seqret & getz

[Bela Tiwari]

>
>I wanted to use SRS for the seqret command but seqret couldn't find getz.
>
>Putting a symbolic link to getz in /emboss/bin worked but it is not
>the nicest thing. Does anyone have a good solution for that problem (eg
>environment variables)?
>


Hello,

Are you sourcing the prep_srs script, which comes with the srs release, in
your environment to set all the SRS variables before running seqret? In
addition to setting variables, this  script should add the relevant SRS
directories to your PATH. Maybe rely on getz being found because it is in
a directory on your PATH, insteady using an alias?

Note that by default, prep_srs puts the SRS directories at the start of
the  PATH, so  if you don't want them there, you might want to edit the
script.


I hope this helps.



Bela




.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.
Dr. Bela Tiwari
Acting Manager

OU Bioinformatics Centre
SWD School of Pathology
South Parks Road
Oxford  OX1 3RE
01865 (2)75507

http://www.molbiol.ox.ac.uk
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