GDR Ingest

Custom logic for slurping external datasets into Broad data repositories.

Building the project

The project is built using sbt. Once the tool is installed, you can compile with:

$ cd ${PROJECT_ROOT}
$ sbt
# Much garbage logging, before dropping into the sbt repl
sbt:gdr-ingest> compile

You can also compile by running sbt compile from the project root in bash, but that will eat the build tool's startup cost on every call.

Running ENCODE ingest

From within the sbt repl, run:

sbt:gdr-ingest> encode-ingest/run --help

You can also run "help" for specific sub-commands to see their options, i.e.

sbt:gdr-ingest> encode-ingest/run prep-ingest --help

Testing ENCODE ingest

There aren't any automated tests (yet). Manual testing has been done by comparing outputs to a test workspace in FireCloud containing a subset of all data.