[DAS] AGP-bases DAS reference server

Tony Cox avc at sanger.ac.uk
Sat May 24 15:17:29 EDT 2003

Dear all,

I have just checked in to the Bio::Das perl beta CVS repository ("Bio-Das2")
a collection of modules that creates a minimal DAS reference server from a
single AGP file (or a directory of one or more files). There is also a
sample server script in the "eg" directory.

Briefly, the server is started using something like:

cd ./eg
./agpserver --dsn ncbi31 --port 3000 --agpfile ./AGP/chr1.agp

It can then be used by a DAS client in the normal way. It is simple (no
frills!) and capable of serving assembly information, entry_points, DSN
info, features across a segment and features by ID. No other DAS commands
are supported yet.

I wrote it because our chromosome finishers needed to be able to view
assemblies as they updated their AGPs. We have a little web-based
ensembl-ish graphical viewer that displays the assembly.

The server uses either DBD::CSV (default) or Mysql for backend SQL storage.
former so that anybody can run a server anywhere without having to be DB
savvy, the latter for better performance. It simply goes:

    --dsn <dsn>                 Name for this DAS datasource
    --agpdir <./dirname>        Directory holding AGP file(s)
    --agpfile <filename>        Single AGP file
    --port <number>             DAS server port (default = 9999)
    --tmpdir <dirname>          CSV temp. directory (default = /tmp)
    [  --backend mysql          Use a mysql backend (default = csv)
        --dbhost <host>         Mysql server hostname
        --dbname <name>         Mysql database name
        --username <user>       Mysql username (needs write access)
        --password <password>   Mysql password
        --dbport <port>         Mysql server port (default =3306)


./agpserver --dsn ncbi31 --agpdir ./TEST --port 3000
Loading AGP file: chrX.agp
Loading AGP file: chrY.agp
Please contact me at this URL: http://hostname:3000/das/dsn/{command}

Please feel free to try it out and pass on comments, etc.


Tony Cox                        Email:avc at sanger.ac.uk
Sanger Institute                WWW:www.sanger.ac.uk
Wellcome Trust Genome Campus    Webmaster
Hinxton                         Tel: +44 1223 834244
Cambs. CB10 1SA                 Fax: +44 1223 494919

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