## File formats:
# All files must be binary indexed format:
# bigWig, bigBed, BAM, VCF

## Folder structure:
myHub/
   hub.txt     -- short description of hub properties
   genomes.txt -- list of genomes included in hub data

   hg19/       -- directory of data for hg19
      trackDb.txt    -- display properties for tracks in this directory
      someTrack.html        -- description text for some track
      someTrackLiver.bigWig -- wiggle plot for some track in liver
      someTrackLiver.bigBed -- BED plot for enriched regions in liver

   hg18/       -- directory of data for hg18
      trackDb.txt -- display properties for tracks in this directory

## hub.txt contents
#  format:
hub          hub_name         [single word name]
shortLabel   hub_short_label  [short name <17 characters]
longLabel    hub_long_label   [longer descriptive label, <80 characters]
genomesFile  genomes_filelist [relative path to genomes.txt file, typically in the hub directory]
email        email_address

# example hub.txt
hub          UCSCHub
shortLabel   UCSC Hub
longLabel    UCSC Genome Informatics Hub for human DNase and RNAseq data
genomesFile  genomes.txt
email        genome@soe.ucsc.edu


## genomes.txt contents
#  format:
genome assembly_database_1          [valid ucsc database name]
trackDb assembly_1_path/trackDb.txt [relative path to trackDb.txt file, typically subdir of hub dir]

genome assembly_database_2
trackDb assembly_2_path/trackDb.txt

# example genomes.txt
genome hg18
trackDb hg18/trackDb.txt

genome hg19
trackDb hg19/trackDb.txt


## trackDB.txt contents
#  format:
track      track_name     
bigDataUrl track_data_URL
shortLabel short_label
longLabel  long_label
type       track_type

# example tracksDb.txt
track      dnaseSignal
bigDataUrl dnaseSignal.bigWig
shortLabel DNAse Signal
longLabel  Depth of alignments of DNAse reads
type       bigWig

track      dnaseReads
bigDataUrl dnaseReads.bam
shortLabel DNAse Reads
longLabel  DNAse reads mapped with MAQ
type       bam

## using nano text editor with pretty colors
There is a file ".nanorc" in this folder with many color syntax definitions,
which makes reading and editing file easier on the eyes.  Copy or append it
to your home directory if you'd like to use it:
Append, which will maintain an existing file:
   cat ./.nanorc >> ~/.nanorc