[med-svn] [Git][med-team/ariba][master] 3 commits: New upstream version 2.12.1+ds

[Sascha Steinbiss]

Sascha Steinbiss pushed to branch master at Debian Med / ariba


Commits:
a2979e81 by Sascha Steinbiss at 2018-06-19T17:09:12+02:00
New upstream version 2.12.1+ds
- - - - -
e03d3355 by Sascha Steinbiss at 2018-06-19T17:09:13+02:00
Update upstream source from tag 'upstream/2.12.1+ds'

Update to upstream version '2.12.1+ds'
with Debian dir a9391d5a5282d2937c7ed2f1758f4ceec356c9a8
- - - - -
94003298 by Sascha Steinbiss at 2018-06-19T18:01:02+02:00
new upstream release

- - - - -


4 changed files:

- Dockerfile
- ariba/ref_genes_getter.py
- debian/changelog
- setup.py


Changes:

=====================================
Dockerfile
=====================================
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,4 +1,4 @@
-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
=====================================
--- a/ariba/ref_genes_getter.py
+++ b/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
=====================================
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,9 @@
+ariba (2.12.1+ds-1) UNRELEASED; urgency=medium
+
+  * New upstream release.
+
+ -- Sascha Steinbiss <satta at debian.org>  Tue, 19 Jun 2018 17:09:34 +0200
+
 ariba (2.12.0+ds-1) unstable; urgency=medium
 
   * New upstream release.


=====================================
setup.py
=====================================
--- a/setup.py
+++ b/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/*']},



View it on GitLab: https://salsa.debian.org/med-team/ariba/compare/5d1142d924d972f1f5de5ea5dca0f69ef3d75e99...94003298665bfce4d8d0c820279f8240baaacc85

-- 
View it on GitLab: https://salsa.debian.org/med-team/ariba/compare/5d1142d924d972f1f5de5ea5dca0f69ef3d75e99...94003298665bfce4d8d0c820279f8240baaacc85
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