Package: t-coffee / 11.00.8cbe486-5

Metadata

Package Version Patches format
t-coffee 11.00.8cbe486-5 3.0 (quilt)

Patch series

view the series file
Patch File delta Description
probconsrna.patch | (download)

t_coffee_source/data_headers/programmes_define.h | 2 1 + 1 - 0 !
1 file changed, 1 insertion(+), 1 deletion(-)

 debian-specific adjustment.
 The program "probconsRNA" is called "probcons-RNA" in Debian.
ncbi blast++_has_dropped_pl_extension.patch | (download)

install | 34 17 + 17 - 0 !
t_coffee_source/data_headers/programmes_define.h | 4 2 + 2 - 0 !
t_coffee_source/perl_header_lib.h | 50 25 + 25 - 0 !
t_coffee_source/programmes_define.h | 4 2 + 2 - 0 !
t_coffee_source/util_lib/util_constraints_list.c | 2 1 + 1 - 0 !
tclinkdb.txt | 34 17 + 17 - 0 !
6 files changed, 64 insertions(+), 64 deletions(-)

 cope with renaming of scripts in ncbi-blast++
 Since ncbi-blast++ has renamed some perl scripts according to
 Debian policy (section 10.4) t-coffee needs to be adapted:
      s/legacy_blast\.pl/legacy_blast/
      s/blastpgp\.pl/blastpgp/


use_debian_packaged_TMalign.patch | (download)

t_coffee_source/makefile | 7 2 + 5 - 0 !
1 file changed, 2 insertions(+), 5 deletions(-)

 there is no need to build tmalign since the debian packaged
 version is used anyway


hardening.patch | (download)

t_coffee_source/makefile | 6 3 + 3 - 0 !
1 file changed, 3 insertions(+), 3 deletions(-)

 propagate hardening options


set_proper_dir_permissions.patch | (download)

t_coffee_source/util_lib/util.c | 13 9 + 4 - 0 !
1 file changed, 9 insertions(+), 4 deletions(-)

 when creating subdirectories in $home do not
 make these world writable but keep users umask


mayhem.patch | (download)

t_coffee_source/util_lib/util.c | 3 2 + 1 - 0 !
1 file changed, 2 insertions(+), 1 deletion(-)

 fix mayhem issue
 The idea behind this patch is that if there is a problem to set the HOME
 directories no additional processes can exist and so we should *really*
 exit.  Somehow the printf_exit() function does some logic which ends up
 in an endless loop and thus forcing the exit will help here.
 .
 Unfortunately this does not solve the issue completely since inside the
 Exit call a "Segmentation fault" happens - so some broken pointer handling
 seems to happen somewhere before.


stable linking inputs.patch | (download)

t_coffee_source/makefile | 2 1 + 1 - 0 !
1 file changed, 1 insertion(+), 1 deletion(-)

 provide stable file order for linking
 This makes the package reproducible.
clustalw2.patch | (download)

install | 20 6 + 14 - 0 !
t_coffee_source/data_headers/programmes_define.h | 2 1 + 1 - 0 !
t_coffee_source/perl_header_lib.h | 16 8 + 8 - 0 !
t_coffee_source/programmes_define.h | 2 1 + 1 - 0 !
t_coffee_source/util_lib/util_constraints_list.c | 10 5 + 5 - 0 !
tclinkdb.txt | 16 8 + 8 - 0 !
6 files changed, 29 insertions(+), 37 deletions(-)

 executable in clustalw 2.x package is named clustalw
 When using bioperl-run test suite it is uncovered that t-coffee is
 wrongly seeking for a clustalw2 executable.  A patch is applied to
 rather seek for clustalw.