[DAS] AGP-bases DAS reference server

[Lincoln Stein]

Hi Tony,

Very good!  I'll put up an announcement on the das web site.

Lincoln

On Saturday 24 May 2003 09:17 am, Tony Cox wrote:
> 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.
> The
> former so that anybody can run a server anywhere without having to be DB
> savvy, the latter for better performance. It simply goes:
>
> ./agpserver
>     --dsn <dsn>                 Name for this DAS datasource
>     --agpdir <./dirname>        Directory holding AGP file(s)
>         or
>     --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)
>     ]
>
> eg:
>
> ./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
>
> ******************************************************
> 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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>
>
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-- 
Lincoln Stein
lstein at cshl.org
Cold Spring Harbor Laboratory
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Cold Spring Harbor, NY 11724
(516) 367-8380 (voice)
(516) 367-8389 (fax)