31e95f0d1dd4ca08feba9b081a356527bd4b45e6 markd Sat Sep 26 20:36:20 2026 -0700 Drop the hand-built Files column from the TSS faceted tables. refs #35528 UCSC will generate the download links in the faceted table, so the Files column each composite built for itself is redundant. Remove downloadCell, the Files header and cell, the Files entry in subtrackUrls, and the DOWNLOAD constant that only fed them. The table is now Tissue, Sample class, Experiment, Cell line on all three composites. writeMetadata no longer needs db or track; the metadata files it writes are byte-identical. Lead each Data Access section with the link to the hgdownload directory, since that is now the way to a single file, and keep the naming convention beside it. Drop the paragraph describing the Files column. diff --git src/hg/makeDb/trackDb/human/hg38/transcriptionStart.ra src/hg/makeDb/trackDb/human/hg38/transcriptionStart.ra index 3637b089375..cf3106f2ffc 100644 --- src/hg/makeDb/trackDb/human/hg38/transcriptionStart.ra +++ src/hg/makeDb/trackDb/human/hg38/transcriptionStart.ra @@ -1,529 +1,529 @@ # Generated by hg/makeDb/outside/proCapNet/proCapNetTrackDb for hg38. # Do not edit by hand, edit the script and regenerate. track transcriptionStart superTrack on show shortLabel Transcription Initiation (TSS) longLabel Transcription initiation (TSS) group rna track encode4ProCap parent transcriptionStart compositeTrack faceted type bigWig shortLabel PRO-cap longLabel PRO-cap nascent RNA transcription start sites from ENCODE 4 metaDataUrl /gbdb/hg38/encode4ProCap/metadata.tsv colorSettingsUrl /gbdb/hg38/encode4ProCap/colors.json primaryKey Cell_line dataTypes procap|"PRO-cap" - subtrackUrls Experiment=https://www.encodeproject.org/experiments/$$/ Files=https://hgdownload.soe.ucsc.edu/gbdb/hg38/encode4ProCap/$$ + subtrackUrls Experiment=https://www.encodeproject.org/experiments/$$/ defaultSortField Cell_line maxCheckboxes 50 noInherit on visibility hide priority 1 track encode4ProCap_A673_procap parent encode4ProCap on container multiWig aggregate solidOverlay showSubtrackColorOnUi on type bigWig autoScale on alwaysZero on maxHeightPixels 100:40:8 windowingFunction maximum color 0,114,178 shortLabel A673 PRO-cap longLabel A673 PRO-cap transcription start sites, plus strand up and minus strand down onlyVisibility full priority 1 track encode4ProCap_A673_procap_pos parent encode4ProCap_A673_procap type bigWig bigDataUrl /gbdb/hg38/encode4ProCap/A673.ENCSR046BCI.pos.bw color 0,114,178 shortLabel A673 PRO-cap + longLabel A673 PRO-cap transcription start sites, plus strand track encode4ProCap_A673_procap_neg parent encode4ProCap_A673_procap type bigWig bigDataUrl /gbdb/hg38/encode4ProCap/A673.ENCSR046BCI.neg.bw color 0,114,178 altColor 0,114,178 shortLabel A673 PRO-cap - longLabel A673 PRO-cap transcription start sites, minus strand track encode4ProCap_Caco-2_procap parent encode4ProCap on container multiWig aggregate solidOverlay showSubtrackColorOnUi on type bigWig autoScale on alwaysZero on maxHeightPixels 100:40:8 windowingFunction maximum color 213,94,0 shortLabel Caco-2 PRO-cap longLabel Caco-2 PRO-cap transcription start sites, plus strand up and minus strand down onlyVisibility full priority 2 track encode4ProCap_Caco-2_procap_pos parent encode4ProCap_Caco-2_procap type bigWig bigDataUrl /gbdb/hg38/encode4ProCap/Caco-2.ENCSR100LIJ.pos.bw color 213,94,0 shortLabel Caco-2 PRO-cap + longLabel Caco-2 PRO-cap transcription start sites, plus strand track encode4ProCap_Caco-2_procap_neg parent encode4ProCap_Caco-2_procap type bigWig bigDataUrl /gbdb/hg38/encode4ProCap/Caco-2.ENCSR100LIJ.neg.bw color 213,94,0 altColor 213,94,0 shortLabel Caco-2 PRO-cap - longLabel Caco-2 PRO-cap transcription start sites, minus strand track encode4ProCap_Calu3_procap