.travis.yml

@@ -6,12 +6,9 @@ addons:
   apt:
     packages:
     - cmake
-language: cpp
 
 before_install:
 - git submodule update --init --recursive
-- test -n $CC  && unset CC
-- test -n $CXX && unset CXX
 
 script:
 - mkdir build
@@ -30,7 +27,7 @@ matrix:
           packages:
             - g++-4.9
             - mpi-default-dev
-      env: COMPILER=g++-4.9
+      env: CXX=g++-4.9
     - compiler: gcc
       addons:
         apt:
@@ -39,7 +36,7 @@ matrix:
           packages:
             - g++-5
             - mpi-default-dev
-      env: COMPILER=g++-5
+      env: CXX=g++-5
     - compiler: gcc
       addons:
         apt:
@@ -48,7 +45,16 @@ matrix:
           packages:
             - g++-6
             - mpi-default-dev
-      env: COMPILER=g++-6
+      env: CXX=g++-6
+    - compiler: gcc
+      addons:
+        apt:
+          sources:
+            - ubuntu-toolchain-r-test
+          packages:
+            - g++-7
+            - mpi-default-dev
+      env: CXX=g++-7
     - compiler: clang
       addons:
         apt:
@@ -58,7 +64,7 @@ matrix:
           packages:
             - clang-3.6
             - mpi-default-dev
-      env: COMPILER=clang++-3.6
+      env: CXX=clang++-3.6
     - compiler: clang
       addons:
         apt:
@@ -68,7 +74,7 @@ matrix:
           packages:
             - clang-3.7
             - mpi-default-dev
-      env: COMPILER=clang++-3.7
+      env: CXX=clang++-3.7
     - compiler: clang
       addons:
         apt:
@@ -78,7 +84,24 @@ matrix:
           packages:
             - clang-3.8
             - mpi-default-dev
-      env: COMPILER=clang++-3.8
-
-
-
+      env: CXX=clang++-3.8
+    - compiler: clang
+      addons:
+        apt:
+          sources:
+            - ubuntu-toolchain-r-test
+            - llvm-toolchain-trusty-3.9
+          packages:
+            - clang-3.9
+            - mpi-default-dev
+      env: CXX=clang++-3.9
+    - compiler: clang
+      addons:
+        apt:
+          sources:
+            - ubuntu-toolchain-r-test
+            - llvm-toolchain-trusty-4.0
+          packages:
+            - clang-4.0
+            - mpi-default-dev
+      env: CXX=clang++-4.0

CMakeLists.txt

@@ -19,6 +19,25 @@ elseif ("${CMAKE_CXX_COMPILER_ID}" STREQUAL "Intel")
   set(CMAKE_COMPILER_IS_ICC 1)
 endif()
 
+
+message("-- Processor is ${CMAKE_SYSTEM_PROCESSOR}")
+
+if(CMAKE_SYSTEM_PROCESSOR MATCHES "amd64.*|x86_64.*|AMD64.*")
+  set(X86_64 1)
+elseif(CMAKE_SYSTEM_PROCESSOR MATCHES "i686.*|i386.*|x86.*|amd64.*|AMD64.*")
+  set(X86 1)
+elseif(CMAKE_SYSTEM_PROCESSOR MATCHES "^(arm.*|ARM.*)")
+  set(ARM 1)
+elseif(CMAKE_SYSTEM_PROCESSOR MATCHES "^(aarch64.*|AARCH64.*)")
+  set(AARCH64 1)
+elseif(CMAKE_SYSTEM_PROCESSOR MATCHES "PPC64*|ppc64*|powerpc64*")
+  set(PPC64 1)
+elseif(CMAKE_SYSTEM_PROCESSOR MATCHES "PPC*|ppc*|powerpc*")
+  set(PPC 1)
+endif()
+
+
+
 set (HHSUITE_VERSION_MAJOR 3)
 set (HHSUITE_VERSION_MINOR 0)
 set (HHSUITE_VERSION_PATCH 0)
@@ -39,12 +58,12 @@ INSTALL(FILES
 include_directories(src)
 include_directories(lib/ffindex/src)
 
