GCG 8.1 clash with SRS

Thure Etzold etzold
Wed Aug 16 10:21:04 EST 1995

>Hi Thure. You are going to have to solve the same problem when you install
>GCG 8.1. How do you plan to handle the multiple versions of srsbuild
>and the programs?

you could just keep two srs trees. The only things that can be 
shared between the two are the indices and the flatfiles

>>the gcg version supports only sequence databases ...prosite is not provided
>That alone makes it desirable to run with the real SRS indices.

the gcg indices ARE real srs indices!

>>>Also, the "LookUp" program (actually a front-end to SRS) has a list of
>>>libraries in the program manual example. What happens to this at sites
>>>with other databases, or without some of the listed databases? (for example,
>>>we do not have genbank or "gb_tags")
>What does LookUp do that SRS can't? Did they change the output format

lookup provides almost the same functionality as getz.

>How closely coupled are GCG and SRS? Can Lookup simply use standard
>SRS indices (with SRS prepared), or does it need source editing and a
>rebuild of LookUp?

lookup comes with a full set of SRS programs for building indices ...the
main difference is the restriction to sequence databanks in GCG formats
so that that SRS will always be happy with lookup's indices but not
the other way round

>So GCG has to run from a separate index directory if a site has any
>database defined in SRS as a "Sequence" database but not in GCG format,
>NRSUB at the EBI for example (at the Sanger Centre it just happens to have
>moved to "Genome" along with other databases). Or have I misunderstood?


>Presumably then GCG's LookUp is picking up "/group=@SEQUENCE_LIBS"
>*only* and is not checking the sequence format? Or is it able to skip
>databases in EMBL flatfile format (for example)?

no those would have to be removed from the group
>This seems to imply needing either a completely separate set of indices
>for GCG, or a lot of playing around with symbolic links (on Unix).

as said in the previous posting you can in you SRS installation specify
the index directory from lookup for those databanks that are supported.


Thure Etzold                                   | EMBL
E-mail: etzold at embl-heidelberg.de              | Postfach 10.2209
Tel: (49) 6221 387529                          | 69012 Heidelberg
Fax: (49) 6221 387517                          | Germany

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