Sierra Project - HIVDB Genotypic Resistance Interpretation Program

Prerequisites

Here're the full development prerequisites of Sierra project:

1. JDK 17 (tested with Oracle Java; also work with OpenJDK).
2. PostAlign Alignment Program. It is an open source codon-aware alignment program written by Philip Tzou (philiptz(at)stanford.edu) of the Stanford HIVDB team. One can retrieve the source code and binary file from the GitHub repository.
3. Docker.

Following system environment is required for running sequence alignment:

• POSTALIGN_PROGRAM: path to the PostAlign command

For host a production server of Sierra project, only Docker is required.

Dependency Lists

Full dependency list of each sub-project can be found in build.gradle file under each sub-project directory. Here's an unfinished list of main dependencies:

• Apache Commons Lang
• Apache Commons Math
• Apache Commons IO
• Apache Log4j
• Google Guava
• Google Gson
• protonpack
• GraphQL-Java
• MySQL Connector/J (dev only)
• c3p0 (dev only)
• junit (dev only)

Note: These dependencies are automatically installed by Gradle which is shipped with this repository. You don't need to install them manually.

Installation

Start Sierra with Docker

Docker images are released publicly for each version of Sierra since 2.2.6. To pull and start a Sierra instance (this is how we host our production server):

docker pull hivdb/sierra:latest
docker run -it --publish=8111:8080 hivdb/sierra dev

After started the instance, the local Sierra web service is accessable through this URL:

http://localhost:8111/sierra/rest/graphql

Before Sierra 3.2, the entry-point was:

http://localhost:8111/WebApplications/rest/graphql

Development with Eclipse IDE

Sierra project uses Gradle to manage the dependencies, build and test. The easiest way to install the whole project is through Eclipse. Here're the steps:

1. Use Git to clone this repository to a local path;
2. In Eclipse, click "File" > "Import...", expand the "Gradle" group, select "Gradle Project", then click "Next >";
3. Eclipse may show a welcome dialog before it starting the import wizard. After the welcome dialog, type sierra local path from step #1 into "Project root directory". Click "Next >";
4. Use all default configurations until finish dialog. Click "Finish" then you have installed sierra in Eclipse.

There may be an issue that you can't find "Gradle Project" in step #2. In this case you can install the latest "Buildship Gradle Integration" with "Help" > "Eclipse Marketplace...". then you can import a Gradle project in Eclipse.

Development server

To start a development server:

make dev

Donation

If you find Sierra useful and wish to donate to the HIVDB team, you can do so through Stanford Make a Gift form. Your contribution will be greatly appreciated.

release

./scripts/release_stable_version <customized version name>