ucsc.dist.yaml

# This is the configuration file for all UCSC and tile-stitching options that are not specific to any genome

# Where is the genome browser accessible from?
# Replace .local with the URL for your local install of the UCSC browser
browser_hosts:
    local: 'http://localhost:58080/'
    authoritative: 'http://genome.ucsc.edu/'

# If the CGI binaries are directly executable from this machine, specify that directory here
# Then, you can use the scrape_method of "cgi_bin", which avoids the overhead of working through the HTTP server
cgi_bin_dir: '/Library/WebServer/CGI-Executables'

# Valid options are "local", "authoritative", or "cgi_bin"
# "authoritative" means you are scraping directly from UCSC's public site.
scrape_method: authoritative

# The usage limits for UCSC's public site are found at http://genome.ucsc.edu/#Conditions
scrape_limit:
    authoritative: 15

# We won't be interested in chromosomes with names that match this pattern
reject_chrs: '^chrM$|^chrUn_|_random$|_\w+_hap\d$'

# Font size for UCSC-rendered text.  Note, changing this affects layout.default.label_width_fn.
text_size: 10

# Give up after fetching this many times
max_fetch_tries: 10

# Only attempt to get tiles for tracks that haven't been updated for at least # seconds
get_if_older_than:
    unfinished: 10
    finished: 100604800

# These are the rules used to setup and extract pixels from the images generated by the UCSC browser
layout:
# The limitations and algo for the UCSC image layout are found in initTl() and trackLayoutSetPicWidth() in kentsrc
# There is one blank pixel on the right side of the pic and two blank pixels between the leftLabel and the track data
# leftLabelWidth = m * hgt.labelWidth + b; at leftLabelWidth + blank from the left, the track data pixels begin
# Note that if the leftLabelWidth is more than half the pix, initTl() overrides your hgt.labelWidth.
# Hence the lower limit for pix here is higher than the actual limit of 320.
    default:
        right_blank: 1
        label_width_fn:
            m: 6
            b: 14
            blank: 2
        hgt.labelWidth: [2, 26]
        pix: [340, 5000]
# These are the limits on actual track data pixels per fetch, derivable from the above limits.
#    let  : x_margin_total = label_width_fn['b'] + label_width_fn['blank'] + right_blank
#    then : pixel_data[0] = pix[0] - (label_width_fn['m'] * hgt.labelWidth[1] + x_margin_total)
#    and  : pixel_htopdata[1] = pix[1] - (label_width_fn['m'] * hgt.labelWidth[0] + x_margin_total)
        pixel_data: [167, 4971]
# We've modified our local copy of kentsrc to support a much higher pix limit.
    local:
        pix: [340, 100000]
        pixel_data: [167, 99971]

# These are the rules used to extract ideograms from the images generated by the UCSC browser.
ideogram:
    scale_from_tracks: 0.8
    crop:
        left: 75
        right: 3

# URLs within the genome browser for various features.  Unless UCSC changes, you should not have to alter these.
browser_urls:
    tracks: 'cgi-bin/hgTracks'
    tables: 'cgi-bin/hgTables'
    track_desc: 'cgi-bin/hgTrackUi'
    dna: 'cgi-bin/hgc?db=%s&c=%s&l=%s&r=%s&g=htcGetDna2&hgSeq.cdsExon=1&hgSeq.padding5=0&hgSeq.padding3=0&hgSeq.casing=upper&hgSeq.maskRepeats=on&hgSeq.repMasking=lower&boolshad.hgSeq.revComp=0&submit=get+DNA'

# Public URLs for downloading certain data from the UCSC browser site
data_urls:
    all_genomes: 'http://hgdownload.cse.ucsc.edu/downloads.html'
    big_zips: 'bigZips'
    chrom_info: 'http://hgdownload.cse.ucsc.edu/goldenPath/%s/database/chromInfo.txt.gz'
    cyto_band: 'http://hgdownload.cse.ucsc.edu/goldenPath/%s/database/cytoBand.txt.gz'

# 
custom_tracks:
    draw_limits:
        squeeze: 1000
        pack: 100

# The genome configuration options that are more likely to be customized by the user should be put toward the top.
genome_config_key_order:
    - species
    - assembly_date
    - output_dir
    - output_tch
    - bppps
    - subdir_for_bppps_under
    - slice_for_bppps_under
    - bppp_limits
    - tile_every
    - init_tracks
    - serve_tracks
    - all_tracks
    - track_desc
    - chr_order
    - default_tracks
    - chr_lengths