[EMBOSS] eprimer3 troubles

Mark Budde markbudde at gmail.com
Mon Apr 29 19:51:12 UTC 2013

I have spent too many hours trying to get eprimer3 to work on my Mac, and
am out of ideas.

I installed primer3 2.3.5 on Mac. I can run it successfulyl with command

When I try and run eprimer3 I get errors.

>From the emboss README:
primer3 from the Whitehead institute must be installed in one or two

EMBOSS application eprimer3 launches primer3_core and expects this to
be version 1.x of the program.

EMBOSS application eprimer32 launches primer32_core and expects this
to be a renamed primer3_core from version 2.x of the program.

primer3's configuration files also need to be installed. The original
application looks by default in /opt/primer3_config

$ eprimer32 -sequence=AAAA

Pick PCR primers and hybridization oligos
Died: eprimer32 uses external program 'primer32_core' which is not in the
     Part of the 'primer3' package, version 2.2.3, available from the
     Whitehead Institute. See: http://primer3.sourceforge.net/ The
     primer3_core application must be renamed to primer32_core

This suggested to me that emboss expects primer32_core to be named
primer32_core, not primer3_core as indicated above.

renaming the program to primer32_core, or typing eprimer3 into the command
line produce the same error:
$ eprimer3 -sequence=AAAA

Pick PCR primers and hybridization oligos
Error: Failed to open filename 'AAAA'
Error: Unable to read sequence 'AAAA'
Died: eprimer3 terminated: Bad value for '-sequence' and no prompt

I get this error regardless of what I put as the sequence, or even if I
input a file.

Does anyone have suggestions or potential diagnostics?

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