diff --git a/data/ucsc.other-tracks.txt b/data/ucsc.other-tracks.txt index 3dcda52d..e69de29b 100644 --- a/data/ucsc.other-tracks.txt +++ b/data/ucsc.other-tracks.txt @@ -1,1050 +0,0 @@ -track ATACseq -superTrack on show -shortLabel ATACseq -longLabel - - track ATACseq_EU_NI - parent ATACseq - container multiWig - shortLabel ATACseq_EU_NI - longLabel - type bigWig - visibility full - aggregate transparentOverlay - showSubtrackColorOnUi on - windowingFunction mean - priority 1 - configurable on - dragAndDrop subTracks - autoScale off - viewLimits 0:40 - alwaysZero on - maxHeightPixels 300:50:10 - color 0,179,116 - - track ATACseq_EU_NI_avg - type bigWig - parent ATACseq_EU_NI - shortLabel ATACseq_EU_NI_avg - longLabel - bigDataUrl https://emc.genome.mcgill.ca/hg19/barreiro/ATACseq_EU_NI_avg.bw - color 135,168,232 - - track ATACseq_EU_NI_stddev - type bigWig - parent ATACseq_EU_NI - shortLabel ATACseq_EU_NI_stddev - longLabel - bigDataUrl 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viewLimits 0:500 - type bigWig - - track RNAseq_EU_NI_rev_stdev - priority 25 - bigDataUrl https://emc.genome.mcgill.ca/hg19/barreiro/RNAseq_EU_NI_rev_stdev.bw - shortLabel RNAseq_EU_NI_rev_stdev - longLabel - parent RNAseq_EU_NI - color 53,144,162 - viewLimits 0:500 - type bigWig - - - track RNAseq_EU_Flu - parent RNAseq - container multiWig - shortLabel RNAseq_EU_Flu - longLabel - type bigWig - visibility full - aggregate transparentOverlay - showSubtrackColorOnUi on - windowingFunction mean - priority 26 - dragAndDrop subTracks - autoScale off - viewLimits 0:500 - alwaysZero on - maxHeightPixels 300:50:10 - color 0,179,116 - - track RNAseq_EU_Flu_fwd_avg - priority 27 - bigDataUrl https://emc.genome.mcgill.ca/hg19/barreiro/RNAseq_EU_Flu_fwd_avg.bw - shortLabel RNAseq_EU_Flu_fwd_avg - longLabel - parent RNAseq_EU_Flu - color 232,135,168 - viewLimits 0:500 - type bigWig - - track RNAseq_EU_Flu_fwd_stdev - priority 28 - bigDataUrl https://emc.genome.mcgill.ca/hg19/barreiro/RNAseq_EU_Flu_fwd_stdev.bw - shortLabel RNAseq_EU_Flu_fwd_stdev - longLabel - parent RNAseq_EU_Flu - color 204,0,01 - viewLimits 0:500 - type bigWig - - track RNAseq_EU_Flu_rev_avg - priority 29 - bigDataUrl https://emc.genome.mcgill.ca/hg19/barreiro/RNAseq_EU_Flu_rev_avg.bw - shortLabel RNAseq_EU_Flu_rev_avg - longLabel - parent RNAseq_EU_Flu - color 237,213,162 - viewLimits 0:500 - type bigWig - - track RNAseq_EU_Flu_rev_stdev - priority 30 - bigDataUrl https://emc.genome.mcgill.ca/hg19/barreiro/RNAseq_EU_Flu_rev_stdev.bw - shortLabel RNAseq_EU_Flu_rev_stdev - longLabel - parent RNAseq_EU_Flu - color 207,153,40 - viewLimits 0:500 - type bigWig - - track RNAseq_AF_NI - parent RNAseq - container multiWig - shortLabel RNAseq_AF_NI - longLabel - type bigWig - visibility full - aggregate transparentOverlay - showSubtrackColorOnUi on - windowingFunction mean - priority 31 - dragAndDrop subTracks - autoScale off - viewLimits 0:500 - alwaysZero on - maxHeightPixels 300:50:10 - color 255,123,0 - - track RNAseq_AF_NI_fwd_avg - priority 32 - bigDataUrl https://emc.genome.mcgill.ca/hg19/barreiro/RNAseq_AF_NI_fwd_avg.bw - shortLabel RNAseq_AF_NI_fwd_avg - longLabel - parent RNAseq_AF_NI - color 135,168,232 - viewLimits 0:500 - type bigWig - - track RNAseq_AF_NI_fwd_stdev - priority 33 - bigDataUrl https://emc.genome.mcgill.ca/hg19/barreiro/RNAseq_AF_NI_fwd_stdev.bw - shortLabel RNAseq_AF_NI_fwd_stdev - longLabel - parent RNAseq_AF_NI - color 53,89,161 - viewLimits 0:500 - type bigWig - - track RNAseq_AF_NI_rev_avg - priority 34 - bigDataUrl https://emc.genome.mcgill.ca/hg19/barreiro/RNAseq_AF_NI_rev_avg.bw - shortLabel RNAseq_AF_NI_rev_avg - longLabel - parent RNAseq_AF_NI - color 148,208,220 - viewLimits 0:500 - type bigWig - - track RNAseq_AF_NI_rev_stdev - priority 35 - bigDataUrl https://emc.genome.mcgill.ca/hg19/barreiro/RNAseq_AF_NI_rev_stdev.bw - shortLabel RNAseq_AF_NI_rev_stdev - longLabel - parent RNAseq_AF_NI - color 53,144,162 - viewLimits 0:500 - type bigWig - - - track RNAseq_AF_Flu - parent RNAseq - container multiWig - shortLabel RNAseq_AF_Flu - longLabel - type bigWig - visibility full - aggregate transparentOverlay - showSubtrackColorOnUi on - windowingFunction mean - priority 36 - dragAndDrop subTracks - autoScale off - viewLimits 0:500 - alwaysZero on - maxHeightPixels 300:50:10 - color 255,123,0 - - track RNAseq_AF_Flu_fwd_avg - priority 37 - bigDataUrl https://emc.genome.mcgill.ca/hg19/barreiro/RNAseq_AF_Flu_fwd_avg.bw - shortLabel RNAseq_AF_Flu_fwd_avg - longLabel - parent RNAseq_AF_Flu - color 232,135,168 - viewLimits 0:500 - type bigWig - - track RNAseq_AF_Flu_fwd_stdev - priority 38 - bigDataUrl https://emc.genome.mcgill.ca/hg19/barreiro/RNAseq_AF_Flu_fwd_stdev.bw - shortLabel RNAseq_AF_Flu_fwd_stdev - longLabel - parent RNAseq_AF_Flu - color 204,0,01 - viewLimits 0:500 - type bigWig - - track RNAseq_AF_Flu_rev_avg - priority 39 - bigDataUrl https://emc.genome.mcgill.ca/hg19/barreiro/RNAseq_AF_Flu_rev_avg.bw - shortLabel RNAseq_AF_Flu_rev_avg - longLabel - parent RNAseq_AF_Flu - color 237,213,162 - viewLimits 0:500 - type bigWig - - track RNAseq_AF_Flu_rev_stdev - priority 40 - bigDataUrl https://emc.genome.mcgill.ca/hg19/barreiro/RNAseq_AF_Flu_rev_stdev.bw - shortLabel RNAseq_AF_Flu_rev_stdev - longLabel - parent RNAseq_AF_Flu - color 207,153,40 - viewLimits 0:500 - type bigWig diff --git a/epivar-prod/docker-compose.yml b/epivar-prod/docker-compose.yml index 461d60e8..6756599c 100644 --- a/epivar-prod/docker-compose.yml +++ b/epivar-prod/docker-compose.yml @@ -41,16 +41,21 @@ services: - EPIVAR_IMPORT_MAX_P_VAL=0.05 - EPIVAR_LOW_COUNT_THRESHOLD=5 volumes: - # dataset configuration: about Markdown file, EpiVar config.js, tracks metadata.json + # dataset configuration: about Markdown file, EpiVar config.js - node1/about.md:/app/data/about.md - node1/config.js:/app/config.js:ro - - node1/metadata.json:/app/data/metadata.json:ro # genotypes: VCF + index file - /flu-infection-data/node1/allSamples.hc.vqsr.mil.snpId.snpeff.dbnsfp.vcf.gz:/app/data/genotypes.vcf.gz:ro - /flu-infection-data/node1/allSamples.hc.vqsr.mil.snpId.snpeff.dbnsfp.vcf.gz.tbi:/app/data/genotypes.vcf.gz.tbi:ro - # tracks: sample bigWigs and writeable volume for on-the-fly merged tracks + # tracks: + # - metadata JSON file, + - node1/metadata.json:/app/data/metadata.json:ro + # - sample bigWigs, - /flu-infection-data/node1/tracks:/tracks:ro + # - writeable volume for on-the-fly merged tracks, - /flu-infection-data/node1/mergedTracks:/mergedTracks + # - other static tracks for showing in the UCSC browser. + - node1/ucsc.other-tracks.txt:/app/data/ucsc.other-tracks.txt:ro epivar-node-1-redis: image: redis:7.2 @@ -92,11 +97,11 @@ services: # dataset configuration: about Markdown file, EpiVar config.js, tracks metadata.json - node2/about.md:/app/data/about.md - node2/config.js:/app/config.js:ro - - node2/metadata.json:/app/data/metadata.json:ro # genotypes: VCF + index file - /flu-infection-data/node2/allSamples.hc.vqsr.mil.snpId.snpeff.dbnsfp.vcf.gz:/app/data/genotypes.vcf.gz:ro - /flu-infection-data/node2/allSamples.hc.vqsr.mil.snpId.snpeff.dbnsfp.vcf.gz.tbi:/app/data/genotypes.vcf.gz.tbi:ro - # tracks: sample bigWigs and writeable volume for on-the-fly merged tracks + # tracks: metadata JSON file, sample bigWigs and writeable volume for on-the-fly merged tracks + - node2/metadata.json:/app/data/metadata.json:ro - /flu-infection-data/node2/tracks:/tracks:ro - /flu-infection-data/node2/mergedTracks:/mergedTracks diff --git a/epivar-prod/node1/ucsc.other-tracks.txt b/epivar-prod/node1/ucsc.other-tracks.txt new file mode 100644 index 00000000..f55ffddc --- /dev/null +++ b/epivar-prod/node1/ucsc.other-tracks.txt @@ -0,0 +1,1050 @@ +track ATACseq +superTrack on show +shortLabel ATACseq +longLabel + + track ATACseq_EU_NI + parent ATACseq + container multiWig + shortLabel ATACseq_EU_NI + longLabel + type bigWig + visibility full + aggregate transparentOverlay + showSubtrackColorOnUi on + windowingFunction mean + priority 1 + configurable on + dragAndDrop subTracks + autoScale off + viewLimits 0:40 + alwaysZero on + maxHeightPixels 300:50:10 + color 0,179,116 + + track ATACseq_EU_NI_avg + type bigWig + parent ATACseq_EU_NI + shortLabel ATACseq_EU_NI_avg + longLabel + bigDataUrl https://emc.genome.mcgill.ca/hg19/barreiro/ATACseq_EU_NI_avg.bw + color 135,168,232 + + track ATACseq_EU_NI_stddev + type bigWig + parent ATACseq_EU_NI + shortLabel ATACseq_EU_NI_stddev + longLabel + bigDataUrl https://emc.genome.mcgill.ca/hg19/barreiro/ATACseq_EU_NI_stdev.bw + color 53,89,161 + + + track ATACseq_EU_Flu + parent ATACseq + container multiWig + shortLabel ATACseq_EU_Flu + longLabel + type bigWig + visibility full + aggregate transparentOverlay + showSubtrackColorOnUi on + windowingFunction mean + priority 2 + configurable on + dragAndDrop subTracks + autoScale off + viewLimits 0:40 + alwaysZero on + maxHeightPixels 300:50:10 + color 0,179,116 + + track ATACseq_EU_Flu_avg + type bigWig + parent ATACseq_EU_Flu + shortLabel ATACseq_EU_Flu_avg + longLabel + bigDataUrl https://emc.genome.mcgill.ca/hg19/barreiro/ATACseq_EU_Flu_avg.bw + color 232,135,168 + + track ATACseq_EU_Flu_stddev + type bigWig + parent ATACseq_EU_Flu + shortLabel ATACseq_EU_Flu_stddev + longLabel + bigDataUrl https://emc.genome.mcgill.ca/hg19/barreiro/ATACseq_EU_Flu_stdev.bw + color 204,0,0 + + + track ATACseq_AF_NI + parent ATACseq + container multiWig + shortLabel ATACseq_AF_NI + longLabel + type bigWig + visibility full + aggregate transparentOverlay + showSubtrackColorOnUi on + windowingFunction mean + priority 3 + configurable on + dragAndDrop subTracks + autoScale off + viewLimits 0:40 + alwaysZero on + maxHeightPixels 300:50:10 + color 255,123,0 + + track ATACseq_AF_NI_avg + type bigWig + parent ATACseq_AF_NI + shortLabel ATACseq_AF_NI_avg + longLabel + bigDataUrl https://emc.genome.mcgill.ca/hg19/barreiro/ATACseq_AF_NI_avg.bw + color 135,168,232 + + track ATACseq_AF_NI_stddev + type bigWig + parent ATACseq_AF_NI + shortLabel ATACseq_AF_NI_stddev + longLabel + bigDataUrl https://emc.genome.mcgill.ca/hg19/barreiro/ATACseq_AF_NI_stdev.bw + color 53,89,161 + + + track ATACseq_AF_Flu + parent ATACseq + container multiWig + shortLabel ATACseq_AF_Flu + longLabel + type bigWig + visibility full + aggregate transparentOverlay + showSubtrackColorOnUi on + windowingFunction mean + priority 4 + configurable on + dragAndDrop subTracks + autoScale off + viewLimits 0:40 + alwaysZero on + maxHeightPixels 300:50:10 + color 255,123,0 + + track ATACseq_AF_Flu_avg + type bigWig + parent ATACseq_AF_Flu + shortLabel ATACseq_AF_Flu_avg + longLabel + bigDataUrl https://emc.genome.mcgill.ca/hg19/barreiro/ATACseq_AF_Flu_avg.bw + color 232,135,168 + + track ATACseq_AF_Flu_stddev + type bigWig + parent ATACseq_AF_Flu + shortLabel ATACseq_AF_Flu_stddev + longLabel + bigDataUrl https://emc.genome.mcgill.ca/hg19/barreiro/ATACseq_AF_Flu_stdev.bw + color 204,0,0 + +track NA1 +type bigWig +visibility full +shortLabel NA1 +longLabel +bigDataUrl https://emc.genome.mcgill.ca/hg19/barreiro/H3K27me3_AF_NI_avg.bw +viewLimits 0:500 +alwaysZero on +maxHeightPixels 300:30:10 +priority 4.5 +color 255,255,255 + + +track H3K27ac +superTrack on show +shortLabel H3K27ac +longLabel + + track H3K27ac_EU_NI + parent H3K27ac + container multiWig + shortLabel H3K27ac_EU_NI + longLabel + type bigWig + visibility full + aggregate transparentOverlay + showSubtrackColorOnUi on + windowingFunction mean + priority 5 + configurable on + dragAndDrop subTracks + autoScale off + viewLimits 0:40 + alwaysZero on + maxHeightPixels 300:50:10 + color 0,179,116 + + track H3K27ac_EU_NI_avg + type bigWig + parent H3K27ac_EU_NI + shortLabel H3K27ac_EU_NI_avg + longLabel + bigDataUrl https://emc.genome.mcgill.ca/hg19/barreiro/H3K27ac_EU_NI_avg.bw + color 135,168,232 + + track H3K27ac_EU_NI_stddev + type bigWig + parent H3K27ac_EU_NI + shortLabel H3K27ac_EU_NI_stddev + longLabel + bigDataUrl https://emc.genome.mcgill.ca/hg19/barreiro/H3K27ac_EU_NI_stdev.bw + color 53,89,161 + + + track H3K27ac_EU_Flu + parent H3K27ac + container multiWig + shortLabel H3K27ac_EU_Flu + longLabel + type bigWig + visibility full + aggregate transparentOverlay + showSubtrackColorOnUi on + windowingFunction mean + priority 6 + configurable on + dragAndDrop subTracks + autoScale off + viewLimits 0:40 + alwaysZero on + maxHeightPixels 300:50:10 + color 0,179,116 + + track H3K27ac_EU_Flu_avg + type bigWig + parent H3K27ac_EU_Flu + shortLabel H3K27ac_EU_Flu_avg + longLabel + bigDataUrl https://emc.genome.mcgill.ca/hg19/barreiro/H3K27ac_EU_Flu_avg.bw + color 232,135,168 + + track H3K27ac_EU_Flu_stddev + type bigWig + parent H3K27ac_EU_Flu + shortLabel H3K27ac_EU_Flu_stddev + longLabel + bigDataUrl https://emc.genome.mcgill.ca/hg19/barreiro/H3K27ac_EU_Flu_stdev.bw + color 204,0,0 + + + track H3K27ac_AF_NI + parent H3K27ac + container multiWig + shortLabel H3K27ac_AF_NI + longLabel + type bigWig + visibility full + aggregate transparentOverlay + showSubtrackColorOnUi on + windowingFunction mean + priority 7 + configurable on + dragAndDrop subTracks + autoScale off + viewLimits 0:40 + alwaysZero on + maxHeightPixels 300:50:10 + color 255,123,0 + + track H3K27ac_AF_NI_avg + type bigWig + parent H3K27ac_AF_NI + shortLabel H3K27ac_AF_NI_avg + longLabel + bigDataUrl https://emc.genome.mcgill.ca/hg19/barreiro/H3K27ac_AF_NI_avg.bw + color 135,168,232 + + track H3K27ac_AF_NI_stddev + type bigWig + parent H3K27ac_AF_NI + shortLabel H3K27ac_AF_NI_stddev + longLabel + bigDataUrl https://emc.genome.mcgill.ca/hg19/barreiro/H3K27ac_AF_NI_stdev.bw + color 53,89,161 + + + track H3K27ac_AF_Flu + parent H3K27ac + container multiWig + shortLabel H3K27ac_AF_Flu + longLabel + type bigWig + visibility full + aggregate transparentOverlay + showSubtrackColorOnUi on + windowingFunction mean + priority 8 + configurable on + dragAndDrop subTracks + autoScale off + viewLimits 0:40 + alwaysZero on + maxHeightPixels 300:50:10 + color 255,123,0 + + track H3K27ac_AF_Flu_avg + type bigWig + parent H3K27ac_AF_Flu + shortLabel H3K27ac_AF_Flu_avg + longLabel + bigDataUrl https://emc.genome.mcgill.ca/hg19/barreiro/H3K27ac_AF_Flu_avg.bw + color 232,135,168 + + track H3K27ac_AF_Flu_stddev + type bigWig + parent H3K27ac_AF_Flu + shortLabel H3K27ac_AF_Flu_stddev + longLabel + bigDataUrl https://emc.genome.mcgill.ca/hg19/barreiro/H3K27ac_AF_Flu_stdev.bw + color 204,0,0 + +track NA2 +type bigWig +visibility full +shortLabel NA2 +longLabel +bigDataUrl https://emc.genome.mcgill.ca/hg19/barreiro/H3K27me3_AF_NI_avg.bw +viewLimits 0:500 +alwaysZero on +maxHeightPixels 300:30:10 +priority 8.5 +color 255,255,255 + + +track H3K4me1 +superTrack on show +shortLabel H3K4me1 +longLabel + + track H3K4me1_EU_NI + parent H3K4me1 + container multiWig + shortLabel H3K4me1_EU_NI + longLabel + type bigWig + visibility full + aggregate transparentOverlay + showSubtrackColorOnUi on + windowingFunction mean + priority 9 + configurable on + dragAndDrop subTracks + autoScale off + viewLimits 0:15 + alwaysZero on + maxHeightPixels 300:50:10 + color 0,179,116 + + track H3K4me1_EU_NI_avg + type bigWig + parent H3K4me1_EU_NI + shortLabel H3K4me1_EU_NI_avg + longLabel + bigDataUrl https://emc.genome.mcgill.ca/hg19/barreiro/H3K4me1_EU_NI_avg.bw + color 135,168,232 + + track H3K4me1_EU_NI_stddev + type bigWig + parent H3K4me1_EU_NI + shortLabel H3K4me1_EU_NI_stddev + longLabel + bigDataUrl https://emc.genome.mcgill.ca/hg19/barreiro/H3K4me1_EU_NI_stdev.bw + color 53,89,161 + + + track H3K4me1_EU_Flu + parent H3K4me1 + container multiWig + shortLabel H3K4me1_EU_Flu + longLabel + type bigWig + visibility full + aggregate transparentOverlay + showSubtrackColorOnUi on + windowingFunction mean + priority 10 + configurable on + dragAndDrop subTracks + autoScale off + viewLimits 0:15 + alwaysZero on + maxHeightPixels 300:50:10 + color 0,179,116 + + track H3K4me1_EU_Flu_avg + type bigWig + parent H3K4me1_EU_Flu + shortLabel H3K4me1_EU_Flu_avg + longLabel + bigDataUrl https://emc.genome.mcgill.ca/hg19/barreiro/H3K4me1_EU_Flu_avg.bw + color 232,135,168 + + track H3K4me1_EU_Flu_stddev + type bigWig + parent