Add instructions for offline use

README.md

@@ -188,3 +188,49 @@ metagraph query -i graph.primary.small.dbg \
 ```
 
 Then, it will save the resulting file in the S3. When all chunks are processed, a dedicated script will merge the results in a single file and send you a notification.
+
+## Instructions for local usage
+
+MetaGraph can be [installed](https://github.com/ratschlab/metagraph#Install) locally for offline use on a Linux or a Mac host using the commands below. Search indexes can be downloaded from [`s3://metagraph-data-public`](s3://metagraph-data-public). For example, chunk `0400` can be downloaded to a working directory as follows:
+```sh
+aws s3 sync s3://metagraph-data-public/all_sra/data/metagenome/0400 .
+```
+Currently, chunks numbered `0001` through to `0400` are available for download. The example query file is located in this repository under [`examples/100_studies_short.fq`](https://github.com/ratschlab/metagraph-open-data/blob/main/examples/100_studies_short.fq).
+
+#### Conda
+```sh
+conda install -c bioconda -c conda-forge metagraph
+conda activate metagraph
+```
+
+Followed by a query on chunk `0400` using the command
+```sh
+metagraph query -i 0400/graph.primary.small.dbg \
+                -a 0400/annotation.clean.row_diff_brwt.annodbg \
+                --query-mode matches \
+                --num-top-labels 10 \
+                --min-kmers-fraction-label 0 \
+                --min-kmers-fraction-graph 0 \
+                examples/100_studies_short.fq
+```
+
+#### Docker
+```sh
+docker pull ghcr.io/ratschlab/metagraph:master
+```
+
+Followed by a query on chunk `0400` using the command
+```sh
+docker run -v ${MNTDIR}:/mnt ghcr.io/ratschlab/metagraph:master query -i 0400/graph.primary.small.dbg \
+                                                                      -a 0400/annotation.clean.row_diff_brwt.annodbg \
+                                                                      --query-mode matches \
+                                                                      --num-top-labels 10 \
+                                                                      --min-kmers-fraction-label 0 \
+                                                                      --min-kmers-fraction-graph 0 \
+                                                                      examples/100_studies_short.fq
+```
+replacing `${MNTDIR}` with the local mount path.
+
+## Additional instructions
+
+For further documentation and usage instructions (including setup instructions using Docker and via source code compilation), please refer to our [Quick start](https://metagraph.ethz.ch/static/docs/quick_start.html) guide in the [MetaGraph documentation](https://metagraph.ethz.ch/static/docs/index.html). The source code is maintained on our [GitHub repository](https://github.com/ratschlab/metagraph).