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Phred and staden integration

jkb at mrc-lmb.cam.ac.uk jkb at mrc-lmb.cam.ac.uk
Mon May 19 03:17:13 EST 2003

In <000901c31ca6$220afc40$a03c0a0a at UALG> gnolasco at ualg.pt ("Gustavo Nolasco") writes:

> Hi,
> after compiling the phred.exe, in what directory should I put it to be
> acessible to pregap4?

If you're talking about windows (which I assume you are as you mention
the .exe extension) then the easiest place may be the same directory
containing the gap4, pregap4, etc binaries.

For all OSes (including windows), the general rule of thumb is if it's 
in your PATH and works properly from the command line then it'll work
from Pregap4.

> how can I configure the enviroment variable so that it can be find by phred
> when running from pregap  as stated in the phred documentation: "set the
> environment
>     variable 'PHRED_PARAMETER_FILE' to the full path name of the file"

Again this is an OS thing. On unix it's normally via setenv or export
commands. On windows it's probably lurking in your user config panel
somewhere, but I'm not sure where...

James Bonfield (jkb at mrc-lmb.cam.ac.uk)   Fax: (+44) 01223 213556
Medical Research Council - Laboratory of Molecular Biology,
Hills Road, Cambridge, CB2 2QH, England.
Also see Staden Package WWW site at http://www.mrc-lmb.cam.ac.uk/pubseq/

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