An embassy-domalign ebuild which solved the issue.

embassy-domalign-0.1.0-r5.ebuild (text/plain), 511 bytes, created by Juergen Rose on 2011-12-24 13:38:50 UTC

# Copyright 1999-2011 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-domalign/embassy-domalign-0.1.0-r4.ebuild,v 1.2 2010/01/01 21:51:36 fauli Exp $

EAPI="4"
SRC_URI="ftp://emboss.open-bio.org/pub/EMBOSS/DOMALIGN-0.1.0.tar.gz"

EBO_DESCRIPTION="Protein domain alignment add-on package"

inherit emboss

KEYWORDS="~amd64 ~x86 ~x86-linux ~ppc-macos"

src_prepare() {
#							epatch "${FILESDIR}/${PF}.patch"
							:
}