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Add mount to loader command
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creisle committed Feb 23, 2022
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12 changes: 9 additions & 3 deletions docs/install.md
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Expand Up @@ -97,15 +97,21 @@ wget https://raw.githubusercontent.com/bcgsc/pori_graphkb_loader/develop/data/vo
Then you can load these terms using the ontology file loader

```bash
docker run --net host bcgsc/pori-graphkb-loader:latest \
docker run --net host \
--mount src=$(pwd)/vocab.json,dst=/data/vocab.json,type=bind \
bcgsc/pori-graphkb-loader:latest \
-u graphkb_importer \
-p secret \
-g http://localhost:8888/api \
-g http://localhost:8080/api \
file \
ontology \
vocab.json
/data/vocab.json
```

!!! Note

Because we are running the loader by itself we need to provide the mount arguments to tell docker that we need access to a file outside of the container itself. When we run this with the snakemake pipeline this is not necessary since snakemake generally takes care of that for you

## Production Instances

### HTTPS
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