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Installation from other sources

The community generously maintains the following methods of installation. For installing from source, please see the relevant section in README.md.

An NCBI API key is required to use this tool. See here for information on how to obtain your own NCBI API key

Conda

datasets-sars-cov-2 is available on BioConda

conda create -n datasets-sars-cov-2 -c conda-forge -c bioconda uscdc-datasets-sars-cov-2

conda activate datasets-sars-cov-2

export NCBI_API_KEY="<your-NCBI-API-key-here>"

# the path to the input TSV may differ depending on how & where you installed conda; below is default location for miniconda3 installed on linux
GenFSGopher.pl --numcpus 8 --compressed --outdir vocvoi-dataset ~/miniconda3/envs/datasets-sars-cov-2/share/uscdc-datasets-sars-cov-2/sars-cov-2-voivoc.tsv

Docker

The StaPH-B working group maintains a docker image for datasets-sars-cov-2. The dockerfile can be found here.

The input TSVs are located here within the StaPH-B docker image: /home/user/datasets-sars-cov-2/datasets/

There is also a BioContainer docker image which contains the (bio)conda environment for this repository. The example below uses the StaPH-B docker image, but similar commands can be used with the BioContainer docker image. The input TSVs are located here within the BioContainer docker image: /usr/local/share/uscdc-datasets-sars-cov-2/

docker pull staphb/datasets-sars-cov-2:latest

# broken into 2 lines for readability
docker run --rm -v $PWD:/data -u $(id -u):$(id -g) staphb/datasets-sars-cov-2:latest /bin/bash -c \
'export NCBI_API_KEY="<your-NCBI-API-key-here>"; GenFSGopher.pl --numcpus 8 --compressed --outdir /data/vocvoi-dataset /home/user/datasets-sars-cov-2/datasets/sars-cov-2-voivoc.tsv'

Singularity

The StaPH-B docker image can be converted to singularity image format and utilitzed in a similar manner.

singularity build staphb.datasets-sars-cov-2.sif docker://staphb/datasets-sars-cov-2:latest

# broken into 3 lines for readabilty
singularity exec -B $PWD:/data --no-home staphb.datasets-sars-cov-2.sif /bin/bash -c \
"export HOME=/home/user; export NCBI_API_KEY="<your-NCBI-API-key-here>"; \
GenFSGopher.pl --numcpus 8 --compressed --outdir /data/vocvoi-dataset /home/user/datasets-sars-cov-2/datasets/sars-cov-2-voivoc.tsv"