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 filePatch | File delta | Description |
---|---|---|
probconsrna.patch | (download) |
t_coffee_source/data_headers/programmes_define.h |
2 1 + 1 - 0 ! |
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 ! |
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 ! |
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 ! |
propagate hardening options |
set_proper_dir_permissions.patch | (download) |
t_coffee_source/util_lib/util.c |
13 9 + 4 - 0 ! |
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 ! |
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 ! |
provide stable file order for linking This makes the package reproducible. |
clustalw2.patch | (download) |
install |
20 6 + 14 - 0 ! |
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. |