This is a backend service for the pheno-matcher project. The server and hpo functions are implmented in rust.
The docker container can be found here: emersonlebleu/pheno_matcher_be_rust-server
Currently there is a amd64 tagged version that is compatable with our CHPC environment.
The docker container will not run as is out of the box for data security reasons. The rust main function will expect an external /data volume to be mounted to the root of your container. This should contain a csv of your patient information in the appropriate format for the application to use.
Other non-sensitive information has been copied to the docker container itself.
For iobio.team purposes this service is hosted in our protected environment and runs in a singularity container.
Instruction on how to use a docker container in our internal team's environment can be found here: CHPC Container Documenation
To run the service you will need to mount or --bind the host folder that contains your data to the /data folder when running your container.
For example the following command:
singularity run --bind /username/datafolder:/data docker://emeronlebleu/pheno_matcher_be_rust-server:amd64
Here we are using a container from the docker hub and running it with singularity. Before we do that however we use the --bind flag and specify the originFolder:containerFolder that should contain our main data.
NOTE: the server will expect this containerFolder to be data at the root of your container as shown in the example.
NOTE: each new version needs to be built, tagged, and added to the docker hub. On CHPC stop the ongoing singularity container and run again with the new docker container.
UPDATE If there is already .sif built you can run something like
singularity run --bind /ssd/emerson/pheno_matcher_be_rust/data/:/data pheno_matcher_be_1.3.sif