parent encode4ProCap on container multiWig aggregate solidOverlay showSubtrackColorOnUi on type bigWig autoScale on alwaysZero on maxHeightPixels 100:40:8 windowingFunction maximum color 0,158,115 shortLabel Calu3 PRO-cap longLabel Calu3 PRO-cap transcription start sites, plus strand up and minus strand down onlyVisibility full priority 3 track encode4ProCap_Calu3_procap_pos parent encode4ProCap_Calu3_procap type bigWig bigDataUrl /gbdb/hg38/encode4ProCap/Calu3.ENCSR935RNW.pos.bw color 0,158,115 shortLabel Calu3 PRO-cap + longLabel Calu3 PRO-cap transcription start sites, plus strand track encode4ProCap_Calu3_procap_neg parent encode4ProCap_Calu3_procap type bigWig bigDataUrl /gbdb/hg38/encode4ProCap/Calu3.ENCSR935RNW.neg.bw color 0,158,115 altColor 0,158,115 shortLabel Calu3 PRO-cap - longLabel Calu3 PRO-cap transcription start sites, minus strand track encode4ProCap_HUVEC_procap parent encode4ProCap on container multiWig aggregate solidOverlay showSubtrackColorOnUi on type bigWig autoScale on alwaysZero on maxHeightPixels 100:40:8 windowingFunction maximum color 204,121,167 shortLabel HUVEC PRO-cap longLabel HUVEC PRO-cap transcription start sites, plus strand up and minus strand down onlyVisibility full priority 4 track encode4ProCap_HUVEC_procap_pos parent encode4ProCap_HUVEC_procap type bigWig bigDataUrl /gbdb/hg38/encode4ProCap/HUVEC.ENCSR098LLB.pos.bw color 204,121,167 shortLabel HUVEC PRO-cap + longLabel HUVEC PRO-cap transcription start sites, plus strand track encode4ProCap_HUVEC_procap_neg parent encode4ProCap_HUVEC_procap type bigWig bigDataUrl /gbdb/hg38/encode4ProCap/HUVEC.ENCSR098LLB.neg.bw color 204,121,167 altColor 204,121,167 shortLabel HUVEC PRO-cap - longLabel HUVEC PRO-cap transcription start sites, minus strand track encode4ProCap_K562_procap parent encode4ProCap on container multiWig aggregate solidOverlay showSubtrackColorOnUi on type bigWig autoScale on alwaysZero on maxHeightPixels 100:40:8 windowingFunction maximum color 230,159,0 shortLabel K562 PRO-cap longLabel K562 PRO-cap transcription start sites, plus strand up and minus strand down onlyVisibility full priority 5 track encode4ProCap_K562_procap_pos parent encode4ProCap_K562_procap type bigWig bigDataUrl /gbdb/hg38/encode4ProCap/K562.ENCSR261KBX.pos.bw color 230,159,0 shortLabel K562 PRO-cap + longLabel K562 PRO-cap transcription start sites, plus strand track encode4ProCap_K562_procap_neg parent encode4ProCap_K562_procap type bigWig bigDataUrl /gbdb/hg38/encode4ProCap/K562.ENCSR261KBX.neg.bw color 230,159,0 altColor 230,159,0 shortLabel K562 PRO-cap - longLabel K562 PRO-cap transcription start sites, minus strand track encode4ProCap_MCF10A_procap parent encode4ProCap on container multiWig aggregate solidOverlay showSubtrackColorOnUi on type bigWig autoScale on alwaysZero on maxHeightPixels 100:40:8 windowingFunction maximum color 86,180,233 shortLabel MCF10A PRO-cap longLabel MCF10A PRO-cap transcription start sites, plus strand up and minus strand down onlyVisibility full priority 6 track encode4ProCap_MCF10A_procap_pos parent encode4ProCap_MCF10A_procap type bigWig bigDataUrl /gbdb/hg38/encode4ProCap/MCF10A.ENCSR799DGV.pos.bw color 86,180,233 shortLabel MCF10A PRO-cap + longLabel MCF10A PRO-cap transcription start sites, plus strand track encode4ProCap_MCF10A_procap_neg parent encode4ProCap_MCF10A_procap type bigWig bigDataUrl /gbdb/hg38/encode4ProCap/MCF10A.ENCSR799DGV.neg.bw color 86,180,233 altColor 86,180,233 shortLabel MCF10A PRO-cap - longLabel MCF10A PRO-cap transcription start sites, minus strand track proCapNet parent transcriptionStart compositeTrack faceted type bigWig shortLabel ProCapNet longLabel ProCapNet predicted PRO-cap metaDataUrl /gbdb/hg38/proCapNet/metadata.tsv colorSettingsUrl /gbdb/hg38/proCapNet/colors.json primaryKey Cell_line dataTypes pred|"Predicted PRO-cap" contrib|"Sequence contribution scores" - subtrackUrls Experiment=https://www.encodeproject.org/annotations/$$/ Files=https://hgdownload.soe.ucsc.edu/gbdb/hg38/proCapNet/$$ + subtrackUrls Experiment=https://www.encodeproject.org/annotations/$$/ defaultSortField Cell_line maxCheckboxes 50 noInherit on visibility hide priority 2 track proCapNet_A673_pred parent proCapNet on container multiWig aggregate solidOverlay showSubtrackColorOnUi on type bigWig autoScale on alwaysZero on maxHeightPixels 100:40:8 windowingFunction maximum color 0,114,178 shortLabel A673 Predicted longLabel A673 ProCapNet predicted PRO-cap, plus strand up and minus strand down onlyVisibility full priority 1 track proCapNet_A673_pred_pos parent proCapNet_A673_pred type bigWig bigDataUrl /gbdb/hg38/proCapNet/pred/A673.proCapNet.pos.bw color 0,114,178 shortLabel A673 Predicted + longLabel A673 ProCapNet predicted PRO-cap, plus strand track proCapNet_A673_pred_neg parent proCapNet_A673_pred type bigWig bigDataUrl /gbdb/hg38/proCapNet/pred/A673.proCapNet.neg.bw color 0,114,178 altColor 0,114,178 negateValues on shortLabel A673 Predicted - longLabel A673 ProCapNet predicted PRO-cap, minus strand track proCapNet_Caco-2_pred parent proCapNet on container multiWig aggregate solidOverlay showSubtrackColorOnUi on type bigWig autoScale on alwaysZero on maxHeightPixels 100:40:8 windowingFunction maximum color 213,94,0 shortLabel Caco-2 Predicted longLabel Caco-2 ProCapNet predicted PRO-cap, plus strand up and minus strand down onlyVisibility full priority 2 track proCapNet_Caco-2_pred_pos parent proCapNet_Caco-2_pred type bigWig bigDataUrl /gbdb/hg38/proCapNet/pred/Caco-2.proCapNet.pos.bw color 213,94,0 shortLabel Caco-2 Predicted + longLabel Caco-2 ProCapNet predicted PRO-cap, plus strand track proCapNet_Caco-2_pred_neg parent proCapNet_Caco-2_pred type bigWig bigDataUrl /gbdb/hg38/proCapNet/pred/Caco-2.proCapNet.neg.bw color 213,94,0 altColor 213,94,0 negateValues on shortLabel Caco-2 Predicted - longLabel Caco-2 ProCapNet predicted PRO-cap, minus strand track proCapNet_Calu3_pred parent proCapNet on container multiWig aggregate solidOverlay showSubtrackColorOnUi on type bigWig autoScale on alwaysZero on maxHeightPixels 100:40:8 windowingFunction maximum color 0,158,115 shortLabel Calu3 Predicted longLabel Calu3 ProCapNet predicted PRO-cap, plus strand up and minus strand down onlyVisibility full priority 3 track proCapNet_Calu3_pred_pos parent proCapNet_Calu3_pred type bigWig bigDataUrl /gbdb/hg38/proCapNet/pred/Calu3.proCapNet.pos.bw color 0,158,115 shortLabel Calu3 Predicted + longLabel Calu3 ProCapNet predicted PRO-cap, plus strand track proCapNet_Calu3_pred_neg parent proCapNet_Calu3_pred type bigWig bigDataUrl /gbdb/hg38/proCapNet/pred/Calu3.proCapNet.neg.bw color 0,158,115 altColor 0,158,115 negateValues on shortLabel Calu3 Predicted - longLabel Calu3 ProCapNet predicted PRO-cap, minus strand track proCapNet_HUVEC_pred parent proCapNet on container multiWig aggregate solidOverlay showSubtrackColorOnUi on type bigWig autoScale on alwaysZero on maxHeightPixels 100:40:8 windowingFunction maximum color 204,121,167 shortLabel HUVEC Predicted longLabel HUVEC ProCapNet predicted PRO-cap, plus strand up and minus strand down onlyVisibility full priority 4 track proCapNet_HUVEC_pred_pos parent proCapNet_HUVEC_pred type bigWig bigDataUrl /gbdb/hg38/proCapNet/pred/HUVEC.proCapNet.pos.bw color 204,121,167 shortLabel HUVEC Predicted + longLabel HUVEC ProCapNet predicted PRO-cap, plus strand track proCapNet_HUVEC_pred_neg parent proCapNet_HUVEC_pred type bigWig bigDataUrl /gbdb/hg38/proCapNet/pred/HUVEC.proCapNet.neg.bw color 204,121,167 altColor 204,121,167 