H3K4me1_EU_Flu + shortLabel H3K4me1_EU_Flu_stddev + longLabel + bigDataUrl https://emc.genome.mcgill.ca/hg19/barreiro/H3K4me1_EU_Flu_stdev.bw + color 204,0,0 + + + track H3K4me1_AF_NI + parent H3K4me1 + container multiWig + shortLabel H3K4me1_AF_NI + longLabel + type bigWig + visibility full + aggregate transparentOverlay + showSubtrackColorOnUi on + windowingFunction mean + priority 11 + configurable on + dragAndDrop subTracks + autoScale off + viewLimits 0:15 + alwaysZero on + maxHeightPixels 300:50:10 + color 255,123,0 + + track H3K4me1_AF_NI_avg + type bigWig + parent H3K4me1_AF_NI + shortLabel H3K4me1_AF_NI_avg + longLabel + bigDataUrl https://emc.genome.mcgill.ca/hg19/barreiro/H3K4me1_AF_NI_avg.bw + color 135,168,232 + + track H3K4me1_AF_NI_stddev + type bigWig + parent H3K4me1_AF_NI + shortLabel H3K4me1_AF_NI_stddev + longLabel + bigDataUrl https://emc.genome.mcgill.ca/hg19/barreiro/H3K4me1_AF_NI_stdev.bw + color 53,89,161 + + + track H3K4me1_AF_Flu + parent H3K4me1 + container multiWig + shortLabel H3K4me1_AF_Flu + longLabel + type bigWig + visibility full + aggregate transparentOverlay + showSubtrackColorOnUi on + windowingFunction mean + priority 12 + configurable on + dragAndDrop subTracks + autoScale off + viewLimits 0:15 + alwaysZero on + maxHeightPixels 300:50:10 + color 255,123,0 + + track H3K4me1_AF_Flu_avg + type bigWig + parent H3K4me1_AF_Flu + shortLabel H3K4me1_AF_Flu_avg + longLabel + bigDataUrl https://emc.genome.mcgill.ca/hg19/barreiro/H3K4me1_AF_Flu_avg.bw + color 232,135,168 + + track H3K4me1_AF_Flu_stddev + type bigWig + parent H3K4me1_AF_Flu + shortLabel H3K4me1_AF_Flu_stddev + longLabel + bigDataUrl https://emc.genome.mcgill.ca/hg19/barreiro/H3K4me1_AF_Flu_stdev.bw + color 204,0,0 + +track NA3 +type bigWig +visibility full +shortLabel NA3 +longLabel +bigDataUrl https://emc.genome.mcgill.ca/hg19/barreiro/H3K27me3_AF_NI_avg.bw +viewLimits 0:500 +alwaysZero on +maxHeightPixels 300:30:10 +priority 12.5 +color 255,255,255 + + +track H3K4me3 +superTrack on show +shortLabel H3K4me3 +longLabel + + track H3K4me3_EU_NI + parent H3K4me3 + container multiWig + shortLabel H3K4me3_EU_NI + longLabel + type bigWig + visibility full + aggregate transparentOverlay + showSubtrackColorOnUi on + windowingFunction mean + priority 13 + configurable on + dragAndDrop subTracks + autoScale off + viewLimits 0:10 + alwaysZero on + maxHeightPixels 300:50:10 + color 0,179,116 + + track H3K4me3_EU_NI_avg + type bigWig + parent H3K4me3_EU_NI + shortLabel H3K4me3_EU_NI_avg + longLabel + bigDataUrl https://emc.genome.mcgill.ca/hg19/barreiro/H3K4me3_EU_NI_avg.bw + color 135,168,232 + + track H3K4me3_EU_NI_stddev + type bigWig + parent H3K4me3_EU_NI + shortLabel H3K4me3_EU_NI_stddev + longLabel + bigDataUrl https://emc.genome.mcgill.ca/hg19/barreiro/H3K4me3_EU_NI_stdev.bw + color 53,89,161 + + + track H3K4me3_EU_Flu + parent H3K4me3 + container multiWig + shortLabel H3K4me3_EU_Flu + longLabel + type bigWig + visibility full + aggregate transparentOverlay + showSubtrackColorOnUi on + windowingFunction mean + priority 14 + configurable on + dragAndDrop subTracks + autoScale off + viewLimits 0:10 + alwaysZero on + maxHeightPixels 300:50:10 + color 0,179,116 + + track H3K4me3_EU_Flu_avg + type bigWig + parent H3K4me3_EU_Flu + shortLabel H3K4me3_EU_Flu_avg + longLabel + bigDataUrl https://emc.genome.mcgill.ca/hg19/barreiro/H3K4me3_EU_Flu_avg.bw + color 232,135,168 + + track H3K4me3_EU_Flu_stddev + type bigWig + parent H3K4me3_EU_Flu + shortLabel H3K4me3_EU_Flu_stddev + longLabel + bigDataUrl https://emc.genome.mcgill.ca/hg19/barreiro/H3K4me3_EU_Flu_stdev.bw + color 204,0,0 + + + track H3K4me3_AF_NI + parent H3K4me3 + container multiWig + shortLabel H3K4me3_AF_NI + longLabel + type bigWig + visibility full + aggregate transparentOverlay + showSubtrackColorOnUi on + windowingFunction mean + priority 15 + configurable on + dragAndDrop subTracks + autoScale off + viewLimits 0:10 + alwaysZero on + maxHeightPixels 300:50:10 + color 255,123,0 + + track H3K4me3_AF_NI_avg + type