<%! def inherit(context): if context.get('use_panels'): return '/webapps/galaxy/base_panels.mako' else: return '/base.mako' %> <%inherit file="${inherit(context)}"/> <%def name="init()"> <% self.has_left_panel=False self.has_right_panel=False self.message_box_visible=False self.active_view="user" self.overlay_visible=False %> <%def name="title()">Custom Database Builds <%def name="stylesheets()"> ${parent.stylesheets()} <%def name="javascripts()"> ${parent.javascripts()} <%def name="center_panel()"> ${self.body()} <%def name="body()"> % if message:

${message}

% elif lines_skipped > 0:

Skipped ${lines_skipped} lines that could not be parsed. (Line was either blank or not 2-column, with 2nd column being an integer)

% endif

Current Custom Builds:

% if dbkeys: % for key, dct in dbkeys.iteritems(): % endfor

${dct['name'] | h}

${key | h}

## ${len(dct["chroms"])} entries ##

    ##                    
    ##                        
    ##                        % for chrom, chrom_len in dct["chroms"].iteritems():
    ##                            
    ##                        % endfor
    ##                    Chrom Length
${chrom | h} ${chrom_len | h}
    ##

% if 'count' in dct: ${dct['count']} % else: Processing % endif

% else:

You currently have no custom builds.

% endif

Show loaded, system-installed builds

${installed_len_files}

Add a Custom Build

## Include hidden param for panels: %if use_panels: %endif ## Custom build via fasta in history.

New Build

Name (eg: Hamster):

Key (eg: hamster_v1):

Definition:

FASTA

Len File

Len Entry

FASTA format

This is a multi-fasta file from your current history that provides the genome sequences for each chromosome/contig in your build.

Here is a snippet from an example multi-fasta file:

    >chr1
    ATTATATATAAGACCACAGAGAGAATATTTTGCCCGG...
    >chr2
    GGCGGCCGCGGCGATATAGAACTACTCATTATATATA...
    ...

Length Format

The length format is two-column, separated by whitespace, of the form:

chrom/contig   length of chrom/contig

For example, the first few entries of mm9.len are as follows:

    chr1    197195432
    chr2    181748087
    chr3    159599783
    chr4    155630120
    chr5    152537259

Trackster uses this information to populate the select box for chrom/contig, and to set the maximum basepair of the track browser. You may either upload a .len file of this format (Len File option), or directly enter the information into the box (Len Entry option).