debian/mmseqs2.install

-obj-x86_64-linux-gnu/src/test usr/share/doc/mmseqs2
+obj-x86_64-linux-gnu/src/test/* usr/share/doc/mmseqs2/test-binaries
+util/bash-completion.sh usr/share/mmseqs2
+README.md usr/share/doc/mmseqs2
+examples usr/share/doc/mmseqs2

debian/patches/fix_util_installation.patch

+Description: Prevent CMake from installing util/
+ We handle this within *.installs outselves
+Author: Shayan Doust <hello@shayandoust.me>
+Last-Update: 2019-07-16
+---
+Index: mmseqs2/util/CMakeLists.txt
+===================================================================
+--- mmseqs2.orig/util/CMakeLists.txt
++++ mmseqs2/util/CMakeLists.txt
+@@ -1,4 +1,4 @@
+-install(PROGRAMS
+-        bash-completion.sh
+-        DESTINATION util
+-        )
++#install(PROGRAMS
++#        bash-completion.sh
++#        DESTINATION util
++#        )

debian/patches/series

+fix_util_installation.patch
 use_system_zstd.patch
 use_system_gzstream.patch

debian/rules

@@ -4,28 +4,8 @@
 export LC_ALL=C.UTF-8
 
 include /usr/share/dpkg/default.mk
-# this provides:
-# DEB_SOURCE: the source package name
-# DEB_VERSION: the full version of the package (epoch + upstream vers. + revision)
-# DEB_VERSION_EPOCH_UPSTREAM: the package's version without the Debian revision
-# DEB_VERSION_UPSTREAM_REVISION: the package's version without the Debian epoch
-# DEB_VERSION_UPSTREAM: the package's upstream version
-# DEB_DISTRIBUTION: the distribution(s) listed in the current entry of debian/changelog
-# SOURCE_DATE_EPOCH: the source release date as seconds since the epoch, as
-#                    specified by <https://reproducible-builds.org/specs/source-date-epoch/>
 
-# for hardening you might like to uncomment this:
-# export DEB_BUILD_MAINT_OPTIONS=hardening=+all
+export DEB_BUILD_MAINT_OPTIONS=hardening=+all
 
 %:
 	dh $@
-
-### When overriding auto_test make sure DEB_BUILD_OPTIONS will be respected
-#override_dh_auto_test:
-#ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
-#	do_stuff_for_testing
-#endif
-
-### If you **really** can not use uscan (even not with mode=git) use a debian/get-orig-script
-#get-orig-source:
-#	. debian/get-orig-source

debian/tests/run-unit-test

@@ -8,9 +8,9 @@ if [ "${AUTOPKGTEST_TMP}" = "" ] ; then
   trap "rm -rf ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM
 fi
 
-cp -r /usr/share/doc/${pkg}/test "${AUTOPKGTEST_TMP}"
+cp -r /usr/share/doc/${pkg}/test-binaries "${AUTOPKGTEST_TMP}"
 
-cd "${AUTOPKGTEST_TMP}"/test
+cd "${AUTOPKGTEST_TMP}"/test-binaries
 rm -r CMakeFiles cmake_install.cmake
 gunzip *
 chmod +x *