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PAG2023 bash script
From GMOD
#!/bin/bash jbrowse create public_html --force cd public_html jbrowse add-assembly data/c_elegans.PRJNA13758.WS286.genomic.fa.gz \ --displayName "C. elegans N2" \ --name c_elegans_PRJNA13758 \ --type bgzipFasta \ --load inPlace \ --refNameAliases test_data/ce_aliases.txt jbrowse add-track data/c_elegans.genes.sorted.gff3.gz \ --name Genes \ --description "Curated genes from WormBase" \ --load inPlace jbrowse text-index --attributes=Name,ID,locus --tracks c_elegans.genes.sorted.gff3 jbrowse add-track https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS286/c_elegans_PRJNA13758/tracks/Curated%20Genes%20\(protein%20coding\)/{refseq}/trackData.jsonz \ --name "Protein coding genes" \ --description "Only protein coding genes from WormBase" jbrowse add-track https://s3.amazonaws.com/wormbase-modencode/test/CeNDR/CB4854.bam \ --name "CeNDR BAM" jbrowse add-track https://storage.googleapis.com/elegansvariation.org/releases/current/WI.current.soft-filtered.vcf.gz \ --name Variants jbrowse add-track https://data.broadinstitute.org/compbio1/PhyloCSFtracks/ce11/latest/PhyloCSF+1.bw \ --name "Frame 1 usage" jbrowse add-track-json '{"type":"MultiQuantitativeTrack","trackId":"multiwiggle_phylo","name":"Forward PhyloCSF","assemblyNames":["c_elegans_PRJNA13758"],"adapter":{"type":"MultiWiggleAdapter", "bigWigs":["https://data.broadinstitute.org/compbio1/PhyloCSFtracks/ce11/latest/PhyloCSF+1.bw", "https://data.broadinstitute.org/compbio1/PhyloCSFtracks/ce11/latest/PhyloCSF+2.bw", "https://data.broadinstitute.org/compbio1/PhyloCSFtracks/ce11/latest/PhyloCSF+3.bw"]}, "displays":[{"type": "MultiLinearWiggleDisplay","displayId": "multiwiggle_phylo-MultiLinearWiggleDisplay"}]}' jbrowse add-assembly data/c_briggsae.PRJNA10731.WS287.genomic.fa.gz \ --displayName "C. briggsae" \ --name c_briggsae_PRJNA10731 \ --type bgzipFasta \ --load inPlace jbrowse add-track data/c_elegans.c_briggsae.paf \ --assemblyNames c_briggsae_PRJNA10731,c_elegans_PRJNA13758 \ --description "A minimap2 comparison of C. elegans and C. briggsae" \ --load inPlace \ --name "C. elegans/C. briggsae Synteny" jbrowse add-track https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS287/c_briggsae_PRJNA10731/tracks/Curated_Genes/{refseq}/trackData.jsonz \ --assemblyNames c_briggsae_PRJNA10731 \ --name "C. briggsae Genes" \ --trackId c_briggsae_genes jbrowse add-track https://s3.amazonaws.com/wormbase-modencode/test/maroilley/candidateSV.vcf.gz \ --name "Structural Variant Candidates VCF" \ --assemblyNames c_elegans_PRJNA13758 \ --category "Structural Variants" jbrowse add-track https://s3.amazonaws.com/wormbase-modencode/test/maroilley/VC109_Het_trim_bwaMEM_sort.bam \ --name "VC109 BAM" \ --assemblyNames c_elegans_PRJNA13758 \ --category "Structural Variants"