/kallisto kallisto --version
or to run the container in an interactive session run,
docker run -it --rm ghcr.io/autamus/kallisto bash
Mounting volumes between the container and your machine
To access files from your machine within the kallisto container you’ll have to mount them using the -v external/path:internal/path
option.
For example,
docker run -v ~/Documents/Data:/Data ghcr.io/autamus/kallisto kallisto /Data/myData.csv
which will mount the ~/Documents/Data
directory on your computer to the /Data
directory within the container.
HPC
If you’re looking to use this container in an HPC environment we recommend using Singularity-HPC to use the container just as any other module on the cluster. Check out the SHPC kallisto container here.