if user has specified gene but not genome, download genome anyway. it's required.
@@ -163,6 +163,10 @@ public class DownloadCommandExecutor extends CommandExecutor {
break;
case EtlCommons.GENE_DATA:
downloadManager.downloadEnsemblGene(sp, spShortName, assembly.getName(), spFolder);
+ if (!dataList.contains(EtlCommons.GENOME_DATA)) {
+ // user didn't specify genome data to download, but we need it for gene data sources
+ downloadManager.downloadReferenceGenome(sp, spShortName, assembly.getName(), spFolder);
+ }
break;
case EtlCommons.VARIATION_DATA:
downloadManager.downloadVariation(sp, spShortName, spFolder);
