[EMBOSS] primer3_core

Koen van der Drift kvddrift at earthlink.net
Tue Sep 14 22:39:46 UTC 2004

On Sep 14, 2004, at 12:30 PM, Paul Baumgartner wrote:

> I removed (#LIBOPTS ='-static') from the Makefile and the compiler 
> generated primer3_core, cp to /sw/bin and run eprimer3 :
> works for stdout
> but outputfiles :
> Output file [hsfau.eprimer3]:
> Error: Unable to open file 'hsfau.eprimer3' for output
> Output file [hsfau.eprimer3]: prim.txt
> Error: Unable to open file 'prim.txt' for output
> Died: eprimer3 terminated: Bad value for '-outfile' and no more retries
> what commands are used for fink (the archive primer3_1.0.0.tar I have 
> here)?
> I installed emboss 2.8.0 by fink commander, but it seems that the 
> component primer3_core is missing


Primer3 is not present in fink right now. And as you can read in the 
eprimer3 docs it needs to be installed separately, so it not missing 
from the emboss package.

The above errors indicate a privileges problem, I suspect because you 
copied primer_core into /sw/lib. Remove it from /sw/bin and put it in 
/usr/local/bin, and try again. I am not familiar with the program, so 
can you mail me (offlist) and example input file, and the CLI command 
to run it. That way I can test it too, and see if I can get to work. If 
so, I might make a fink package for it.


- Koen.

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