[EMBOSS] How to search the arhives ?

[pmr at ebi.ac.uk]

Hi Mark,

> This is probably a stupid question but I did not find a way to search
> the emboss archives. I've found them, though, but only to access the
> chunks by date. Not very efficient if you don't know the date of the
> post anymore :-(

Hmmmm ... the archives have moved a couiple of times. I keep copies of the
important mails, but I've moved twice too so they are hard to search.

While I'm figuring out how to search, I'll try answering again to see if I
give the same reply :-)

> I was actually looking for a post Peter once send about how to hardcode
> the clustalw option '-outorder=input' in emma. I think you had to set an
> environmental variable, but I don't recall which one that was.
> One thing I tried was to set 'clustalw -outorder=input' in the acd file,
> but that did not work out.

I suspect it was to define EMBOSS_CLUSTALW to be :

setenv EMBOSS_CLUSTALW "clustalw -outorder=input"

Works for me! (If you already define this variable to set the full path or
executable name for clustalw, preserve that part in the new value)

I suppose adding this as an option to emma would be reasonable. yet
another emma option - maybe this was one added since emma was originally
written (to test just how far we could stretch ACD :-) I will look for any
other new clustalw options at the same time.

regards,

Peter