debian/copyright

 Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
 Upstream-Name: mmseqs2
-Source: <path_to_download>
-Comment: **** Before manually editing this file you should give ****
-           scan-copyrights
-         **** available in cme + lib-config-model-dpkg-perl     ****
-         **** package a try.  For existing copyright files try  ****
-           cme update dpkg-copyright
+Source: https://github.com/soedinglab/MMseqs2
+Files-Excluded: lib/gzstream, lib/zstd
+Comment: The system-wide option of these libraries are much preferred than that in lib/
 
 Files: *
-Copyright: 20xx-20yy <upstream>
-License: <license>
+Copyright: 2016 Söding Lab <https://mpibpc.mpg.de/soeding>
+License: GPLv3
+
+Files: lib/alp/*
+Copyright: 2008 John Spouge
+License: public_domain
+
+Files: lib/cadode/*
+Copyright: 2008 Michiaki Hamada
+License: public_domain
+
+Files: lib/kseq2/*
+Copyright: 2009 Milot Mirdita
+License: MIT
+
+Files: lib/ksw2/*
+Copyright: 2009 Attractive Chaos <attractor@live.co.uk>
+License: MIT
+
+Files: lib/omptl/*
+Copyright: 2006-2011 Fokko Beekhof <Fokko.Beekhof@unige.ch>
+License: LGPL
+
+Files: lib/tinyexpr/*
+Copyright: 2015-2018 Lewin van Winkle
+License: Zlib-Libpng License
 
 Files: debian/*
 Copyright: 2019 Shayan Doust <hello@shayandoust.me>
-License: <license>
+License: GPLv3
+
+License: GPLv3
+ This program is free software: you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+ .
+ This program is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ GNU General Public License for more details.
+ .
+ You should have received a copy of the GNU General Public License
+ along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
+License: LGPL
+ This version of the GNU Lesser General Public License incorporates
+ the terms and conditions of version 3 of the GNU General Public
+ License, supplemented by the additional permissions listed below.
+ .
+   0. Additional Definitions.
+ .
+ As used herein, "this License" refers to version 3 of the GNU Lesser
+ General Public License, and the "GNU GPL" refers to version 3 of the GNU
+ General Public License.
+ .
+ "The Library" refers to a covered work governed by this License,
+ other than an Application or a Combined Work as defined below.
+ .
+ An "Application" is any work that makes use of an interface provided
+ by the Library, but which is not otherwise based on the Library.
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+ .
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+ .
+ The object code form of an Application may incorporate material from
+ a header file that is part of the Library.  You may convey such object
+ code under terms of your choice, provided that, if the incorporated
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+    Library is used in it and that the Library and its use are
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+ received it does not specify a version number of the GNU Lesser
+ General Public License, you may choose any version of the GNU Lesser
+ General Public License ever published by the Free Software Foundation.
+ .
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+ 
+License: MIT
+ Permission is hereby granted, free of charge, to any person obtaining a
+ copy of this software and associated documentation files (the "Software"),
+ to deal in the Software without restriction, including without limitation
+ the rights to use, copy, modify, merge, publish, distribute, sublicense,
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+ OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+ MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
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+ TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE 
+ SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+
+License: public_domain
+                      PUBLIC DOMAIN NOTICE
+         National Center for Biotechnology Information
+ .
+ With the exception of certain third-party files summarized below, this
+ software is a "United States Government Work" under the terms of the
+ United States Copyright Act.  It was written as part of the authors'
+ official duties as United States Government employees and thus cannot
+ be copyrighted.  This software is freely available to the public for
+ use. The National Library of Medicine and the U.S. Government have not
+ placed any restriction on its use or reproduction.
+ .
+ Although all reasonable efforts have been taken to ensure the accuracy
+ and reliability of the software and data, the NLM and the U.S.
+ Government do not and cannot warrant the performance or results that
+ may be obtained by using this software or data. The NLM and the U.S.
+ Government disclaim all warranties, express or implied, including
+ warranties of performance, merchantability or fitness for any
+ particular purpose.
+ .
+ Please cite the author in any work or product based on this material.

debian/mmseqs2.install

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

debian/rules

@@ -9,3 +9,14 @@ export DEB_BUILD_MAINT_OPTIONS=hardening=+all
 
 %:
 	dh $@
+
+override_dh_install:
+	dh_install
+	cp src/test/*.index debian/mmseqs2/usr/lib/mmseqs2/test
+	cp src/test/dataGap debian/mmseqs2/usr/lib/mmseqs2/test
+	cp src/test/dataLinear debian/mmseqs2/usr/lib/mmseqs2/test
+
+	# We also remove unneeded files & folders like CMake
+	rm -r debian/mmseqs2/usr/lib/mmseqs2/test/CMakeFiles \
+		debian/mmseqs2/usr/lib/mmseqs2/test/*.cmake \
+		debian/mmseqs2/usr/lib/mmseqs2/test/Makefile

debian/tests/run-unit-test

@@ -8,12 +8,9 @@ if [ "${AUTOPKGTEST_TMP}" = "" ] ; then
   trap "rm -rf ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM
 fi
 
-cp -r /usr/share/doc/${pkg}/test-binaries "${AUTOPKGTEST_TMP}"
+cp -r /usr/lib/${pkg}/test "${AUTOPKGTEST_TMP}"
 
-cd "${AUTOPKGTEST_TMP}"/test-binaries
-rm -r CMakeFiles cmake_install.cmake
-gunzip *
-chmod +x *
+cd "${AUTOPKGTEST_TMP}"/test
 
 # Notice: Some tests have been excluded as they have user directories hard-coded.
 # ... Maybe a patch soon to rectify this.