Problems with EMBOSS and Staden package...

Peter Rice nospam at theebi.ac.uk
Wed Mar 10 04:51:13 EST 2004

R. Fisher wrote:

> I'm running into errors trying to access the EMBOSS package from spin.
>  I've run the utility to create the links under the Emboss menu in
> spin, but several commands fail due to unknown qualifier errors. 
> PEPNET runs OK, for example, but if I try to run emma on the same
> sequence(s), I get an error stating "Error produced by emboss:  died: 
> unknown qualifier -inseqs".  I've checked my installation of EMBOSS,
> and the programs run fine on their own.  I suspect that the scripts to
> create the Staden-EMBOSS link may be out of date...all the returned
> errors seem to contain invalid parameters....

The current spin is set up for an older version of EMBOSS.

When the Staden package disappeared I was working on updating this - but 
as I was updating the EMBOSS graphics to work better with SPIN it did 
not need SPIN changes at the time.

Since that time, EMBOSS command line qualifiers have been "standardised" 
- which means many have changed their names.

I have now volunteered to update the files for the next EMBOSS release - 
they will probably be distributed with EMBOSS, but also committed to 
SourceForge so there will be files in a future SPIN release too.

I will announce the availability on this list. Assume some time in April.


Peter Rice

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