problem with wildcard in emboss applications.

[ableasby at hgmp.mrc.ac.uk]

Ted,

Thanks for the message. It would probably be best posted to emboss-bug
but as its here I'd probably best clarify to all this group which are
bugs and which aren't.

1.  As far as I could see only 'contacts' and 'swissparse' weren't
shown by wossname -alpha and that is fixed in the next release. acdc
will not show up as its a developers application and doesn't have an
acd file.  Similarly runJemboss.csh is not an EMBOSS application but a
Jemboss script so again doesn't appear. Yes, prima is now made
obsolete, thankfully.
The rest of them are now programs so I expect you may have and
emboss_acd definition lying around in an emboss.default or .embossrc
file which is pointing to an old installation. 

2. In executing some of the above programs, I've encountered some of the
following errors:

a) acd: Error - must specify an application to compile
That's an informative message. The syntax should be "acdc applicationname"
which enables developers to test their acd files.

b) contacts: yes, see above, fixed for the next release
   If you install the contacts.acd file manually it will fix it.

c) extractfeat
   Can't reproduce this. Is this an old emboss_data definition you
   have somewhere?

d) primer3. That's not a bug and again is informative. Primer3 in
   EMBOSS is a wrapper to make the original program easier to use.
   You must have that program installed and in your path. The message
   is telling you where to get it.

e) swissparse: yes, see above, fixed for the next release


Cheers
Alan