Dockerfile

-FROM ubuntu:17.04
+FROM ubuntu:17.10
 
 RUN apt-get update
 RUN apt-get install --no-install-recommends -y \
@@ -29,7 +29,7 @@ ENV ARIBA_BOWTIE2=$PWD/bowtie2-2.2.9/bowtie2 ARIBA_CDHIT=cdhit-est MPLBACKEND="a
 
 RUN git clone https://github.com/sanger-pathogens/ariba.git \
   && cd ariba \
-  && git checkout v2.10.1 \
+  && git checkout v2.12.0 \
   && python3 setup.py test \
   && python3 setup.py install
 

ariba/ref_genes_getter.py

@@ -190,7 +190,7 @@ class RefGenesGetter:
 
     @classmethod
     def _get_genetic_epi_database_from_bitbucket(cls, db_name, outdir, git_commit=None):
-        assert db_name in {'plasmidfinder', 'resfinder', 'virulence_finder'}
+        assert db_name in {'plasmidfinder', 'resfinder', 'virulencefinder'}
         cmd = 'git clone ' + 'https://bitbucket.org/genomicepidemiology/' + db_name + '_db.git ' + outdir
         common.syscall(cmd)
 
@@ -497,13 +497,13 @@ class RefGenesGetter:
             except:
                 raise Error('Error mkdir/chdir ' + tmpdir)
 
-            zipfile = 'plasmidfinder.zip'
+            zipfile = 'virulencefinder.zip'
             cmd = 'curl -X POST --data "folder=virulencefinder&filename=virulencefinder.zip" -o ' + zipfile + ' https://cge.cbs.dtu.dk/cge/download_data.php'
             print('Downloading data with:', cmd, sep='\n')
             common.syscall(cmd)
             common.syscall('unzip ' + zipfile)
         else:
-            RefGenesGetter._get_genetic_epi_database_from_bitbucket('plasmidfinder', tmpdir, git_commit=self.version)
+            RefGenesGetter._get_genetic_epi_database_from_bitbucket('virulencefinder', tmpdir, git_commit=self.version)
             os.chdir(tmpdir)
 
         print('Combining downloaded fasta files...')

debian/changelog

+ariba (2.12.1+ds-1) UNRELEASED; urgency=medium
+
+  * New upstream release.
+
+ -- Sascha Steinbiss <satta@debian.org>  Tue, 19 Jun 2018 17:09:34 +0200
+
 ariba (2.12.0+ds-1) unstable; urgency=medium
 
   * New upstream release.

setup.py

@@ -55,7 +55,7 @@ vcfcall_mod = Extension(
 setup(
     ext_modules=[minimap_mod, fermilite_mod, vcfcall_mod],
     name='ariba',
-    version='2.12.0',
+    version='2.12.1',
     description='ARIBA: Antibiotic Resistance Identification By Assembly',
     packages = find_packages(),
     package_data={'ariba': ['test_run_data/*']},