+add_subdirectory(lib/ffindex)
 add_subdirectory(src)
 add_subdirectory(data)
 add_subdirectory(scripts)
 add_subdirectory(test)
 #add_subdirectory(doc)
-add_subdirectory(lib/ffindex)
 
 
 SET (CPACK_GENERATOR "DEB;TGZ;ZIP;RPM")

README

@@ -16,6 +16,7 @@ For full documentation see the user guide in hhsuite-userguide.pdf
 To compile from source, you will need:
  * a recent C/C++ compiler
  * CMake 2.8.12 or later
+ * pdbx python library for example from https://github.com/soedinglab/pdbx
 
 *****************************************************************************
 2. Installation

README.md

@@ -10,12 +10,20 @@
 
 The HH-suite is an open-source software package for sensitive protein sequence searching based on the pairwise alignment of hidden Markov models (HMMs).
 
+## WARNING ##
+We had to rename our repository for ffindex, so it might be necessary to run the following commands to update the submodule in your clone:
+
+	git pull
+	git submodule deinit
+	git submodule init
+
 
 ## Requirements
 
 To compile from source, you will need:
  * a recent C/C++ compiler
  * [CMake](http://cmake.org/) 2.8.12 or later
+ * install [pdbx python library](https://github.com/soedinglab/pdbx)
 
 
 ## Installation

debian/README.source

 hhsuite for Debian
 ------------------
 
+The ffindex package features an MQP library to work with OpenMPI.
+But only when OpenMPI is found to be installed.
+The ffindex packages builds with OpenMPI but does not export that
+library. To overcome this hurdle please deinstall the OpenMPI packages
+for building this package.
+
 Patches
 .......
 Patches are documented in their headers.

debian/changelog

+hhsuite (3.0~beta3+dfsg-1) unstable; urgency=medium
+
+  * Team upload.
+
+  * New upstream version.
+  * d/control
+    - compliance with policy 4.2
+    - adapted Vcs URLs to salsa.d.o
+  * Caveat: Does not compile with openmpi libraries discovered.
+    See README.source.
+
+ -- Steffen Moeller <moeller@debian.org>  Thu, 02 Aug 2018 17:42:28 +0200
+
 hhsuite (3.0~beta2+dfsg-4) UNRELEASED; urgency=medium
 
   * debian/upstream/metadata:

debian/control

@@ -6,15 +6,15 @@ Uploaders: Laszlo Kajan <lkajan@debian.org>,
 Section: science
 Priority: optional
 Build-Depends: debhelper (>= 10),
-               libffindex0-dev (>= 0.9.9.6-2),
+               libffindex0-dev (>= 0.9.9.7+soedinglab),
                cmake,
                texlive-latex-base,
                texlive-latex-recommended,
                imagemagick,
                help2man
-Standards-Version: 3.9.8
-Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/hhsuite.git
-Vcs-Git: https://anonscm.debian.org/git/debian-med/hhsuite.git
+Standards-Version: 4.2.0
+Vcs-Browser: https://salsa.debian.org/med-team/hhsuite.git
+Vcs-Git: https://salsa.debian.org/med-team/hhsuite.git
 Homepage: http://toolkit.genzentrum.lmu.de/sections/search
 
 Package: hhsuite

debian/patches/build-own-manual-PDF.patch

 Description: build own manual PDF
  The LaTeX source is now included, so we can build the manual directly.
 Author: Sascha Steinbiss <satta@debian.org>
---- a/CMakeLists.txt
-+++ b/CMakeLists.txt
-@@ -29,7 +29,6 @@
+Index: hhsuite/CMakeLists.txt
+===================================================================
+--- hhsuite.orig/CMakeLists.txt
++++ hhsuite/CMakeLists.txt
+@@ -48,7 +48,6 @@ set(CMAKE_LIBRARY_OUTPUT_DIRECTORY ${CMA
  set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/bin)
  
