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EGCG w/ GCG9?

pmr at sanger.ac.uk pmr at sanger.ac.uk
Wed Mar 19 11:34:45 EST 1997


In article <5goqb7$2ju at acebo.sdi.uam.es> txomsy at cnb.uam.es (Jose R. Valverde) writes:
>   In article <browns02-1703971555510001 at mcrcr1.med.nyu.edu>,
>	   browns02 at mcrcr.med.nyu.edu (Stuart M. Brown) writes:
>   > After installation of GCG version 9, my EGCG programs no longer work.
>   > 
>	   You are out of luck to use EGCG8 with GCG 9 for the moment. But
>   it does not mean you can't use EGCG8.
>
>	   The only problem I have seen for now is a damn format change in
>   GCG9 files: mismatches or empty positions are now marked with a ~ instead
>   of a ., which breaks some EGCG programs like PRETTYBOX.

Ah, you have found one of those little differences. SeqLab has an
extra gap character (for gaps at the ends of sequences) so all code
that looked for '.' now has to do more work.

The changes to the default matrix files are tricky too. You have to
remember which GCG version you are using if you have 8.1 and 9.0 both
around.

>	   I wonder if GCG is not trying to end with EGCG so they can put
>   those programs in their package themselves... nay, too paranoic! Sure!
>   Or not?

So far, GCG have been nicely co-operative. As for putting the programs
in the GCG package themselves, the EGCG readme files do not allow it.

Of course, that doesn't mean it can't be arranged for some EGCG
programs to be included in GCG with the author's permission ...

For those cases where EGCG has a minor change to a GCG program, there
is really no problem with GCG doing something similar. Past examples
include "fetch without the sequence", and "map writing out the enzyme
file".  That last one was slipped into GCG 9.0. I believe John Devereux
himself was the author - at least that was the story I heard at the
Heidelberg User Focus meeting, but I don't know for sure until I see
the source code :-)
--
------------------------------------------------------------------------
Peter Rice                           | Informatics Division,
E-mail: pmr at sanger.ac.uk             | The Sanger Centre,
Tel: (44) 1223 494967                | Wellcome Trust Genome Campus,
Fax: (44) 1223 494919                | Hinxton, Cambridge, CB10 1SA,
URL: http://www.sanger.ac.uk/~pmr/   | England



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