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}