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.\"
.IX Title "MAKE_DAS_CONF 1p"
.TH MAKE_DAS_CONF 1p "2018-10-03" "perl v5.26.2" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
.\" way too many mistakes in technical documents.
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.SH "NAME"
make_das_conf.pl \- Create GBrowse config files from DAS sources
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 1
\&  % make_das_conf.pl http://genome.cse.ucsc.edu/cgi\-bin/das/hg16 > /usr/local/apache/conf/gbrowse.conf/ucsc.conf
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
This script generates a rough draft configuration file suitable for
browsing a remote \s-1DAS\s0 server.
.PP
To use this script, give it the \s-1URL\s0 of a \s-1DAS\s0 server.  If you point it
at the \s-1DAS\s0 base \s-1URL\s0 (without the data source name), as in
\&\*(L"http://genome.cse.ucsc.edu/cgi\-bin/das\*(R", it will print a list of
valid data sources to standard output.  If you give it a complete \s-1DAS
URL,\s0 as in \*(L"http://genome.cse.ucsc.edu/cgi\-bin/das/hg16\*(R", it will
print a gbrowse configuration file to standard output.
.PP
You will probably want to tweak the configuration file after you
generate it.  In particular, you will want to customize the glyph
types associated with each track and adjust the list of examples given
in the instructions (by default this script uses the complete list of
entry points, which may be rather long).
.PP
Also be aware that this script creates a set of aggregators that may
or may not be correct.  Consider the case of a \s-1DAS\s0 server which uses
the canonical structure for a spliced mRNA:
.PP
.Vb 2
\&     main method:   mRNA
\&     subparts:      5\*(Aq\-UTR, CDS, 3\*(Aq\-UTR
.Ve
.PP
This conversion script will generate the following set of aggregators:
.PP
.Vb 4
\&   mRNA{mRNA}
\&   5\*(Aq\-UTR{5\*(Aq\-UTR}
\&   CDS{CDS}
\&   3\*(Aq\-UTR{3\*(Aq\-UTR}
.Ve
.PP
It will also generate a total of four tracks, one each for the mRNA
and each of its parts.
.PP
This is, of course, incorrect. You will want to consolidate these into
a single aggregator:
.PP
.Vb 1
\&   mRNA{5\*(Aq\-UTR,3\*(Aq\-UTR,CDS/mRNA}
.Ve
.SH "SEE ALSO"
.IX Header "SEE ALSO"
Bio::DB::GFF, bulk_load_gff.pl, load_gff.pl
.SH "AUTHOR"
.IX Header "AUTHOR"
Lincoln Stein <lstein@cshl.org>.
.PP
Copyright (c) 2002 Cold Spring Harbor Laboratory
.PP
This library is free software; you can redistribute it and/or modify
it under the same terms as Perl itself.  See \s-1DISCLAIMER\s0.txt for
disclaimers of warranty.