akmorrow13
commented
5 years ago 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 https://github.com/hammerlab/pileup.js/issues/506
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