This is described in README.

1. ":gene_table" is simple genePred table with named columns e.g. https://chopchop.cbu.uib.no/genomes/isoforms/hg38.gene_table You could transform gff&gtf into genePred by using tools like http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/gtfToGenePred

2. To use the symbols you have to have them in the proper column in the genePred table, you could process the table to replace the ensemble gene names, or something like this might work

   gtfToGenePred -genePredExt -geneNameAsName2 gencode.v29.annotation.gtf hg38.genePred
   

3. Paths to the reference files are specified in the config.json

{  
  "PATH": {  
    "PRIMER3": "./primer3_core",  
    "BOWTIE": "bowtie/bowtie",  
    "TWOBITTOFA": "./twoBitToFa",  
    "TWOBIT_INDEX_DIR": "/your/full/path/to/2bit_folder",  
    "BOWTIE_INDEX_DIR": "/your/full/path/to/ebwt_folder",  
    "ISOFORMS_INDEX_DIR": "/your/full/path/to/ebwt_transcriptome_folder_and_2bit_of_genome",  
    "ISOFORMS_MT_DIR": "/your/full/path/to/vienna_MT_folder",  
    "GENE_TABLE_INDEX_DIR": "/your/full/path/to/genePred_folder"  
  },  
  "THREADS": 1  
}