  INSTALL(FILES
@@ -11,12 +13,12 @@ Author: Sascha Steinbiss <satta@debian.org>
    LICENSE
    README
    PERMISSIONS OWNER_READ OWNER_WRITE GROUP_READ WORLD_READ
-@@ -43,7 +42,7 @@
+@@ -63,7 +62,7 @@ add_subdirectory(src)
  add_subdirectory(data)
  add_subdirectory(scripts)
  add_subdirectory(test)
 -#add_subdirectory(doc)
 +add_subdirectory(doc)
- #add_subdirectory(lib/ffindex)
  
  
+ SET (CPACK_GENERATOR "DEB;TGZ;ZIP;RPM")

debian/patches/disable-AVX-SSE.patch

 Description: do not use AVX to build binaries 
 Author: Sascha Steinbiss <satta@debian.org>
---- a/src/CMakeLists.txt
-+++ b/src/CMakeLists.txt
-@@ -9,22 +9,22 @@
- endif()
+Index: hhsuite/src/CMakeLists.txt
+===================================================================
+--- hhsuite.orig/src/CMakeLists.txt
++++ hhsuite/src/CMakeLists.txt
+@@ -12,22 +12,22 @@ endif()
+ if(X86 OR X86_64)
  
  #SSE
 -if(${HAVE_AVX2})
@@ -32,10 +34,12 @@ Author: Sascha Steinbiss <satta@debian.org>
 +    endif(${HAVE_SSSE3_EXTENSIONS})
  endif()
  
- 
---- a/cmake/CheckSSEFeatures.cmake
-+++ b/cmake/CheckSSEFeatures.cmake
-@@ -209,23 +209,23 @@
+ else() #
+Index: hhsuite/cmake/CheckSSEFeatures.cmake
+===================================================================
+--- hhsuite.orig/cmake/CheckSSEFeatures.cmake
++++ hhsuite/cmake/CheckSSEFeatures.cmake
+@@ -209,23 +209,23 @@ macro(PCL_CHECK_FOR_SSE)
      set(CMAKE_REQUIRED_FLAGS)
  
      if(CMAKE_COMPILER_IS_GNUCC OR CMAKE_COMPILER_IS_GNUCXX OR CMAKE_COMPILER_IS_CLANG)

debian/patches/disable-ffindex-build.patch

 Description: do not try to build ffindex
 Author: Sascha Steinbiss <satta@debian.org>
---- a/CMakeLists.txt
-+++ b/CMakeLists.txt
-@@ -37,14 +37,14 @@
+Index: hhsuite/CMakeLists.txt
+===================================================================
+--- hhsuite.orig/CMakeLists.txt
++++ hhsuite/CMakeLists.txt
+@@ -56,9 +56,9 @@ INSTALL(FILES
  )
  
  include_directories(src)
 -include_directories(lib/ffindex/src)
 +#include_directories(lib/ffindex/src)
  
+-add_subdirectory(lib/ffindex)
++#add_subdirectory(lib/ffindex)
  add_subdirectory(src)
  add_subdirectory(data)
  add_subdirectory(scripts)
- add_subdirectory(test)
- #add_subdirectory(doc)
--add_subdirectory(lib/ffindex)
-+#add_subdirectory(lib/ffindex)
- 
- 
- SET (CPACK_GENERATOR "DEB;TGZ;ZIP;RPM")

debian/patches/fix-namespace.patch

-Description: add stdlib.h to header
- This fixes compilation with Debian's ffindex headers.
-Author: Sascha Steinbiss <satta@debian.org>
---- a/src/hhdatabase.h
-+++ b/src/hhdatabase.h
-@@ -15,6 +15,7 @@
- class FFindexDatabase;
- 
- extern "C" {
-+#include <stdlib.h>
- #include <ffindex.h>
- }
- 

