hivdb/sierra-testing repository overview

⁠Sierra Project - HIVDB Genotypic Resistance Interpretation Program

Sierra-HIV is an open source software released under GPL-3.0 license. Access our GitHub repository: https://github.com/hivdb/sierra⁠

⁠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.