diff --git a/INSTALL.md b/INSTALL.md new file mode 100644 index 0000000..e59a6e0 --- /dev/null +++ b/INSTALL.md @@ -0,0 +1,44 @@ +# 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](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](https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities/) + +## Conda +*datasets-sars-cov-2* is available on [BioConda](https://bioconda.github.io/recipes/uscdc-datasets-sars-cov-2/README.html) +```bash +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="" + +# 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](https://staphb.org/) maintains a [docker image](https://hub.docker.com/r/staphb/datasets-sars-cov-2) for *datasets-sars-cov-2*. The dockerfile can be found [here](https://github.com/StaPH-B/docker-builds/tree/master/datasets-sars-cov-2/). + +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](https://quay.io/repository/biocontainers/uscdc-datasets-sars-cov-2?tab=tags) 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/` +```bash +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=""; 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. +```bash +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=""; \ +GenFSGopher.pl --numcpus 8 --compressed --outdir /data/vocvoi-dataset /home/user/datasets-sars-cov-2/datasets/sars-cov-2-voivoc.tsv" +``` diff --git a/README.md b/README.md index e5d32b1..c3a9cdc 100644 --- a/README.md +++ b/README.md @@ -19,46 +19,12 @@ Technical Outreach and Assistance for States Team (TOAST) developed benchmark da ## Installation & Usage -An NCBI API key is required to use this tool. [See here for information on how to obtain your own NCBI API key](https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities/) +### Other installation methods -### Conda -*datasets-sars-cov-2* is available on [BioConda](https://bioconda.github.io/recipes/uscdc-datasets-sars-cov-2/README.html) -```bash -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="" - -# 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](https://staphb.org/) maintains a [docker image](https://hub.docker.com/r/staphb/datasets-sars-cov-2) for *datasets-sars-cov-2*. The dockerfile can be found [here](https://github.com/StaPH-B/docker-builds/tree/master/datasets-sars-cov-2/). - -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](https://quay.io/repository/biocontainers/uscdc-datasets-sars-cov-2?tab=tags) 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/` -```bash -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=""; 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. -```bash -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=""; \ -GenFSGopher.pl --numcpus 8 --compressed --outdir /data/vocvoi-dataset /home/user/datasets-sars-cov-2/datasets/sars-cov-2-voivoc.tsv" -``` +Some methods of installation are maintained by the community. +Although we do not have direct control over them, we would like to list them for convenience. +Visit [INSTALL.md](INSTALL.md) for these methods. ### From Source Code