bigWig + parent H3K4me3_AF_NI + shortLabel H3K4me3_AF_NI_avg + longLabel + bigDataUrl https://emc.genome.mcgill.ca/hg19/barreiro/H3K4me3_AF_NI_avg.bw + color 135,168,232 + + track H3K4me3_AF_NI_stddev + type bigWig + parent H3K4me3_AF_NI + shortLabel H3K4me3_AF_NI_stddev + longLabel + bigDataUrl https://emc.genome.mcgill.ca/hg19/barreiro/H3K4me3_AF_NI_stdev.bw + color 53,89,161 + + + track H3K4me3_AF_Flu + parent H3K4me3 + container multiWig + shortLabel H3K4me3_AF_Flu + longLabel + type bigWig + visibility full + aggregate transparentOverlay + showSubtrackColorOnUi on + windowingFunction mean + priority 16 + configurable on + dragAndDrop subTracks + autoScale off + viewLimits 0:10 + alwaysZero on + maxHeightPixels 300:50:10 + color 255,123,0 + + track H3K4me3_AF_Flu_avg + type bigWig + parent H3K4me3_AF_Flu + shortLabel H3K4me3_AF_Flu_avg + longLabel + bigDataUrl https://emc.genome.mcgill.ca/hg19/barreiro/H3K4me3_AF_Flu_avg.bw + color 232,135,168 + + track H3K4me3_AF_Flu_stddev + type bigWig + parent H3K4me3_AF_Flu + shortLabel H3K4me3_AF_Flu_stddev + longLabel + bigDataUrl https://emc.genome.mcgill.ca/hg19/barreiro/H3K4me3_AF_Flu_stdev.bw + color 204,0,0 + +track NA4 +type bigWig +visibility full +shortLabel NA4 +longLabel +bigDataUrl https://emc.genome.mcgill.ca/hg19/barreiro/H3K27me3_AF_NI_avg.bw +viewLimits 0:500 +alwaysZero on +maxHeightPixels 300:30:10 +priority 16.5 +color 255,255,255 + + +track H3K27me3 +superTrack on show +shortLabel H3K27me3 +longLabel + + track H3K27me3_EU_NI + parent H3K27me3 + container multiWig + shortLabel H3K27me3_EU_NI + longLabel + type bigWig + visibility full + aggregate transparentOverlay + showSubtrackColorOnUi on + windowingFunction mean + priority 17 + configurable on + dragAndDrop subTracks + autoScale off + viewLimits 0:10 + alwaysZero on + maxHeightPixels 300:50:10 + color 0,179,116 + + track H3K27me3_EU_NI_avg + type bigWig + parent H3K27me3_EU_NI + shortLabel H3K27me3_EU_NI_avg + longLabel + bigDataUrl https://emc.genome.mcgill.ca/hg19/barreiro/H3K27me3_EU_NI_avg.bw + color 135,168,232 + + track H3K27me3_EU_NI_stddev + type bigWig + parent H3K27me3_EU_NI + shortLabel H3K27me3_EU_NI_stddev + longLabel + bigDataUrl https://emc.genome.mcgill.ca/hg19/barreiro/H3K27me3_EU_NI_stdev.bw + color 53,89,161 + + + track H3K27me3_EU_Flu + parent H3K27me3 + container multiWig + shortLabel H3K27me3_EU_Flu + longLabel + type bigWig + visibility full + aggregate transparentOverlay + showSubtrackColorOnUi on + windowingFunction mean + priority 18 + configurable on + dragAndDrop subTracks + autoScale off + viewLimits 0:10 + alwaysZero on + maxHeightPixels 300:50:10 + color 0,179,116 + + track H3K27me3_EU_Flu_avg + type bigWig + parent H3K27me3_EU_Flu + shortLabel H3K27me3_EU_Flu_avg + longLabel + bigDataUrl https://emc.genome.mcgill.ca/hg19/barreiro/H3K27me3_EU_Flu_avg.bw + color 232,135,168 + + track H3K27me3_EU_Flu_stddev + type bigWig + parent H3K27me3_EU_Flu + shortLabel H3K27me3_EU_Flu_stddev + longLabel + bigDataUrl https://emc.genome.mcgill.ca/hg19/barreiro/H3K27me3_EU_Flu_stdev.bw + color 204,0,0 + + + track H3K27me3_AF_NI + parent H3K27me3 + container multiWig + shortLabel H3K27me3_AF_NI + longLabel + type bigWig + visibility full + aggregate transparentOverlay + showSubtrackColorOnUi on + windowingFunction mean + priority 19 + configurable on + dragAndDrop subTracks + autoScale off + viewLimits 0:10 + alwaysZero on + maxHeightPixels 300:50:10 + color 255,123,0 + + track H3K27me3_AF_NI_avg + type bigWig + parent H3K27me3_AF_NI + shortLabel H3K27me3_AF_NI_avg + longLabel + bigDataUrl https://emc.genome.mcgill.ca/hg19/barreiro/H3K27me3_AF_NI_avg.bw + color 135,168,232 + + track H3K27me3_AF_NI_stddev + type bigWig + parent H3K27me3_AF_NI + shortLabel H3K27me3_AF_NI_stddev + longLabel + bigDataUrl https://emc.genome.mcgill.ca/hg19/barreiro/H3K27me3_AF_NI_stdev.bw + color 53,89,161 + + + track H3K27me3_AF_Flu + parent H3K27me3 + container multiWig + shortLabel H3K27me3_AF_Flu + longLabel + type bigWig + visibility full + aggregate transparentOverlay + showSubtrackColorOnUi on + windowingFunction mean + priority 20 + configurable on + dragAndDrop subTracks + autoScale off + viewLimits 0:10 + alwaysZero on + maxHeightPixels 300:50:10 + color 255,123,0 + + track H3K27me3_AF_Flu_avg + type bigWig + parent H3K27me3_AF_Flu + shortLabel H3K27me3_AF_Flu_avg + longLabel + bigDataUrl https://emc.genome.mcgill.ca/hg19/barreiro/H3K27me3_AF_Flu_avg.bw + color 232,135,168 + + track H3K27me3_AF_Flu_stddev + type bigWig + parent H3K27me3_AF_Flu + shortLabel H3K27me3_AF_Flu_stddev + longLabel + bigDataUrl https://emc.genome.mcgill.ca/hg19/barreiro/H3K27me3_AF_Flu_stdev.bw + color 204,0,0 + +track NA5 +type bigWig +visibility full +shortLabel NA5 +longLabel +bigDataUrl https://emc.genome.mcgill.ca/hg19/barreiro/H3K27me3_AF_NI_avg.bw +viewLimits 0:500 +alwaysZero on +maxHeightPixels 300:30:10 +priority 20.5 +color 255,255,255 + +hub hub1 +shortLabel Track Collections +longLabel Track Collections +useOneFile on +email genome-www@soe.ucsc.edu + +genome hg19 + +track RNAseq +superTrack on show +shortLabel RNAseq +longLabel + + track RNAseq_EU_NI + parent RNAseq + container multiWig + shortLabel RNAseq_EU_NI + longLabel + type bigWig + visibility full + aggregate transparentOverlay + showSubtrackColorOnUi on + windowingFunction mean + priority 21 + dragAndDrop subTracks + autoScale off + viewLimits 0:500 + alwaysZero on + maxHeightPixels 300:50:10 + color 0,179,116 + + track RNAseq_EU_NI_fwd_avg + priority 22 + bigDataUrl https://emc.genome.mcgill.ca/hg19/barreiro/RNAseq_EU_NI_fwd_avg.bw + shortLabel RNAseq_EU_NI_fwd_avg + longLabel + parent RNAseq_EU_NI + color 135,168,232 + viewLimits 0:500 + type bigWig + + track RNAseq_EU_NI_fwd_stdev + priority 23 + bigDataUrl https://emc.genome.mcgill.ca/hg19/barreiro/RNAseq_EU_NI_fwd_stdev.bw + shortLabel RNAseq_EU_NI_fwd_stdev + longLabel + parent RNAseq_EU_NI + color 53,89,161 + viewLimits 0:500 + type bigWig + + track RNAseq_EU_NI_rev_avg + priority 24 + bigDataUrl https://emc.genome.mcgill.ca/hg19/barreiro/RNAseq_EU_NI_rev_avg.bw + shortLabel RNAseq_EU_NI_rev_avg + longLabel + parent RNAseq_EU_NI + color 148,208,220 + viewLimits 0:500 + type bigWig + + track RNAseq_EU_NI_rev_stdev + priority 25 + bigDataUrl https://emc.genome.mcgill.ca/hg19/barreiro/RNAseq_EU_NI_rev_stdev.bw + shortLabel RNAseq_EU_NI_rev_stdev + longLabel + parent RNAseq_EU_NI + color 53,144,162 + viewLimits 0:500 + type bigWig + + + track RNAseq_EU_Flu + parent RNAseq + container multiWig + shortLabel RNAseq_EU_Flu + longLabel + type bigWig + visibility full + aggregate transparentOverlay + showSubtrackColorOnUi on + windowingFunction mean + priority 26 + dragAndDrop subTracks + autoScale off + viewLimits 0:500 + alwaysZero on + maxHeightPixels 300:50:10 + color 0,179,116 + + track RNAseq_EU_Flu_fwd_avg + priority 27 + bigDataUrl https://emc.genome.mcgill.ca/hg19/barreiro/RNAseq_EU_Flu_fwd_avg.bw + shortLabel RNAseq_EU_Flu_fwd_avg + longLabel + parent RNAseq_EU_Flu + color 232,135,168 + viewLimits 0:500 + type bigWig + + track RNAseq_EU_Flu_fwd_stdev + priority 28 + bigDataUrl https://emc.genome.mcgill.ca/hg19/barreiro/RNAseq_EU_Flu_fwd_stdev.bw + shortLabel RNAseq_EU_Flu_fwd_stdev + longLabel + parent RNAseq_EU_Flu + color 204,0,01 + viewLimits 0:500 + type bigWig + + track RNAseq_EU_Flu_rev_avg + priority 29 + bigDataUrl https://emc.genome.mcgill.ca/hg19/barreiro/RNAseq_EU_Flu_rev_avg.bw + shortLabel RNAseq_EU_Flu_rev_avg + longLabel + parent RNAseq_EU_Flu + color 237,213,162 + viewLimits 0:500 + type bigWig + + track RNAseq_EU_Flu_rev_stdev + priority 30 + bigDataUrl https://emc.genome.mcgill.ca/hg19/barreiro/RNAseq_EU_Flu_rev_stdev.bw + shortLabel RNAseq_EU_Flu_rev_stdev + longLabel + parent RNAseq_EU_Flu + color 207,153,40 + viewLimits 0:500 + type bigWig + + track RNAseq_AF_NI + parent RNAseq + container multiWig + shortLabel RNAseq_AF_NI + longLabel + type bigWig + visibility full + aggregate transparentOverlay + showSubtrackColorOnUi on + windowingFunction mean + priority 