debian/patches/fix_type_mismatch_in_printf.patch

-Author: Daniel Shahaf  <danielsh@apache.org>
-Last-Update: Wed, Jan 18, 2017 at 15:22:26 +0000
-Bug-Debian: https://bugs.debian.org/851764
-Description: hhblits.cpp uses the %i printf(3) conversion to format a 'double' value
- Thats undefined and prints garbage - the patch inserts the correct format
- (and also fixes the doc about the correct default value
-
---- a/doc/hhsuite-userguide.tex
-+++ b/doc/hhsuite-userguide.tex
-@@ -1466,7 +1466,7 @@
-  -maxfilt                  max number of hits allowed to pass 2nd prefilter (default=20000)   
-  -min_prefilter_hits       min number of hits to pass prefilter (default=100)               
-  -prepre_smax_thresh       min score threshold of ungapped prefilter (default=10)               
-- -pre_evalue_thresh        max E-value threshold of Smith-Waterman prefilter score (default=0)
-+ -pre_evalue_thresh        max E-value threshold of Smith-Waterman prefilter score (default=1000.0)
-  -pre_bitfactor            prefilter scores are in units of 1 bit / pre_bitfactor (default=4)
-  -pre_gap_open             gap open penalty in prefilter Smith-Waterman alignment (default=20)
-  -pre_gap_extend           gap extend penalty in prefilter Smith-Waterman alignment (default=4)
---- a/src/hhblits.cpp
-+++ b/src/hhblits.cpp
-@@ -330,7 +330,7 @@
-     printf(" -maxfilt                  max number of hits allowed to pass 2nd prefilter (default=%i)   \n", par.maxnumdb);
-     printf(" -min_prefilter_hits       min number of hits to pass prefilter (default=%i)               \n", par.min_prefilter_hits);
-     printf(" -prepre_smax_thresh       min score threshold of ungapped prefilter (default=%i)               \n", par.preprefilter_smax_thresh);
--    printf(" -pre_evalue_thresh        max E-value threshold of Smith-Waterman prefilter score (default=%i)\n", par.prefilter_evalue_thresh);
-+    printf(" -pre_evalue_thresh        max E-value threshold of Smith-Waterman prefilter score (default=%.1f)\n", par.prefilter_evalue_thresh);
-     printf(" -pre_bitfactor            prefilter scores are in units of 1 bit / pre_bitfactor (default=%i)\n", par.prefilter_bit_factor);
-     printf(" -pre_gap_open             gap open penalty in prefilter Smith-Waterman alignment (default=%i)\n", par.prefilter_gap_open);
-     printf(" -pre_gap_extend           gap extend penalty in prefilter Smith-Waterman alignment (default=%i)\n", par.prefilter_gap_extend);
-

