debian/changelog

 hhsuite (3.1.0-1) UNRELEASED; urgency=medium
 
+  * Team upload.
   * New upstream release.
     "Added hhsearch_omp, hhsearch_mpi, hhalign_omp and haling_mpi binaries
      Removed non-GPLv3 compatible code
      ffindex_apply_mpi will not crash anymore on systems with low amount of
        virtual memory"
+  * The non-GPLv3 code was in src/hhprefilter.cpp; now gone
+  * Mark hhsuite-data as Multi-Arch: foreign
+  * Drop hhsuite-doc: documentation moved by upstream to
+    https://github.com/soedinglab/hh-suite/wiki
+  * Removed '-march=native'
 
  -- Michael R. Crusoe <michael.crusoe@gmail.com>  Thu, 28 Feb 2019 08:16:48 -0600
 

debian/control

@@ -8,8 +8,6 @@ Priority: optional
 Build-Depends: debhelper (>= 11~),
                libffindex0-dev (>= 0.9.9.8),
                cmake,
-               texlive-latex-base,
-               texlive-latex-recommended,
                imagemagick,
                help2man
 Standards-Version: 4.3.0
@@ -21,6 +19,7 @@ Package: hhsuite
 Architecture: amd64
 Depends: ${shlibs:Depends},
          ${misc:Depends},
+         ${perl:Depends},
          ffindex (>= 0.9.9.8),
          hhsuite-data (= ${source:Version}),
          python
@@ -46,6 +45,7 @@ Description: sensitive protein sequence searching based on HMM-HMM alignment
 
 Package: hhsuite-data
 Architecture: all
+Multi-Arch: foreign
 Depends: ${misc:Depends}
 Description: sensitive protein sequence searching based on HMM-HMM alignment (data)
  HH-suite is an open-source software package for sensitive protein sequence

debian/copyright

@@ -3,12 +3,14 @@ Upstream-Name: hhsuite
 Upstream-Contact: Andreas Hauser <hauser@genzentrum.lmu.de>
                   Johannes Soeding <soeding@genzentrum.lmu.de>
 Source: ftp://toolkit.lmb.uni-muenchen.de/HH-suite/releases/hhsuite-([0-9.]+)\.tar\.gz
+File-Excluded: scripts/hhpred/
+               lib/ffindex/
 
 Files: *
 Copyright: 2006, 2012 Johannes Soeding
            2012 Michael Remmert
            2012 Andreas Hauser <hauser@genzentrum.lmu.de>
-           2006, 2009, 2012 Andreas Biegert
+           2006, 2009-2012 Andreas Biegert
            2009-2012 Christof Angermueller
 License: GPL-3.0+
 
@@ -16,13 +18,25 @@ Files: src/cs/getopt_pp.h src/cs/getopt_pp.cc
 Copyright: 2007, 2008  Daniel Gutson, FuDePAN
 License: GPL-3.0+
 
+Files: src/hhprefilter.h
+Copyright: 2012-2015, Boston College.
+License: Expat
+
 Files: debian/*
 Copyright: 2012 Laszlo Kajan <lkajan@rostlab.org>
+           2019 Michael R. Crusoe <michael.crusoe@gmail.com>
 License: GPL-3.0+
 
+Files: cmake/xxdi.pl
+Copyright: 2013, Linux Foundation
+ 2013, Greg Kroah-Hartman <gregkh@linuxfoundation.org>
+License: GPL-2
+
 Files: cmake/FindASan.cmake cmake/FindMSan.cmake cmake/FindTSan.cmake cmake/FindUBSan.cmake
 Copyright: 2013 Matthew Arsenault
-License: MIT
+License: Expat
+
+License: Expat
  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
@@ -41,15 +55,6 @@ License: MIT
  OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
  THE SOFTWARE.
 
-Files: doc/UseLATEX.cmake
-Copyright: 2004 Sandia Corporation
-License: Sandia
- Under the terms of Contract DE-AC04-94AL85000, there is a non-exclusive
- license for use of this work by or on behalf of the
- U.S. Government. Redistribution and use in source and binary forms, with
- or without modification, are permitted provided that this Notice and any
- statement of authorship are reproduced on all copies.
-
 License: GPL-3.0+
  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

debian/upstream/metadata

@@ -26,6 +26,18 @@ Reference:
    URL: http://bioinformatics.oxfordjournals.org/content/21/7/951.abstract
    eprint: "http://bioinformatics.oxfordjournals.org/content/\
     21/7/951.full.pdf+html"
+ - Author: >
+     Martin Steinegger and Markus Meier and Milot Mirdita and Harald Voehringer
+    and Stephan J. Haunsberger and Johannes Söding
+   Title: >
+     HH-suite3 for fast remote homology detection and deep protein
+     annotation
+   Journal: bioRxiv
+   publisher: Cold Spring Harbor Laboratory
+   Year: 2019
+   DOI: 10.1101/560029
+   URL: https://www.biorxiv.org/content/early/2019/02/25/560029
+   eprint: https://www.biorxiv.org/content/early/2019/02/25/560029.full.pdf
 Registry:
  - Name: OMICtools
    Entry: OMICS_28407