negateValues on shortLabel HUVEC Predicted - longLabel HUVEC ProCapNet predicted PRO-cap, minus strand track proCapNet_K562_pred parent proCapNet on container multiWig aggregate solidOverlay showSubtrackColorOnUi on type bigWig autoScale on alwaysZero on maxHeightPixels 100:40:8 windowingFunction maximum color 230,159,0 shortLabel K562 Predicted longLabel K562 ProCapNet predicted PRO-cap, plus strand up and minus strand down onlyVisibility full priority 5 track proCapNet_K562_pred_pos parent proCapNet_K562_pred type bigWig bigDataUrl /gbdb/hg38/proCapNet/pred/K562.proCapNet.pos.bw color 230,159,0 shortLabel K562 Predicted + longLabel K562 ProCapNet predicted PRO-cap, plus strand track proCapNet_K562_pred_neg parent proCapNet_K562_pred type bigWig bigDataUrl /gbdb/hg38/proCapNet/pred/K562.proCapNet.neg.bw color 230,159,0 altColor 230,159,0 negateValues on shortLabel K562 Predicted - longLabel K562 ProCapNet predicted PRO-cap, minus strand track proCapNet_MCF10A_pred parent proCapNet on container multiWig aggregate solidOverlay showSubtrackColorOnUi on type bigWig autoScale on alwaysZero on maxHeightPixels 100:40:8 windowingFunction maximum color 86,180,233 shortLabel MCF10A Predicted longLabel MCF10A ProCapNet predicted PRO-cap, plus strand up and minus strand down onlyVisibility full priority 6 track proCapNet_MCF10A_pred_pos parent proCapNet_MCF10A_pred type bigWig bigDataUrl /gbdb/hg38/proCapNet/pred/MCF10A.proCapNet.pos.bw color 86,180,233 shortLabel MCF10A Predicted + longLabel MCF10A ProCapNet predicted PRO-cap, plus strand track proCapNet_MCF10A_pred_neg parent proCapNet_MCF10A_pred type bigWig bigDataUrl /gbdb/hg38/proCapNet/pred/MCF10A.proCapNet.neg.bw color 86,180,233 altColor 86,180,233 negateValues on shortLabel MCF10A Predicted - longLabel MCF10A ProCapNet predicted PRO-cap, minus strand track proCapNet_A673_contrib parent proCapNet off type bigWig bigDataUrl /gbdb/hg38/proCapNet/contrib/A673.proCapNet-contrib.bw logo on autoScale on alwaysZero on maxHeightPixels 100:40:8 color 0,114,178 shortLabel A673 Contribution longLabel A673 ProCapNet sequence-contribution scores onlyVisibility full priority 11 track proCapNet_Caco-2_contrib parent proCapNet off type bigWig bigDataUrl /gbdb/hg38/proCapNet/contrib/Caco-2.proCapNet-contrib.bw logo on autoScale on alwaysZero on maxHeightPixels 100:40:8 color 213,94,0 shortLabel Caco-2 Contribution longLabel Caco-2 ProCapNet sequence-contribution scores onlyVisibility full priority 12 track proCapNet_Calu3_contrib parent proCapNet off type bigWig bigDataUrl /gbdb/hg38/proCapNet/contrib/Calu3.proCapNet-contrib.bw logo on autoScale on alwaysZero on maxHeightPixels 100:40:8 color 0,158,115 shortLabel Calu3 Contribution longLabel Calu3 ProCapNet sequence-contribution scores onlyVisibility full priority 13 track proCapNet_HUVEC_contrib parent proCapNet off type bigWig bigDataUrl /gbdb/hg38/proCapNet/contrib/HUVEC.proCapNet-contrib.bw logo on autoScale on alwaysZero on maxHeightPixels 100:40:8 color 204,121,167 shortLabel HUVEC Contribution longLabel HUVEC ProCapNet sequence-contribution scores onlyVisibility full priority 14 track proCapNet_K562_contrib parent proCapNet off type bigWig bigDataUrl /gbdb/hg38/proCapNet/contrib/K562.proCapNet-contrib.bw logo on autoScale on alwaysZero on maxHeightPixels 100:40:8 color 230,159,0 shortLabel K562 Contribution longLabel K562 ProCapNet sequence-contribution scores onlyVisibility full priority 15 track proCapNet_MCF10A_contrib parent proCapNet off type bigWig bigDataUrl /gbdb/hg38/proCapNet/contrib/MCF10A.proCapNet-contrib.bw logo on autoScale on alwaysZero on maxHeightPixels 100:40:8 color 86,180,233 shortLabel MCF10A Contribution longLabel MCF10A ProCapNet sequence-contribution scores onlyVisibility full priority 16