How to get around changing .i files while indexing offline

Rodrigo Lopez rls at ebi.ac.uk
Thu Sep 23 03:42:10 EST 1999


Hi,

The instructions for using the SRS indices at the EBI have been updated.
Peter is quite right in pointing out that they should work with the GCG
formatted EMBL but EBI cannot take any responsibility if these don't work
with your particular flavour of GCG, UNIX and most importantly, SRS. When
doing the reallocating you can follow it's progress by doing:

% getz -stat embl

and you will see the action taken is 'reallocating' rather than 'indexing'.

There is another way of achieving what you want:

1. Start a new UNIX session
2. If you know how to use $SRSOFFINX you simply use it.
OR: Check you srsdb.i for or add/edit something like this:

   $libloc:[@EMBL_DB dir:"$dataRootF/embl/"]
      indexDir:"$dataRootS/srsindex/"
      offDir:"/ebi/services/ext/data/embl/"]

offDir is the location of the new embl files you want to index.
$SRSOFFINX is the location where you will store temporarily the index files.

3. Do an srscheck embl.

4. check the content of $SRSETC/srsupdate

If everything is to your satisfaction you can start the indexing and
continue to query the old embl database in the meantime.

FYI: We will be providing indices for SRS6 in the near future.

R:)



Peter Rice <pmr at sanger.ac.uk> wrote in message
news:subaeqfxpy1.fsf at sanger.ac.uk...
> tdeboer at hgmp.mrc.ac.uk writes:
> > How do I get around changing and recompiling the .i files when I want=20
> > to both index the new database offline and still be able to retrieve=20
> > entries from the former release, without having to revert to using
two=20
> > completely seperate macines ?
>
> In general it is a problem, but for EMBL there is a solution.
>
> The SRS index files are on the FTP server at the EBI. You can simply
> FTP them over and make them live with the new embl.i. The instructions
> are a little out of date (these are the index files for the flat file
> version, but it still has a reference to 'GCG formatted files').
>
> The README says they cannot be reallocated for GCG formatted databases.
> Not sure why - the EBI files used to be for GCG databases and I could
> reallocate them for flat files with "srsbuild -r embl" given a little
> care in updating the file names in embl.i.
>
> The accession number index has a long-standing bug that misses
> secondary accession numbers. I have a fixed embl.is file at Sanger but
> you would need to be careful about rebuilding the links if you reindex
> the accession numbers. srscheck misses the change and I had to relink
> by hand.
>
>
>
> --
> ----------------------------------------------------------------------
> Peter Rice                | Informatics Division, The Sanger Centre,
> E-mail: pmr at sanger.ac.uk  | Wellcome Trust Genome Campus,
> Tel: (44) 1223 494967     | Hinxton, Cambridge, CB10 1SA, England
> Fax: (44) 1223 494919     | URL: http://www.sanger.ac.uk/Users/pmr/






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