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Developer SOPs


These SOPs describe developer related processes, including setup guides, tutorials, and best practices. This wiki is growing, so please contribute to it. If you find anything difficult to setup or learn, then make sure you document it or revise existing documentation so future co-ops can get started faster.

This is not meant to be an all-inclusive resource. We can’t possibly cover all the knowledge a co-op here might need to know, so the programmer’s ability to research is ever important.

Brief Overview of Development

The VBRC creates and maintains a set of Java tools used in the analysis and curation of viral genomes. These tools are available from this website as Java Web Start applications.

All of our code is stored in a BitBucket repository and we tend to code in IntelliJ. Currently, the codebase is comprised of a large number of legacy maintenance applications and a few active/new ones. Older projects use Apache Ant builds and manual dependency management, while newer projects use Maven for dependency management and packaging. Other technologies used are Spring and Spring JDBC.

On the webserver side, we use a MySQL database and run Apache2 for this wordpress-based website. There is another application server which runs jobs.

You will also end up helping the co-op researchers with their work by fixing bugs in their tools, creating new tools or scripts, editing files, maintaining the database, and updating the website. If you’re looking for a project, check out the ongoing development tasks.

Please read the practices article before you get started. See also the administrator SOPs. All passwords can be found in the red binder (please keep it up to date).


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