DomainAnnotation is a SDK port of the old Gene Families service, which finds domains (from public protein domain libraries such as COGs and Pfam) in proteins in a user-supplied genome.
SETUP:
DomainAnnotation requires binaries from HMMER and RPS-BLAST, which are retrieved using the "download_3rd_party_bins.sh" script, and used to format the libraries. It also adds them to the Docker image. This is done automatically as part of the "make" process.
DomainAnnotation requires several public PSSM and HMM libraries, which are retrieved using the "prepare_3rd_party_dbs.sh" script. The script also formats the libraries for use by HMMER or RPS-BLAST. This is done automatically as part of the "make" process.
The libraries have to be parsed and stored in DomainModelSet objects in a public KBase workspace called "KBasePublicGeneDomains." This needs to be done once every time a new version of the libraries is desired (and once each per KBase environment, e.g., ci vs appdev vs production). The code to do this is in domainannotation.DomainModelLibPreparation and needs to be run by a developer with write access to that workspace.
Once the libraries are downloaded using the script above, the
developer needs to set environment variables: KB_AUTH_TOKEN (e.g., to
kbase-whoami -t) and KB_DEPLOYMENT_CONFIG (e.g., to
"/kb/dev_container/modules/kb_sdk/DomainAnnotation/test_local/workdir/config.properties"),
then run "make prepare-library-objects" to create the workspace and
all the library objects needed for this to run.