Makefile | 79 39 + 40 - 0 !
1 file changed, 39 insertions(+), 40 deletions(-)

 patch to top level makefile
  * Make Makefile DESTDIR-aware.
  * Fix install mode of data files.

scripts/HHPaths.pm | 11 7 + 4 - 0 !
src/hhdecl.C | 4 2 + 2 - 0 !
2 files changed, 9 insertions(+), 6 deletions(-)

 set hhsuite paths.
 Set paths to hhsuite components - as installed on Debian - correctly in absence of the (now superflouos) HHLIB environment variable.

src/hhblits.C | 7 6 + 1 - 0 !
src/hhsearch.C | 1 1 + 0 - 0 !
2 files changed, 7 insertions(+), 1 deletion(-)

 fix paths in help pages
 Fix issues where the path in help pages is taken from the build-time location of the executables.

src/Makefile | 8 4 + 4 - 0 !
1 file changed, 4 insertions(+), 4 deletions(-)

 assorted patches
  * Set paths to hhsuite components for Perl scripts.
  * Add a Makefile to generate data/do_not_delete.phr,do_not_delete.pin,do_not_delete.psq .

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/hhblitsdb.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 !
11 files changed, 11 insertions(+), 11 deletions(-)

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

src/pngwriter.cc | 4 2 + 2 - 0 !
1 file changed, 2 insertions(+), 2 deletions(-)

 fix unused variables warning

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

 remove unnecessary libz link

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/hhblitsdb.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 !
11 files changed, 11 insertions(+), 11 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

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

 fix version where it is not up to date

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

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