Download : docker pull ghcr.io/autamus/hisat2 Compressed Size : 32MB
HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (whole-genome, transcriptome, and exome sequencing data) against the general human population (as well as against a single reference genome).
To download the latest version of hisat2 run,
docker pull ghcr.io/autamus/hisat2:latest
or to download a specific version of hisat2 run,
docker pull ghcr.io/autamus/hisat2:2.2.0
To run the container as an application run,
docker run --rm ghcr.io/autamus/hisat2 hisat2 --version
or to run the container in an interactive session run,
docker run -it --rm ghcr.io/autamus/hisat2 bash
Mounting volumes between the container and your machine
To access files from your machine within the hisat2 container you’ll have to mount them using the
-v external/path:internal/path option.
docker run -v ~/Documents/Data:/Data ghcr.io/autamus/hisat2 hisat2 /Data/myData.csv
which will mount the
~/Documents/Data directory on your computer to the
/Data directory within the container.
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 hisat2 container here.