The following commit has been merged in the master branch:
commit d073bc0d95815308318ddead03b7f643e16167d8
Author: Charles Plessy <[email protected]>
Date:   Thu Jun 21 14:25:01 2012 +0900

    Separate architecture-dependant and independant targets in debian/rules.
    
    This makes the package buildable again on our build farm.

diff --git a/debian/rules b/debian/rules
index f44dcd9..234f1db 100755
--- a/debian/rules
+++ b/debian/rules
@@ -43,7 +43,7 @@ override_dh_clean:
        [ ! -d debian/testbackup ] || ( $(RM) --recursive test ; mv 
debian/testbackup test )
        dh_clean  --exclude=feattext.html~ config.status test-stamp 
install-stamp
 
-override_dh_auto_install:
+override_dh_auto_install-arch:
        ### Binaries and data go to a temporary dir before being moved to their 
own package ###
        $(MAKE) -C emboss install DESTDIR=$(EMBOSS-TMP)
 
@@ -70,6 +70,7 @@ override_dh_auto_install:
        # Remove this file when the relicenced file becomes part of the 
upstream tarball.
        uudecode -o 
$(CURDIR)/debian/emboss-doc/usr/share/EMBOSS/doc/manuals/EMBOSS_qg.pdf 
$(CURDIR)/debian/EMBOSS_qg_new.pdf.uu
 
+override_dh_auto_install-indep:
        $(MAKE) -C jemboss install DESTDIR=$(CURDIR)/debian/jemboss 
bindir=/usr/bin
        # install target seems to remove executable flag which is claimed by 
lintian
        find $(CURDIR)/debian/jemboss/usr/share/EMBOSS/jemboss/utils -type f 
-not -executable -name "*sh" -exec chmod a+x \{\} \;

-- 
The European Molecular Biology Open Software Suite.

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