Don't use to refer to running or building a program on a particular platform or operating system. Use on instead.
It's OK to use against in content for a technical audience to discuss evaluating a value against an expression or running a query against a database.
Examples
Run queries on HDInsight using Hadoop, HBase, or Apache Storm clusters to
extract meaning from structured and unstructured data in Azure Storage.
Use Elastic Database jobs to run T-SQL scripts against all of the databases in an elastic database pool.