debian/control

@@ -21,7 +21,8 @@ Depends: ${python3:Depends},
          ${misc:Depends},
          ncbi-blast+,
          mash,
-         kaptive
+         kaptive,
+         kaptive-data
 Recommends: python3-biopython
 Description: tool to screen Klebsiella genome assemblies
  Kleborate is a tool to screen Klebsiella genome assemblies for:

debian/patches/series

 python3.patch
 fix_get_resource_paths.patch
+use_debian_installed_kaptive.patch

debian/patches/use_debian_installed_kaptive.patch

+Author: Andreas Tille <tille@debian.org>
+Last-Update: Tue, 24 Sep 2019 12:36:03 +0200
+Description: Make sure Debian packaged kaptive will be found
+
+--- a/kleborate/kleborate.py
++++ b/kleborate/kleborate.py
+@@ -353,13 +353,13 @@ def get_resource_paths():
+ 
+ def get_kaptive_paths():
+ 	this_file = os.path.realpath(__file__)
+-	kaptive_dir = os.path.join(os.path.dirname(os.path.dirname(this_file)), 'kaptive')
++	kaptive_dir = '/usr/bin'
+ 	if not os.path.isdir(kaptive_dir):
+ 		sys.exit('Error: could not find Kaptive directory. Did you git clone with --recursive?')
+ 	kaptive_py = os.path.join(kaptive_dir, 'kaptive.py')
+ 	if not os.path.isfile(kaptive_py):
+ 		sys.exit('Error: could not find kaptive.py')
+-	db_dir = os.path.join(kaptive_dir, 'reference_database')
++	db_dir = '/usr/share/kaptive/reference_database'
+ 	kaptive_k_db = os.path.join(db_dir, 'Klebsiella_k_locus_primary_reference.gbk')
+ 	if not os.path.isfile(kaptive_k_db):
+ 		sys.exit('Error: could not find Klebsiella_k_locus_primary_reference.gbk')