Steffen Möller pushed to branch master at Debian Med / gubbins
Commits:
c62bd388 by Steffen Moeller at 2020-01-09T02:34:14+01:00
Fixes
- - - - -
3 changed files:
- debian/changelog
- debian/control
- debian/patches/gubbins_exe_in_usr_lib.patch
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,12 @@
+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 <moel...@debian.org> Thu, 09 Jan 2020 02:31:16 +0100
+
gubbins (2.4.0-1) unstable; urgency=medium
* Team upload.
=====================================
debian/control
=====================================
@@ -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.
=====================================
debian/patches/gubbins_exe_in_usr_lib.patch
=====================================
@@ -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
@@ -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)
View it on GitLab:
https://salsa.debian.org/med-team/gubbins/commit/c62bd388f4e5ea7a28ff28bbb1cc8743bfdf1fbf
--
View it on GitLab:
https://salsa.debian.org/med-team/gubbins/commit/c62bd388f4e5ea7a28ff28bbb1cc8743bfdf1fbf
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