debian/patches/perl_interpreter

 Description: patch Perl interpreter as required by Polich 5.1
  Perl Script Magic - http://www.debian.org/doc/packaging-manuals/perl-policy/ch-programs.html#s-hash_bang
 Author: Laszlo Kajan <lkajan@rostlab.org>
---- a/scripts/addss.pl
-+++ b/scripts/addss.pl
-@@ -1,4 +1,4 @@
--#!/usr/bin/env perl
-+#!/usr/bin/perl
- #
- # addss.pl
- # Add PSIPRED secondary structure prediction (and DSSP annotation) to an MSA or HMMER file.
---- a/scripts/create_profile_from_hhm.pl
-+++ b/scripts/create_profile_from_hhm.pl
+Index: hhsuite/scripts/create_profile_from_hhm.pl
+===================================================================
+--- hhsuite.orig/scripts/create_profile_from_hhm.pl
++++ hhsuite/scripts/create_profile_from_hhm.pl
 @@ -1,4 +1,4 @@
 -#!/usr/bin/env perl
 +#!/usr/bin/perl
  # 
  # create_profile_from_hhm.pl 
  # Create a profile (.prf) from a given HHM file
---- a/scripts/create_profile_from_hmmer.pl
-+++ b/scripts/create_profile_from_hmmer.pl
-@@ -1,4 +1,4 @@
--#!/usr/bin/env perl
-+#!/usr/bin/perl
- #
- # create_profile_from_hmmer.pl 
- # Create a profile (.prf) from a given HMMER/HMMER3 file
---- a/scripts/hhmakemodel.pl
-+++ b/scripts/hhmakemodel.pl
-@@ -1,4 +1,4 @@
--#! /usr/bin/env perl
-+#!/usr/bin/perl
- #
- # hhmakemodel.pl 
- # Generate a model from an output alignment of hhsearch. 
---- a/scripts/multithread.pl
-+++ b/scripts/multithread.pl
-@@ -1,4 +1,4 @@
--#!/usr/bin/env perl
-+#!/usr/bin/perl
- #
- # multithread.pl: 
- # Run a command with different file names as arguments on multiple threads in parallel 
---- a/scripts/pdb2fasta.pl
-+++ b/scripts/pdb2fasta.pl
-@@ -1,4 +1,4 @@
--#! /usr/bin/env perl
-+#!/usr/bin/perl
- #
- # pdb2fasta.pl - generate FASTA nonredundant sequence file from SEQRES records of globbed pdb files.
- 
---- a/scripts/pdbfilter.pl
-+++ b/scripts/pdbfilter.pl
-@@ -1,4 +1,4 @@
--#! /usr/bin/env perl
-+#!/usr/bin/perl
- # pdbfilter.pl - Read pdb or SCOP sequences from infile and write representative set of sequences to outfile
- 
- #
---- a/scripts/reformat.pl
-+++ b/scripts/reformat.pl
-@@ -1,4 +1,4 @@
--#! /usr/bin/env perl
-+#!/usr/bin/perl
- 
- # reformat.pl 
- # Reformat a multiple alignment file
---- a/scripts/renumberpdb.pl
-+++ b/scripts/renumberpdb.pl
-@@ -1,4 +1,4 @@
--#!/usr/bin/env perl
-+#!/usr/bin/perl
- # renumberpdb.pl - generate a PDB file with renumbered indices that match residue indices in input sequence
- # Usage:   renumberpdb.pl [options] infile [outfile] 
- # Example: renumberpdb.pl d1hz4a_.a3m d1hz4a_.pdb
---- a/scripts/splitfasta.pl
-+++ b/scripts/splitfasta.pl
-@@ -1,4 +1,4 @@
--#! /usr/bin/env perl
-+#!/usr/bin/perl
- # splitfasta.pl 
- # Split a file with multiple, FASTA formatted sequences into many single-sequence FASTA files
- #

debian/patches/series

 perlscript_uselib
 perl_interpreter
 add_Makefile_in_data.patch
-spelling.patch
 disable-ffindex-build.patch
-fix-namespace.patch
 drop-fmemopen.h.patch
 build-own-manual-PDF.patch
 set-default-HHLIB-dir.patch
 disable-AVX-SSE.patch
-fix_type_mismatch_in_printf.patch

debian/patches/set-default-HHLIB-dir.patch

@@ -2,13 +2,15 @@ Description: set default HHLIB
  hhsuite needs to access some static data in /usr/share. This patch sets the
  correct search path if it is not given by the user in HHLIB environment var.
 Author: Sascha Steinbiss <satta@debian.org>
---- a/src/hhdecl.cpp
-+++ b/src/hhdecl.cpp
-@@ -13,7 +13,7 @@
+Index: hhsuite/src/hhdecl.cpp
+===================================================================
+--- hhsuite.orig/src/hhdecl.cpp
++++ hhsuite/src/hhdecl.cpp
+@@ -13,7 +13,7 @@ void Parameters::SetDefaultPaths() {
  	if (getenv("HHLIB"))
  		strcpy(hhlib, getenv("HHLIB"));
  	else
--		strcpy(hhlib, "/usr/lib");
+-		strcpy(hhlib, "/usr/lib/hhsuite");
 +		strcpy(hhlib, "/usr/share/hhsuite");
  
  	strcat(strcpy(hhdata, hhlib), "/data");

