[med-svn] [Git][med-team/gubbins][master] Fixes

[Steffen Möller]

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 <moeller at 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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