[Request for review] smalt

[Nilesh Patra <nilesh@debian.org>]

Hi,

I was trying to make smalt cross-buildable. First off, it tries to
install test/sequenceReverseComplement_test which is generated only when
tests are run. This breaks nocheck profile so I went ahead and filed a
bug #985071 with severity:important

Now, the python3 B-D is used only for tests, so I simply annotated it
with <!nocheck> -- otherwise this causes cross-satisfiability issues. Next, it was using build compiler for compilation, so
I forced the build system in d/rules to not do that.

It cross builds in my chroot at the moment, but I'm not sure if it is optimal. Reason being
"./configure" is still hardcoded in d/rules. Since this uses a very
hacky way to pass some options, I'm not sure of a way to replace it by
dh_auto_configure.
I am also not sure if a replacement is even needed at this point. Hence,
I'd really appreciate any reviews. (I've commented test/sequenceReverseComplement_test just for the sake of running cross build successfully)

diff --git a/debian/control b/debian/control
index 11c05ad..56d8a8b 100644
--- a/debian/control
+++ b/debian/control
@@ -5,7 +5,7 @@ Section: science
 Priority: optional
 Build-Depends: debhelper-compat (= 12),
                zlib1g-dev,
-               python3,
+               python3 <!nocheck>,
                samtools,
                libbambamc-dev
 Standards-Version: 4.4.1
diff --git a/debian/rules b/debian/rules
index 2b12d2b..3394f33 100755
--- a/debian/rules
+++ b/debian/rules
@@ -1,6 +1,7 @@
 #!/usr/bin/make -f
 
 # DH_VERBOSE := 1
+-include /usr/share/dpkg/buildtools.mk
 export DEB_BUILD_MAINT_OPTIONS = hardening=+all
 
 # autoreconf is needed to make the patch to test/Makefile.am effective
@@ -12,7 +13,7 @@ override_dh_autoreconf:
 
 override_dh_auto_configure:
 	# see upstream INSTALL file
-	CONFIG_SHELL=/bin/bash /bin/bash ./configure CONFIG_SHELL=/bin/bash
+	CONFIG_SHELL=/bin/bash /bin/bash ./configure CONFIG_SHELL=/bin/bash CC="$(CC)"
 
 override_dh_auto_install:
 	# upstream install does install more files than needed
diff --git a/debian/smalt.install b/debian/smalt.install
index 6482bfe..9be53db 100644
--- a/debian/smalt.install
+++ b/debian/smalt.install
@@ -1,2 +1,2 @@
 src/smalt				usr/bin
-test/sequenceReverseComplement_test	usr/lib/smalt/test
+#test/sequenceReverseComplement_test	usr/lib/smalt/test


Cheers,
Nilesh