problem with wildcard in emboss applications.

[Ted Chiang]

Alan,

Thanks for the patch.  We've installed and tested the 'wildcard' function
for seqret and a number of other emboss applications and it seems to work
well.

We've conducted some further tests of emboss2.1.0 after our recent
installation, and I noticed some bugs that might be of interest.

1. I noticed that emboss2.1.0 has a few new applications not present in
earlier version (1.13), however 'wossname' does not seem to be able to
pick them up. ie.

	%wossname -alphabet

fails to list the following programs which are in the
/blah/emboss2.1.0/bin directory:

> acdc
> contacts
> extractfeat
> infoalign
> listor
> mwfilter
  (prima (1.13)--> primer3(2.1) -->this is a program replacement, I guess)
> runJemboss.csh
> seqretallfeat
> swissparse
> trimest


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


======================================================================
$/tools/emboss2.1.0/bin/acdc

   EMBOSS An error in acdc.c at line 36:
Error - must specify an application to compile
=======================================================================
$/tools/emboss2.1.0/bin/contacts

   EMBOSS An error in ajacd.c at line 1207:
acdfile '/tools/emboss2.1.0/share/EMBOSS/acd/contacts.acd' not opened
=========+============================================================
$/tools/emboss2.1.0/bin/extractfeat
Warning: Efeatures.embl: tag note (feature 3'clip) not in Etags file
Warning: Efeatures.embl: tag partial (feature 3'clip) not in Etags file
Warning: Efeatures.embl: tag standard_name (feature 3'clip) not in Etags
file
======================================================================
$/tools/emboss2.1.0/bin/primer3
Picks PCR primers and hybridization oligos
Input sequence(s): AF104304
Output file [af104304.primer3]: 

   EMBOSS An error in primer3.c at line 316:
The program 'primer3_core' must be on the path.
It is part of the 'primer3' package,
available from the Whitehead Institute.
See: http://www-genome.wi.mit.edu/
Broken pipe
======================================================================
$/tools/emboss2.1.0/bin/swissparse   

   EMBOSS An error in ajacd.c at line 1207:
acdfile '/tools/emboss2.1.0/share/EMBOSS/acd/swissparse.acd' not opened
======================================================================



---->If you could please help us in solving some of these problems, we
would really appreciate it.  I presume some of them may be due to
installation nuances on our side...

thanks.

-Ted


=====================================
Ted Chiang
Bioinformatics Supercomputing Centre
Hospital for Sick Children, Toronto
ext. 7028
tchiang at bioinfo.sickkids.on.ca



On Mon, 7 Jan 2002 ableasby at hgmp.mrc.ac.uk wrote:

> Ted,
> 
> Ah, its a GenBank thing. Specifically the horrible header information
> at the start of each distribution file. I've put a replacement
> ajseqread.c file in:
> 
>   ftp://ftp.uk.embnet.org/pub/EMBOSS/patchfiles/ajseqread.c
> 
> Put that in the ajax directory and "make install" again and you
> should be OK. Being good Europeans we can tend to forget about some
> genbank nuances. Apologies.
> 
> Alan
> 
> PS: This probably means a new distribution soon incorporating the
>     patch and the srs patch.
> 
>