Q&A: SRS5.1 and applications

Tim Dudgeon dudgeon at britbio.co.uk
Wed Jan 14 12:12:33 EST 1998


In the light of previous postings to this newsgroup here is another minor
fix to SRS5.1 that people might find useful.

I've encountered a problem with configuring applications in SRS5.1
whereby you do not get all the applications that are configured in
DNASEQ_DATA:$datatype.applications or PROTSEQ_DATA:$datatype.applications
(defined in srsgen.i).

For instance, if you include BLAST_APP and CLUSTALW_APP as your only
applications you only get BLAST accessible in SRSWWW when you have the
results of a protein database query. The reason is that PROTSEQ_DATA
contains the following:

PROTSEQ_DATA:$DataType:[ProteinSequence
  applications:{@?BLAST_APP @?SW_APP @?FASTA_APP @?CLUSTALW_APP
    @?PPSEARCH_APP
  }
]

and as SW_APP is not defined ($libloc:[@SW_DB dir:"" indexDir:""] is
commented out in srsdb.i) you only get BLAST, as any misssing application
appears to prevent SRS 'reading on' to get the full list. To solve the
problem remove any unused applications, i.e.

PROTSEQ_DATA:$DataType:[ProteinSequence
  applications:{@?BLAST_APP @?CLUSTALW_APP
  }
]


Hope this helps.

Tim

--
Dr. Tim Dudgeon				Phone: 01865 748747
British Biotech Pharmaceuticals Plc.	FAX:   01865 717598
Watlington Road, Oxford, OX4 5LY, UK	email: dudgeon at britbio.co.uk

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