Update installation docs (#26)

* fixed 01 test bug; updated checksums; added null tree target

* installation modification

* m

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="<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](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="<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.
+```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="<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"
+```

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="<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](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="<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.
-```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="<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"
-```
+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