debian/patches/spelling.patch

-Description: Fix spelling
-Author: Andreas Tille <tille@debian.org>
-Last-Update: Sat, 13 Aug 2016 07:27:28 +0200
-
---- a/src/cs/context_profile-inl.h
-+++ b/src/cs/context_profile-inl.h
-@@ -106,7 +106,7 @@
-     assert(len & 1);
-     if (nalph != Abc::kSize)
-         throw Exception("Alphabet size of serialized context profile should be %d"
--                        "but is acutally %d!", Abc::kSize, nalph);
-+                        "but is actually %d!", Abc::kSize, nalph);
- 
-     // If everything went fine we can resize our data memmbers
-     probs.Resize(len);
---- a/doc/hhsuite-userguide.tex
-+++ b/doc/hhsuite-userguide.tex
-@@ -1575,7 +1575,7 @@
-  -neffmax ]1,20] skip further search iterations when diversity Neff of query MSA 
-                 becomes larger than neffmax (default=10.0)
-  -cpu <int>     number of CPUs to use (for shared memory SMPs) (default=2)      
-- -scores <file> write scores for all pairwise comparisions to file               
-+ -scores <file> write scores for all pairwise comparisons to file               
-  -atab   <file> write all alignments in tabular layout to file                   
-  -maxres <int>  max number of HMM columns (def=20001)             
-  -maxmem [1,inf[ limit memory for realignment (in GB) (def=3.0)          
-@@ -1706,7 +1706,7 @@
- Other options:                                                                   
-  -v <int>       verbose mode: 0:no screen output  1:only warings  2: verbose (def=2)
-  -cpu <int>     number of CPUs to use (for shared memory SMPs) (default=2)      
-- -scores <file> write scores for all pairwise comparisions to file               
-+ -scores <file> write scores for all pairwise comparisons to file               
-  -atab   <file> write all alignments in tabular layout to file                   
-  -maxres <int>  max number of HMM columns (def=20001)             
-  -maxmem [1,inf[ limit memory for realignment (in GB) (def=3.0)          
---- a/src/cs/crf_state-inl.h
-+++ b/src/cs/crf_state-inl.h
-@@ -44,7 +44,7 @@
-     assert(len & 1);
-     if (nalph != Abc::kSize)
-         throw Exception("Alphabet size of serialized CRF state should be %d"
--                        "but is acutally %d!", Abc::kSize, nalph);
-+                        "but is actually %d!", Abc::kSize, nalph);
- 
-     // If everything went fine we can resize our data memmbers
-     context_weights.Resize(len);
---- a/src/hhblits.cpp
-+++ b/src/hhblits.cpp
-@@ -457,7 +457,7 @@
-   printf("                becomes larger than neffmax (default=%.1f)\n", par.neffmax);
-   printf(" -cpu <int>     number of CPUs to use (for shared memory SMPs) (default=%i)      \n", par.threads);
-   if (all) {
--	printf(" -scores <file> write scores for all pairwise comparisions to file               \n");
-+	printf(" -scores <file> write scores for all pairwise comparisons to file               \n");
- 	  printf(" -filter_matrices filter matrices for similarity to output at most 100 matrices\n");
-     printf(" -atab   <file> write all alignments in tabular layout to file                   \n");
-     printf(" -maxres <int>  max number of HMM columns (def=%5i)             \n", par.maxres);
---- a/src/hhsearch.cpp
-+++ b/src/hhsearch.cpp
-@@ -241,7 +241,7 @@
-   printf(" -v <int>       verbose mode: 0:no screen output  1:only warings  2: verbose (def=%i)\n", par.v);
-   printf(" -cpu <int>     number of CPUs to use (for shared memory SMPs) (default=%i)      \n", par.threads);
-   if (all) {
--  printf(" -scores <file> write scores for all pairwise comparisions to file               \n");
-+  printf(" -scores <file> write scores for all pairwise comparisons to file               \n");
-     printf(" -atab   <file> write all alignments in tabular layout to file                   \n");
-     printf(" -maxres <int>  max number of HMM columns (def=%5i)             \n", par.maxres);
-     printf(" -maxmem [1,inf[ limit memory for realignment (in GB) (def=%.1f)          \n", par.maxmem);

debian/rules

@@ -27,8 +27,11 @@ override_dh_installman: $(HHMANPAGES)
 $(HHMANPAGES): %.1 : debian/tmp/usr/bin/%
 	unset LD_PRELOAD && export LD_LIBRARY_PATH=debian/tmp/usr/lib && export HHLIB=. && help2man --no-info --help-option '-h all' --version-string $(VERSION) -n "$$n_$*" '$<' | sed -e 's/\(^\|[^\]\)-/\1\\-/g;' > '$@'
 
