[med-svn] [Git][med-team/kleborate][master] 2 commits: Make sure Debian packaged kaptive will be found

[Andreas Tille]

Andreas Tille pushed to branch master at Debian Med / kleborate


Commits:
47d29ab5 by Andreas Tille at 2019-09-27T10:53:06Z
Make sure Debian packaged kaptive will be found

- - - - -
bba0a761 by Andreas Tille at 2019-09-27T10:53:06Z
Also use kaptive-data which contains the needed .gbk files

- - - - -


3 changed files:

- debian/control
- debian/patches/series
- + debian/patches/use_debian_installed_kaptive.patch


Changes:

=====================================
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
=====================================
@@ -1,2 +1,3 @@
 python3.patch
 fix_get_resource_paths.patch
+use_debian_installed_kaptive.patch


=====================================
debian/patches/use_debian_installed_kaptive.patch
=====================================
@@ -0,0 +1,22 @@
+Author: Andreas Tille <tille at 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')



View it on GitLab: https://salsa.debian.org/med-team/kleborate/compare/c0a759b5643a169207eb1cc72dce6760adef4779...bba0a7611bebe6b36ac08a8210f5a1a87724a01c

-- 
View it on GitLab: https://salsa.debian.org/med-team/kleborate/compare/c0a759b5643a169207eb1cc72dce6760adef4779...bba0a7611bebe6b36ac08a8210f5a1a87724a01c
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