pandaseq

Download        : docker pull ghcr.io/autamus/pandaseq
Compressed Size : 28MB

Description

PANDASEQ is a program to align Illumina reads, optionally with PCR primers embedded in the sequence, and reconstruct an overlapping sequence.

Usage

Pull (Download)

To download the latest version of pandaseq run,

docker pull ghcr.io/autamus/pandaseq:latest

or to download a specific version of pandaseq run,

docker pull ghcr.io/autamus/pandaseq:2.11

Run

To run the container as an application run,

docker run --rm ghcr.io/autamus/pandaseq pandaseq --version

or to run the container in an interactive session run,

docker run -it --rm ghcr.io/autamus/pandaseq bash

Mounting volumes between the container and your machine

To access files from your machine within the pandaseq 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/pandaseq pandaseq /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 pandaseq container here.