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Installation

Dependencies

The pipeline require only a UNIX system, Nextflow and either Docker or Singularity. Please, for installing these tools refer to their manual.

Downloading the pipeline

You can easily get a copy of the pipeline or update with:

# download or update to the latest version
nextflow pull deng-lab/viroprofiler

# download a specific version (ex. 1.0)
nextflow pull deng-lab/viroprofiler -r v1.0

# download a specific branch (ex. dev)
nextflow pull deng-lab/viroprofiler -r dev

Warning

The pipeline requires a UNIX system, therefore, Windows users may successfully use this pipeline via the Linux subsystem for window. Nextflow team has made available a nice tutorial about this issue.

Downloading docker images

The docker images used by the pipeline are:

docker pull denglab/viroprofiler-base        ;
docker pull denglab/viroprofiler-binning     ;
docker pull denglab/viroprofiler-abundance   ;
docker pull denglab/viroprofiler-geneannot   ;
docker pull denglab/viroprofiler-vibrant     ;
docker pull denglab/viroprofiler-taxa        ;
docker pull denglab/viroprofiler-host        ;
docker pull denglab/viroprofiler-replicyc    ;

Using singularity

Docker and singularity images are downloaded on the fly. Be sure to properly set NXF_SINGULARITY_LIBRARYDIR env variable to a writable directory if using Singularity. This will make that the downloaded images are resuable through different executions. Read more at: https://www.nextflow.io/docs/latest/singularity.html#singularity-docker-hub

For example, to download the images for singularity you may:

# apply this command to each image
# just change the "/" and ":" to "-".
# ex. Image denglab/viroprofiler-base becomes denglab-viroprofiler-base.img
singularity pull --dir $NXF_SINGULARITY_LIBRARYDIR denglab-viroprofiler-base.img docker://denglab/viroprofiler-base:latest
singularity pull --dir $NXF_SINGULARITY_LIBRARYDIR denglab-viroprofiler-binning.img docker://denglab/viroprofiler-binning:latest
singularity pull --dir $NXF_SINGULARITY_LIBRARYDIR denglab-viroprofiler-abundance.img docker://denglab/viroprofiler-abundance:latest
singularity pull --dir $NXF_SINGULARITY_LIBRARYDIR denglab-viroprofiler-geneannot.img docker://denglab/viroprofiler-geneannot:latest
singularity pull --dir $NXF_SINGULARITY_LIBRARYDIR denglab-viroprofiler-vibrant.img docker://denglab/viroprofiler-vibrant:latest
singularity pull --dir $NXF_SINGULARITY_LIBRARYDIR denglab-viroprofiler-taxa.img docker://denglab/viroprofiler-taxa:latest
singularity pull --dir $NXF_SINGULARITY_LIBRARYDIR denglab-viroprofiler-host.img docker://denglab/viroprofiler-host:latest
singularity pull --dir $NXF_SINGULARITY_LIBRARYDIR denglab-viroprofiler-replicyc.img docker://denglab/viroprofiler-replicyc:latest

Testing your installation

After that, you can run the pipeline with a testing dataset by selecting one of the available profiles:

  1. Docker
    • nextflow run denglab/viroprofiler -profile docker,test
  2. Singularity
    • nextflow run denglab/viroprofiler -profile singularity,test

About NF profiles

Please read more about how to proper select NF profiles to better understand it.