WormBase / website-jbrowse-gff

Dockerfile for processing GFF data for JBrowse
MIT License
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add creation of blast config (assemblies->tracks) #5

Open scottcain opened 6 months ago

scottcain commented 6 months ago

For the blast server, it would be good to have a file that gives a two column file (assemblies\tcomma delimited track list). Need to get the list of tracks desired (from @adamjohnwright)

The place to do this list building isn't immediately obvious--it could happen here (which would be after the config.json is created for each assembly) or in website-genome-browsers/jbrowse2, where the list would be created as the config.json is constructed. I'm leading towards the latter (the script that builds config.json already has S3 access built in to it--so it could just put this blast config file somewhere in the s3 bucket when placing the config.json.

scottcain commented 6 months ago

Looking at https://github.com/alliance-genome/agr_blast_service_configuration/blob/main/conf/WB/databases.WB.WS292.json shows me that the tracks of interest are

          "tracks" : [
               "$ASSEMBLY_curated_genes",
               "$ASSEMBLY_protein_motifs",
               "$ASSEMBLY_classical_alleles"
            ],

@adamjohnwright : Do you have a preference for how these data a presented? I mentioned doing two tab delimited columns but I could also do json if you'd prefer, like:

{
   "bioproject" : "$BIOPROJECT",
    "tracks" : [
               "$ASSEMBLY_curated_genes",
               "$ASSEMBLY_protein_motifs",
               "$ASSEMBLY_classical_alleles"
      ]
}
adamjohnwright commented 6 months ago

Probably both would work but I lean towards json

scottcain commented 6 months ago

I'm going to suggest adding genblastg_cds_predictions as a track to add as well since the C. elegans Hawaiian strain doesn't have any of the other three tracks.