embInitP documentation?

pmr at ebi.ac.uk pmr at ebi.ac.uk
Sat Jun 25 19:24:53 UTC 2005

Hi C...

> I'm new to EMBOSS, but I've read a good bit of the documentation on
> the website, and also have delved into the source code.


> I want to create a program that doesn't exist in the pre-existing
> EMBOSS software repository structure - that is, I want the binary to
> live in any arbitrary place I want.

Ah .... I know that problem.

> It looks as if embInitP() may be meant to handle a situation like this:

Yes, but as I noticed last month it's not perfect in the current release.

> What exactly a package name is, and how it is used to find the ACD
> file, seems to be left as an exercise to the reader.

In which case, we should give him something better to read!

The package is there so that an EMBASSY package (EMBOSS-associated
software, maybe with its own licence) can be linked to the EMBOSS
libraries and have somewhere to live.

Currently, we distribute these in embassy/[packagename]/ and the package
variable was there so the ACD file could be found if the program was not
installed. EMBOSS will look in embassy/[packagename]/emboss_acd/ to find
the ACD file.

Putting a symlink in there, and having your ACD file in an emboss_acd
directory, should help.

If you run your program with -debug on the command line, it should produce
a report to [programname].dbg showing where it is looking for your ACD

For EMBOSS 3.0.0 (due out, as tradition dictates, on 15th July) we have
extended the EMBASSY packages to include a "myemboss" package. This is
intended for anyone to develop their own programs in an EMBOSS development
environment (you need aclocal, autoconf, automake and libtool on your
system - all free and saves an enormous amount of makefile editing). With
MYEMBOSS installed you can do this:

write your application in the myemboss source directory

put your ACD file in the myemboss/emboss_acd directory

use "myemboss" in your embInitP call

define EMBOSS_MYEMBOSSACDROOT to point to where your myemboss/emboss_acd
directory is.

You can easily use some other package name if appropriate (for example,
you may be developing your own "EMBASSY" package - we have several with
only one program).

Hope that helps. If you need it urgently, I could send you a patch to the
ajacd.c source file that will look for the new package ACDROOT variable.

Otherwise, you would have to wait 3 weeks (or dive into the CVS developers
copy :-)

> Thanks, and thanks for this awesome software (I'm assuming the emboss
> authors read this list...)

You found us! I wrote embInitP :-)

Peter Rice

More information about the emboss-dev mailing list