Loading debian/changelog +9 −0 Original line number Diff line number Diff line gubbins (2.4.0-2) unstable; urgency=medium * Team upload. * Fix run_gubbins wrapper (Sascha Steinbiss) * raxml needed as default method at runtime - turned back into hard dependency (suggested by Sascha) -- Steffen Moeller <moeller@debian.org> Thu, 09 Jan 2020 02:31:16 +0100 gubbins (2.4.0-1) unstable; urgency=medium * Team upload. Loading debian/control +3 −3 Original line number Diff line number Diff line Loading @@ -28,10 +28,10 @@ Architecture: any Depends: ${shlibs:Depends}, ${misc:Depends}, ${python3:Depends}, python3 Recommends: iqtree, fasttree, python3, raxml Recommends: iqtree, fasttree Description: phylogenetic analysis of genome sequences Gubbins supports rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences. Loading debian/patches/gubbins_exe_in_usr_lib.patch +12 −13 Original line number Diff line number Diff line Loading @@ -5,19 +5,6 @@ Description: gubbins executable prints that it is not intended for direct usage it prints that it is intended to be called from run_gubbins. So it makes sense to rather install it to /usr/lib/gubbins instead of /usr/bin. Index: gubbins/python/gubbins/common.py =================================================================== --- gubbins.orig/python/gubbins/common.py +++ gubbins/python/gubbins/common.py @@ -48,7 +48,7 @@ def parse_and_run(input_args, program_de printer = utils.VerbosePrinter(True, "\n") # Check if the Gubbins C-program is available. If so, print a welcome message. Otherwise exit. - gubbins_exec = 'gubbins' + gubbins_exec = '/usr/lib/gubbins/gubbins' if utils.which(gubbins_exec) is None: # Check if the Gubbins C-program is available in its source directory (for tests/Travis) gubbins_bundled_exec = os.path.abspath(os.path.join(current_directory, '../src/gubbins')) Index: gubbins/src/main.c =================================================================== --- gubbins.orig/src/main.c Loading @@ -31,3 +18,15 @@ Index: gubbins/src/main.c fprintf (stream, "Usage: %s [options] alignment_file\n", program_name); fprintf (stream, "Version: %s\n", PACKAGE_VERSION); fprintf (stream, Index: gubbins/python/gubbins/common.py =================================================================== --- gubbins.orig/python/gubbins/common.py +++ gubbins/python/gubbins/common.py @@ -48,6 +48,7 @@ def parse_and_run(input_args, program_de printer = utils.VerbosePrinter(True, "\n") # Check if the Gubbins C-program is available. If so, print a welcome message. Otherwise exit. + os.environ["PATH"] = os.environ["PATH"] + ":/usr/lib/gubbins/" gubbins_exec = 'gubbins' if utils.which(gubbins_exec) is None: # Check if the Gubbins C-program is available in its source directory (for tests/Travis) Loading
debian/changelog +9 −0 Original line number Diff line number Diff line gubbins (2.4.0-2) unstable; urgency=medium * Team upload. * Fix run_gubbins wrapper (Sascha Steinbiss) * raxml needed as default method at runtime - turned back into hard dependency (suggested by Sascha) -- Steffen Moeller <moeller@debian.org> Thu, 09 Jan 2020 02:31:16 +0100 gubbins (2.4.0-1) unstable; urgency=medium * Team upload. Loading
debian/control +3 −3 Original line number Diff line number Diff line Loading @@ -28,10 +28,10 @@ Architecture: any Depends: ${shlibs:Depends}, ${misc:Depends}, ${python3:Depends}, python3 Recommends: iqtree, fasttree, python3, raxml Recommends: iqtree, fasttree Description: phylogenetic analysis of genome sequences Gubbins supports rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences. Loading
debian/patches/gubbins_exe_in_usr_lib.patch +12 −13 Original line number Diff line number Diff line Loading @@ -5,19 +5,6 @@ Description: gubbins executable prints that it is not intended for direct usage it prints that it is intended to be called from run_gubbins. So it makes sense to rather install it to /usr/lib/gubbins instead of /usr/bin. Index: gubbins/python/gubbins/common.py =================================================================== --- gubbins.orig/python/gubbins/common.py +++ gubbins/python/gubbins/common.py @@ -48,7 +48,7 @@ def parse_and_run(input_args, program_de printer = utils.VerbosePrinter(True, "\n") # Check if the Gubbins C-program is available. If so, print a welcome message. Otherwise exit. - gubbins_exec = 'gubbins' + gubbins_exec = '/usr/lib/gubbins/gubbins' if utils.which(gubbins_exec) is None: # Check if the Gubbins C-program is available in its source directory (for tests/Travis) gubbins_bundled_exec = os.path.abspath(os.path.join(current_directory, '../src/gubbins')) Index: gubbins/src/main.c =================================================================== --- gubbins.orig/src/main.c Loading @@ -31,3 +18,15 @@ Index: gubbins/src/main.c fprintf (stream, "Usage: %s [options] alignment_file\n", program_name); fprintf (stream, "Version: %s\n", PACKAGE_VERSION); fprintf (stream, Index: gubbins/python/gubbins/common.py =================================================================== --- gubbins.orig/python/gubbins/common.py +++ gubbins/python/gubbins/common.py @@ -48,6 +48,7 @@ def parse_and_run(input_args, program_de printer = utils.VerbosePrinter(True, "\n") # Check if the Gubbins C-program is available. If so, print a welcome message. Otherwise exit. + os.environ["PATH"] = os.environ["PATH"] + ":/usr/lib/gubbins/" gubbins_exec = 'gubbins' if utils.which(gubbins_exec) is None: # Check if the Gubbins C-program is available in its source directory (for tests/Travis)