31 + dragAndDrop subTracks + autoScale off + viewLimits 0:500 + alwaysZero on + maxHeightPixels 300:50:10 + color 255,123,0 + + track RNAseq_AF_NI_fwd_avg + priority 32 + bigDataUrl https://emc.genome.mcgill.ca/hg19/barreiro/RNAseq_AF_NI_fwd_avg.bw + shortLabel RNAseq_AF_NI_fwd_avg + longLabel + parent RNAseq_AF_NI + color 135,168,232 + viewLimits 0:500 + type bigWig + + track RNAseq_AF_NI_fwd_stdev + priority 33 + bigDataUrl https://emc.genome.mcgill.ca/hg19/barreiro/RNAseq_AF_NI_fwd_stdev.bw + shortLabel RNAseq_AF_NI_fwd_stdev + longLabel + parent RNAseq_AF_NI + color 53,89,161 + viewLimits 0:500 + type bigWig + + track RNAseq_AF_NI_rev_avg + priority 34 + bigDataUrl https://emc.genome.mcgill.ca/hg19/barreiro/RNAseq_AF_NI_rev_avg.bw + shortLabel RNAseq_AF_NI_rev_avg + longLabel + parent RNAseq_AF_NI + color 148,208,220 + viewLimits 0:500 + type bigWig + + track RNAseq_AF_NI_rev_stdev + priority 35 + bigDataUrl https://emc.genome.mcgill.ca/hg19/barreiro/RNAseq_AF_NI_rev_stdev.bw + shortLabel RNAseq_AF_NI_rev_stdev + longLabel + parent RNAseq_AF_NI + color 53,144,162 + viewLimits 0:500 + type bigWig + + + track RNAseq_AF_Flu + parent RNAseq + container multiWig + shortLabel RNAseq_AF_Flu + longLabel + type bigWig + visibility full + aggregate transparentOverlay + showSubtrackColorOnUi on + windowingFunction mean + priority 36 + dragAndDrop subTracks + autoScale off + viewLimits 0:500 + alwaysZero on + maxHeightPixels 300:50:10 + color 255,123,0 + + track RNAseq_AF_Flu_fwd_avg + priority 37 + bigDataUrl https://emc.genome.mcgill.ca/hg19/barreiro/RNAseq_AF_Flu_fwd_avg.bw + shortLabel RNAseq_AF_Flu_fwd_avg + longLabel + parent RNAseq_AF_Flu + color 232,135,168 + viewLimits 0:500 + type bigWig + + track RNAseq_AF_Flu_fwd_stdev + priority 38 + bigDataUrl https://emc.genome.mcgill.ca/hg19/barreiro/RNAseq_AF_Flu_fwd_stdev.bw + shortLabel RNAseq_AF_Flu_fwd_stdev + longLabel + parent RNAseq_AF_Flu + color 204,0,01 + viewLimits 0:500 + type bigWig + + track RNAseq_AF_Flu_rev_avg + priority 39 + bigDataUrl https://emc.genome.mcgill.ca/hg19/barreiro/RNAseq_AF_Flu_rev_avg.bw + shortLabel RNAseq_AF_Flu_rev_avg + longLabel + parent RNAseq_AF_Flu + color 237,213,162 + viewLimits 0:500 + type bigWig + + track RNAseq_AF_Flu_rev_stdev + priority 40 + bigDataUrl https://emc.genome.mcgill.ca/hg19/barreiro/RNAseq_AF_Flu_rev_stdev.bw + shortLabel RNAseq_AF_Flu_rev_stdev + longLabel + parent RNAseq_AF_Flu + color 207,153,40 + viewLimits 0:500 + type bigWig diff --git a/example.docker-compose.yml b/example.docker-compose.yml index 30010a88..dd8f70cb 100644 --- a/example.docker-compose.yml +++ b/example.docker-compose.yml @@ -14,19 +14,24 @@ services: - EPIVAR_IMPORT_MAX_P_VAL=0.05 - EPIVAR_LOW_COUNT_THRESHOLD=5 volumes: - # dataset configuration: about Markdown file, EpiVar config.js, tracks metadata.json + # dataset configuration: about Markdown file, EpiVar config.js - /path/to/about.md:/app/data/about.md # about file - /path/to/config.js:/app/config.js:ro # dataset configuration file, see config.example.js - - /path/to/metadata.json:/app/metadata.json:ro # genotypes: VCF + index file - /path/to/genotypes.vcf.gz:/app/data/genotypes.vcf.gz:ro - /path/to/genotypes.vcf.gz.tbi:/app/data/genotypes.vcf.gz.tbi:ro - # TODO - - /path/to/input-files:/app/input-files # input files directory - - /path/to/ucsc.tracks:/app/data/ucsc.other-tracks.txt # static track hub with other relevant tracks - # tracks: sample bigWigs and writeable volume for on-the-fly merged tracks - - /path/to/tracks:/tracks + # peaks files + - /path/to/matrices:/app/input-files/matrices:ro + - /path/to/qtls:/app/input-files/qtls:ro + # tracks: + # - metadata JSON file, + - /path/to/metadata.json:/app/data/metadata.json:ro + # - sample bigWigs, + - /path/to/tracks:/tracks:ro + # - writeable volume for on-the-fly merged tracks, - volumes/mergedTracks:/mergedTracks + # - other static tracks for showing in the UCSC browser. + - /path/to/ucsc.other-tracks.txt:/app/data/ucsc.other-tracks.txt:ro epivar-redis: image: redis:7.2