install prob ga4gh_repo add-referenceset

[jpdna]

I'm trying to follow the instructions here: http://ga4gh-reference-implementation.readthedocs.io/en/latest/demo.html and am getting the error below

$ ga4gh_repo add-referenceset registry.db hs37d5.fa.gz -d "NCBI37 assembly of the human genome" --species '{"id": "9606", "term": "Homo sapiens", "source_name": "NCBI", "source_version: "1.0"}'  --name NCBI37 --sourceUri "ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz"
usage: ga4gh_repo [-h] [--version]
                  {init,verify,list,add-dataset,remove-dataset,add-referenceset,remove-referenceset,add-readgroupset,add-ontology,remove-ontology,remove-readgroupset,add-variantset,remove-variantset,add-featureset,remove-featureset,add-biosample,remove-biosample,add-individual,remove-individual,add-rnaquantification,init-rnaquantificationset,add-rnaquantificationset,remove-rnaquantificationset,add-phenotypeassociationset,remove-phenotypeassociationset}
                  ...
ga4gh_repo: error: unrecognized arguments: --species {"id": "9606", "term": "Homo sapiens", "source_name": "NCBI", "source_version: "1.0"}

[david4096]

Thanks @jpdna ! Two problems have come together here. First, RTD is failing so our "latest" docs are actually aging quickly. The species field was added recently and so the released version, 0.3.5 that you get from pip, does not include this. The release notes for 0.3.6 are not completely clear on this point.

To get past it just leave off that flag! The old flag -ncbiTaxonId 9606 will also work. These docs (stable) currently track the latest released version whereas latest is (usually) master.

[david4096]

If you're building from source the latest RTD has been updated now! http://ga4gh-reference-implementation.readthedocs.io/en/latest/datarepo.html#command-line