scripts/addss.pl | 2 1 + 1 - 0 !
scripts/create_profile_from_hhm.pl | 2 1 + 1 - 0 !
scripts/create_profile_from_hmmer.pl | 2 1 + 1 - 0 !
scripts/hhmakemodel.pl | 2 1 + 1 - 0 !
scripts/multithread.pl | 2 1 + 1 - 0 !
scripts/pdb2fasta.pl | 2 1 + 1 - 0 !
scripts/pdbfilter.pl | 2 1 + 1 - 0 !
scripts/reformat.pl | 2 1 + 1 - 0 !
scripts/renumberpdb.pl | 2 1 + 1 - 0 !
scripts/splitfasta.pl | 2 1 + 1 - 0 !
10 files changed, 10 insertions(+), 10 deletions(-)

 perl script use lib
  * Set paths to hhsuite components for Perl scripts.

scripts/addss.pl | 2 1 + 1 - 0 !
scripts/create_profile_from_hhm.pl | 2 1 + 1 - 0 !
scripts/create_profile_from_hmmer.pl | 2 1 + 1 - 0 !
scripts/hhmakemodel.pl | 2 1 + 1 - 0 !
scripts/multithread.pl | 2 1 + 1 - 0 !
scripts/pdb2fasta.pl | 2 1 + 1 - 0 !
scripts/pdbfilter.pl | 2 1 + 1 - 0 !
scripts/reformat.pl | 2 1 + 1 - 0 !
scripts/renumberpdb.pl | 2 1 + 1 - 0 !
scripts/splitfasta.pl | 2 1 + 1 - 0 !
10 files changed, 10 insertions(+), 10 deletions(-)

 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

data/Makefile | 11 11 + 0 - 0 !
1 file changed, 11 insertions(+)

 add makefile to data

doc/hhsuite-userguide.tex | 4 2 + 2 - 0 !
src/cs/context_profile-inl.h | 2 1 + 1 - 0 !
src/cs/crf_state-inl.h | 2 1 + 1 - 0 !
src/hhblits.cpp | 2 1 + 1 - 0 !
src/hhsearch.cpp | 2 1 + 1 - 0 !
5 files changed, 6 insertions(+), 6 deletions(-)

 fix spelling

CMakeLists.txt | 4 2 + 2 - 0 !
1 file changed, 2 insertions(+), 2 deletions(-)

 do not try to build ffindex

src/hhdatabase.h | 1 1 + 0 - 0 !
1 file changed, 1 insertion(+)

 add stdlib.h to header
 This fixes compilation with Debian's ffindex headers.

src/cs/cstranslate_app.h | 2 1 + 1 - 0 !
1 file changed, 1 insertion(+), 1 deletion(-)

 drop include for fmemopen
 According to the comments in the included files, this wrapper is only required for MacOS X and BSD.

CMakeLists.txt | 3 1 + 2 - 0 !
1 file changed, 1 insertion(+), 2 deletions(-)

 build own manual pdf
 The LaTeX source is now included, so we can build the manual directly.

src/hhdecl.cpp | 2 1 + 1 - 0 !
1 file changed, 1 insertion(+), 1 deletion(-)

 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.

cmake/CheckSSEFeatures.cmake | 34 17 + 17 - 0 !
src/CMakeLists.txt | 16 8 + 8 - 0 !
2 files changed, 25 insertions(+), 25 deletions(-)

 do not use avx to build binaries 

doc/hhsuite-userguide.tex | 2 1 + 1 - 0 !
src/hhblits.cpp | 2 1 + 1 - 0 !
2 files changed, 2 insertions(+), 2 deletions(-)

 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