I have Emboss installed on our development serve...

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I have Emboss installed on our development server and I'm preparing a dispatch which will send it out to about 20 remote sites.

I ran the configure with the --prefix option to install to a private directory. I also collected all the data files (rebase, transfac etc.) to another directory and extracted the information from them with the relevant programs.

My intention was to simply transfer the Emboss install directory and the Data directory to all sites, using symlinks where necessary so that the directory paths corresponded.

However, when testing this I have found a couple of problems;

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.

A) 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 22 Nov 2000)

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