AGP-bases DAS reference server available

Posted on May 23, 2003 by Chris Dagdigian

Tony writes: 

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

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