jbrowse add-assembly meliloti_data/genome_files/sinorhizobium_meliloti_2011.fa.gz --load inPlace --name "Sinorhizobium meliloti 2011" --displayName "Reference sequence" -t bgzipFasta

jbrowse add-track meliloti_data/annotation_files/sinorhizobium_meliloti_2011.gff.gz --load inPlace --name "Annotation" --category "Annotation files" --description "Sinorhizobium meliloti 2011" --config '{"displays": [ { "type": "LinearBasicDisplay", "displayId": "sinorhizobium_meliloti_2011.gff-LinearBasicDisplay", "renderer": { "type": "SvgFeatureRenderer", "color1": "jexl:get(feature,'\'strand\'')==-1?'\'red\'':'\'blue\''"}}]}' --overwrite
jbrowse text-index --attributes Name,ID,locus_tag


jbrowse add-track test_data/coverage_files/RIBO-csrA-1.min.forward.global.bw --load inPlace --name "RIBO-csrA-1 (fwd)" --category "Experiment 1" --description "Coverage file Forward strand (+)." --config '{"displays" : [ { "type": "LinearWiggleDisplay", "displayId": "RIBO-csrA-1.min.forward.global-LinearWiggleDisplay", "renderers" : { "XYPlotRenderer" : { "type": "XYPlotRenderer", "posColor" : "rgba(190,190,190,1)", "negColor": "rgba(190,190,190,1)" }}}]}' --description "Ribo-seq file for csrA condition" --overwrite

jbrowse add-track test_data/coverage_files/RIBO-csrA-1.min.reverse.global.bw --load inPlace --name "RIBO-csrA-1 (rev)" --category "Experiment 1" --description "Coverage file Reverse strand (-)." --config '{"displays" : [ { "type": "LinearWiggleDisplay", "displayId": "RIBO-csrA-1.min.reverse.global-LinearWiggleDisplay", "renderers" : { "XYPlotRenderer" : { "type": "XYPlotRenderer", "posColor" : "rgba(190,190,190,1)", "negColor": "rgba(190,190,190,1)" }}}]}' --description "Ribo-seq file for csrA condition" --overwrite

jbrowse add-track test_data/coverage_files/RNA-csrA-1.min.forward.global.bw --load inPlace --name "RNA-csrA-1 (fwd)" --category "Experiment 1" --description "Coverage file Forward strand (+)." --config '{"displays" : [ { "type": "LinearWiggleDisplay", "displayId": "RNA-csrA-1.min.forward.global-LinearWiggleDisplay", "renderers" : { "XYPlotRenderer" : { "type": "XYPlotRenderer", "posColor" : "rgba(190,190,190,1)", "negColor": "rgba(190,190,190,1)" }}}]}' --description "Ribo-seq file for csrA condition" --overwrite
jbrowse add-track test_data/coverage_files/RNA-csrA-1.min.reverse.global.bw --load inPlace --name "RNA-csrA-1 (rev)" --category "Experiment 1" --description "Coverage file Reverse strand (-)." --config '{"displays" : [ { "type": "LinearWiggleDisplay", "displayId": "RNA-csrA-1.min.reverse.global-LinearWiggleDisplay", "renderers" : { "XYPlotRenderer" : { "type": "XYPlotRenderer", "posColor" : "rgba(190,190,190,1)", "negColor": "rgba(190,190,190,1)" }}}]}' --description "Ribo-seq file for csrA condition" --overwrite



jbrowse add-track test_data/coverage_files/RIBO-WT-1.min.forward.global.bw --load inPlace --name "RIBO-WT-1 (fwd)" --category "Experiment 1" --description "Coverage file Forward strand (+)." --config '{"displays" : [ { "type": "LinearWiggleDisplay", "displayId": "RIBO-WT-1.min.forward.global-LinearWiggleDisplay", "renderers" : { "XYPlotRenderer" : { "type": "XYPlotRenderer", "posColor" : "rgba(190,190,190,1)", "negColor": "rgba(190,190,190,1)" }}}]}' --description "Ribo-seq file for WT condition" --overwrite
jbrowse add-track test_data/coverage_files/RIBO-WT-1.min.reverse.global.bw --load inPlace --name "RIBO-WT-1 (rev)" --category "Experiment 1" --description "Coverage file Reverse strand (-)." --config '{"displays" : [ { "type": "LinearWiggleDisplay", "displayId": "RIBO-WT-1.min.reverse.global-LinearWiggleDisplay", "renderers" : { "XYPlotRenderer" : { "type": "XYPlotRenderer", "posColor" : "rgba(190,190,190,1)", "negColor": "rgba(190,190,190,1)" }}}]}' --description "Ribo-seq file for WT condition" --overwrite

jbrowse add-track test_data/coverage_files/RNA-WT-1.min.forward.global.bw --load inPlace --name "RNA-WT-1 (fwd)" --category "Experiment 1" --description "Coverage file Forward strand (+)." --config '{"displays" : [ { "type": "LinearWiggleDisplay", "displayId": "RNA-WT-1.min.forward.global-LinearWiggleDisplay", "renderers" : { "XYPlotRenderer" : { "type": "XYPlotRenderer", "posColor" : "rgba(190,190,190,1)", "negColor": "rgba(190,190,190,1)" }}}]}' --description "Ribo-seq file for WT condition" --overwrite
jbrowse add-track test_data/coverage_files/RNA-WT-1.min.reverse.global.bw --load inPlace --name "RNA-WT-1 (rev)" --category "Experiment 1" --description "Coverage file Reverse strand (-)." --config '{"displays" : [ { "type": "LinearWiggleDisplay", "displayId": "RNA-WT-1.min.reverse.global-LinearWiggleDisplay", "renderers" : { "XYPlotRenderer" : { "type": "XYPlotRenderer", "posColor" : "rgba(190,190,190,1)", "negColor": "rgba(190,190,190,1)" }}}]}' --description "Ribo-seq file for WT condition" --overwrite