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 <[email protected]>
+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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