Protocols supported with -genes in mango-submit

[prakashmstpt]

When I am using a file option with -genes both on local HDFS it does not work. If I use http it works.
My question is what are supported protocols for -genes?
Does not work:
/home/sm/mango-distribution-0.0.1//bin/mango-submit --packages org.apache.parquet:parquet-hadoop:1.8.2
-- /home/gm/workspace/mango_testing/mango_test_files//hg19.2bit -port 3333 -genes /user/gm/workspace/mango_testing/mango_test_files//ensGene.bb
-features /user/gm/workspace/mango_testing/mango_test_files//gtex_gene_expression.bed,
/user/gm/workspace/mango_testing/mango_test_files//ucsc_genes_hg19.bed
-variants /user/gm/workspace/mango_testing/mango_test_files//1000gSNPs.vcf
-reads /user/gm/workspace/mango_testing/mango_test_files//HG00096.chrom11.ILLUMINA.bwa.GBR.low_coverage.20120522.bam
Works :
/home/sm/mango-distribution-0.0.1//bin/mango-submit --packages org.apache.parquet:parquet-hadoop:1.8.2
-- /home/gm/workspace/mango_testing/mango_test_files//hg19.2bit -port 3333 -genes http://www.biodalliance.org/datasets/ensGene.bb
-features /user/gm/workspace/mango_testing/mango_test_files//gtex_gene_expression.bed,
/user/gm/workspace/mango_testing/mango_test_files//ucsc_genes_hg19.bed
-variants /user/gm/workspace/mango_testing/mango_test_files//1000gSNPs.vcf
-reads /user/gm/workspace/mango_testing/mango_test_files//HG00096.chrom11.ILLUMINA.bwa.GBR.low_coverage.20120522.bam

[akmorrow13]

Unfortunately right now, the only supported protocol for -genes is http. Supporting local bed/bigbed files through a JSON API requires modifying pileup.js GeneTrack code to support JSON formats. I have made an issue here for this in pileup hammerlab/pileup.js#506