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@@ -188,3 +188,52 @@ metagraph query -i graph.primary.small.dbg \ | |
``` | ||
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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. | ||
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### Instructions for offline usage | ||
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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: | ||
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```sh | ||
aws s3 cp metagraph-data-public/all_sra/data/metagenome/0001 . --recursive | ||
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``` | ||
Currently, chunks numbered `0001` through to `0400` are available for download. The example query file can be downloaded as follows: | ||
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```sh | ||
aws s3 cp examples/100_studies_short.fq . | ||
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``` | ||
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#### Conda | ||
```sh | ||
conda install -c bioconda -c conda-forge metagraph | ||
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conda activate metagraph | ||
``` | ||
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Followed by a query on chunk `0001` using the command | ||
```sh | ||
metagraph query -i 0001/graph.primary.small.dbg \ | ||
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-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 | ||
``` | ||
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#### Docker | ||
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```sh | ||
docker pull ghcr.io/ratschlab/metagraph:master | ||
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``` | ||
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Followed by a query on chunk `0001` using the command | ||
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```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. | ||
There was a problem hiding this comment. Choose a reason for hiding this commentThe reason will be displayed to describe this comment to others. Learn more. We should probably provide some specific examples on what should be used as |
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## Additional instructions | ||
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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). |
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