This is the command make_das_confp that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
PROGRAM:
NAME
make_das_conf.pl - Create GBrowse config files from DAS sources
SYNOPSIS
% make_das_conf.pl http://genome.cse.ucsc.edu/cgi-bin/das/hg16 > /usr/local/apache/conf/gbrowse.conf/ucsc.conf
DESCRIPTION
This script generates a rough draft configuration file suitable for browsing a remote DAS
server.
To use this script, give it the URL of a DAS server. If you point it at the DAS base URL
(without the data source name), as in "http://genome.cse.ucsc.edu/cgi-bin/das", it will
print a list of valid data sources to standard output. If you give it a complete DAS URL,
as in "http://genome.cse.ucsc.edu/cgi-bin/das/hg16", it will print a gbrowse configuration
file to standard output.
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).
Also be aware that this script creates a set of aggregators that may or may not be
correct. Consider the case of a DAS server which uses the canonical structure for a
spliced mRNA:
main method: mRNA
subparts: 5'-UTR, CDS, 3'-UTR
This conversion script will generate the following set of aggregators:
mRNA{mRNA}
5'-UTR{5'-UTR}
CDS{CDS}
3'-UTR{3'-UTR}
It will also generate a total of four tracks, one each for the mRNA and each of its parts.
This is, of course, incorrect. You will want to consolidate these into a single
aggregator:
mRNA{5'-UTR,3'-UTR,CDS/mRNA}
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