IUBio GIL .. BIOSCI/Bionet News .. Biosequences .. Software .. FTP

How to get around changing .i files while indexing offline

Rodrigo Lopez rls at ebi.ac.uk
Fri Sep 24 10:00:54 EST 1999

Oh Dear! The joys of working late. If was talking about SRS6.x. I'm sorry
for the previous posting.

However, a judicious use of the environment variable that determine where
the index and icarus files are as well as building the srs section somewhere
else can do the trick with SRS5.x. Thure and I did it here a while back
during an emergency and it worked. It required quite a lot of cool (real
sweat!) from my part to go through it :-) It can get quite complicated and
this is indeed what has appeared 'transparently' in SRS6.x


Tim Cutts <timc at chiark.greenend.org.uk> wrote in message
news:xCy*c-S+n at news.chiark.greenend.org.uk...
> In article <newscache$b68iif$ptj at pointy-haired-boss>,
> Rodrigo Lopez <rls at ebi.ac.uk> wrote:
> >Hi,
> >
> >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
> >
> >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.
> No, Rodrigo, that doesn't work, as he said in his initial posting,
> because the embl.i file has to be edited for the new divisions.  This
> then means that even though you're building offline, the old inices will
> start returning the wrong entries, because the embl.i file has changed.
> You need to have an offline version o the database definition as well,
> and SRS does not have that.  There are two solutions:
> 1)  Have a parallel installation of SRS on the same machine which you
> use only for index building.  You can then copy the index files across
> once its done, update the embl.i file in your online SRS, run srssection
> and hey presto.  You do need to be very careful that the .i files are
> exactly the same on both installations.
> 2)  Use the same scheme, but with completely separate machines.
> I believe this is supposed to be fixed in SRS 6, but for commercial
> sites like mine, buying a new faster machine is more cost-effective than
> upgrading SRS.
> Tim.

More information about the Bio-srs mailing list

Send comments to us at archive@iubioarchive.bio.net