Extracted data information

[Peter Rice]

"simon andrews (BITS)" wrote:
> 1) Although the Emboss programs work, I can't see any of the extracted data.
> For instance remap gives the error;
> 
>            EMBOSS An error in remap.c at line 167:
>         Cannot locate enzyme file. Run REBASEEXTRACT
> 
> This is despite the fact that I have both the Emboss install and the Data
> directories in the same place as on the development machine (which works).
> 
> 2) The other major problem is that I can no longer see my databases defined
> in emboss.default.  Again, the file exists, and is in the same place as on
> the development machine, but the box it is transferred to gives an empty
> list from showdb.
> 
> Does anyone know where Emboss stores the information about the location of
> these files?  It can't have installed anything outside the original
> installation directory (wasn't installed as root), so I'm guessing that the
> problem stems from the program resolving symlinks at some point.

It is inside the binaries ...

EMBOSS 'knows' the location of the files because it is picked up during the
configure, when you build your copy, and included in the binaries.

You can see it during compilation, especially of ajnam.c (where it is used):

-DAJAX_FIXED_ROOT=\"/full/source/path\" -DPREFIX=\"/install/prefix/path\" 

To copy binaries, you need to define environment variable(s) to override the
compile-time definitions, unless you can make the path (e.g. /usr/local) the
same for the installations at each site.

emboss.default can set environment variables too, but you need to tell EMBOSS
where to find that file.

     setenv EMBOSS_ROOT /dir/for/default/file

and then, in the emboss.default file you can set:

     SET EMBOSS_ACDROOT /install/dir/share/EMBOSS/acd

or (this overrides it) you can use another environment variable:

     SET EMBOSS_ACDROOT /install/dir/share/EMBOSS/acd




-- 
------------------------------------------------
Peter Rice, LION Bioscience Ltd, Cambridge, UK
peter.rice at uk.lionbioscience.com +44 1223 224723