-override_dh_clean:
+override_dh_auto_clean:
+	dh_auto_clean
 	rm -f $(HHMANPAGES)
+	find . -name "*.rej" -delete
+	find . -name "*~" -delete
 	dh_clean
 
 override_dh_auto_build:

scripts/CMakeLists.txt

@@ -24,6 +24,9 @@ INSTALL(PROGRAMS
 	ffindex.py
 	a3m.py
 	get_a3m_size.py
-	is_huge_a3m.py
+	pdbfilter.py
+	cif2fasta.py
+	hhmakemodel.py
+  hh_reader.py
 	DESTINATION scripts
 )

scripts/HHPaths.pm

@@ -28,9 +28,10 @@ package HHPaths;
 use vars qw(@ISA @EXPORT @EXPORT_OK %EXPORT_TAGS $VERSION);
 use Exporter;
 our $v;
-our $VERSION = "version 2.0.16 (February 2013)";
+our $VERSION = "version 3.0.0 (15-03-2015)";
 our @ISA     = qw(Exporter);
 our @EXPORT  = qw($VERSION $hhlib $hhdata $hhbin $hhscripts $execdir $datadir $ncbidir $dummydb $pdbdir $dsspdir $dssp $cs_lib $context_lib $v);
+push @EXPORT, qw($hhshare $hhbdata);
 
 ##############################################################################################
 # PLEASE COMPLETE THE PATHS ... TO PSIPRED AND OLD-STYLE BLAST (NOT BLAST+) (NEEDED FOR PSIPRED) 
@@ -54,11 +55,13 @@ our $dssp    =  "/cluster/databases/dssp/bin/dsspcmbi";  # where is the dssp bin
 # The lines below probably do not need to be changed
 
 # Setting paths for hh-suite perl scripts
-our $hhlib    = $ENV{"HHLIB"};     # main hh-suite directory
-our $hhdata   = $hhlib."/data";    # path to data directory for hhblits, example files
+our $hhlib    = $ENV{"HHLIB"} || "/usr/lib/hhsuite";     # main hh-suite directory
+our $hhshare  = $ENV{"HHLIB"} || "/usr/share/hhsuite";   # main hh-suite directory
+our $hhdata   = $hhshare."/data";  # path to arch indep data directory for hhblits, example files
+our $hhbdata  = $hhlib."/data";    # path to arch dep data directory for hhblits, example files
 our $hhbin    = $hhlib."/bin";     # path to cstranslate (path to hhsearch, hhblits etc. should be in environment variable PATH)
-our $hhscripts= $hhlib."/scripts"; # path to hh perl scripts (addss.pl, reformat.pl, hhblitsdb.pl etc.)
-our $dummydb  = $hhdata."/do_not_delete"; # Name of dummy blast db for PSIPRED (single sequence formatted with NCBI formatdb)
+our $hhscripts= $hhshare."/scripts"; # path to hh perl scripts (addss.pl, reformat.pl, hhblitsdb.pl etc.)
+our $dummydb  = $hhbdata."/do_not_delete"; # Name of dummy blast db for PSIPRED (single sequence formatted with NCBI formatdb)
 
 # HHblits data files
 our $cs_lib = "$hhdata/cs219.lib";
@@ -72,7 +75,7 @@ $ENV{"PATH"} = $hhscripts.":".$ENV{"PATH"}; # Add hh scripts directory to enviro
 ################################################################################################
 sub System()
 {
-    if ($v>=2) {printf("\$ %s\n",$_[0]);} 
+    if ($v>=2) {printf(STDERR "\$ %s\n",$_[0]);} 
     system($_[0]);
     if ($? == -1) {
 	die("\nError: failed to execute '$_[0]': $!\n\n");