diff --git a/docs/install.md b/docs/install.md index 9aa1e07..e96fe02 100644 --- a/docs/install.md +++ b/docs/install.md @@ -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