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49 changes: 49 additions & 0 deletions README.md
Original file line number Diff line number Diff line change
Expand Up @@ -188,3 +188,52 @@ 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 offline usage

MetaGraph can be installed 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 `0001` can be downloaded to a working directory as follows:
```sh
aws s3 cp metagraph-data-public/all_sra/data/metagenome/0001 . --recursive
```
Currently, chunks numbered `0001` through to `0400` are available for download. The example query file can be downloaded as follows:
```sh
aws s3 cp examples/100_studies_short.fq .
```

#### Conda
```sh
conda install -c bioconda -c conda-forge metagraph
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Last time I checked, bioconda image was quite behind the git trunk. In particular, the query above wouldn't work due to incompatible CLI arguments. Should we do something about it before merging?

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yes, I'm creating the new release now

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I removed the conda instructions for now since there's still some work being done on upgrading the package.

conda activate metagraph
```

Followed by a query on chunk `0001` using the command
```sh
metagraph query -i 0001/graph.primary.small.dbg \
-a 0001/annotation.clean.row_diff_brwt.annodbg \
--query-mode matches \
--num-top-labels 10 \
--min-kmers-fraction-label 0 \
--min-kmers-fraction-graph 0 \
100_studies_short.fq
```

#### Docker
```sh
docker pull ghcr.io/ratschlab/metagraph:master
```

Followed by a query on chunk `0001` using the command
```sh
docker run -v ${MNTDIR}:/mnt ghcr.io/ratschlab/metagraph:master query -i 0001/graph.primary.small.dbg \
-a 0001/annotation.clean.row_diff_brwt.annodbg \
--query-mode matches \
--num-top-labels 10 \
--min-kmers-fraction-label 0 \
--min-kmers-fraction-graph 0 \
100_studies_short.fq
```
replacing `${MNTDIR}` with the local mount path.
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We should probably provide some specific examples on what should be used as ${MNTDIR}.


## 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).