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SOPRANO App

SOPRANO has a browser-based user interface powered by streamlit. This can be deployed from the command line via soprano-app. This will present the user with a visual way of interacting with the CLI utilities. It also offers a light-weight version of the pipeline; though this is restricted to single-sample pipeline runs, with no KDE as described in the CLI.

Data sources

By default, the application will serve options for the example annotated mutation and immunopeptidome files shipped with SOPRANO. Additional files can be detected by the application by their placement in the ./app_sources folders:

./app_sources/annotated_inputs

VEP annotated mutation files placed in this directory will be detected, so long as they have the extension pattern *anno*. E.g., mutations.anno or mutations.annotated.

./app_sources/immunopeptidomes

User defined immunopeptidomes BED files placed in this directory will be detected, so long as they have the extension .bed. E.g., immuno.bed.

./app_sources/coordinate_files

User defined BED files that can be used for randomization will be detected, so long as they have the extension .bed. E.g., randoms.bed.

Note: Quantities generated on-the-fly during an app session will be cached into these folders.

Serving the application via Docker

The application can also be constructed as a docker image, and served more generally this way. This can be manually constructed from the repository root via

docker build -t soprano .

To interact with data sources, users should bind mount whilst running the application, for example, with

docker run -d -p 8501:8501 --name SOPRANO_APP -v "$(pwd)"/ensembl_downloads:/app/ensembl_downloads soprano

Public content

Alternatively, there is a publicly available image that can be pulled down directly, and executed in the same way. A version of this application is running at the ICR that you can view here.

Notes on the containerized app

Data in general will not persist between sessions. For example, an annotated mutation file will not be saved directly onto your file system. Users are therefore encouraged to download any results that they want to use via the appropriate buttons.