[med-svn] [Git][med-team/ariba][upstream] New upstream version 2.14.4+ds

[Sascha Steinbiss]

Sascha Steinbiss pushed to branch upstream at Debian Med / ariba


Commits:
4b898686 by Sascha Steinbiss at 2019-09-26T08:24:34Z
New upstream version 2.14.4+ds
- - - - -


3 changed files:

- CHANGELOG.md
- ariba/ref_genes_getter.py
- setup.py


Changes:

=====================================
CHANGELOG.md
=====================================
@@ -1,5 +1,12 @@
 # Change Log
 
+[v2.14.4](https://github.com/sanger-pathogens/ariba/tree/v2.14.4) (2019-09-24)
+[Full Changelog](https://github.com/sanger-pathogens/ariba/compare/v2.14.3...v2.14.4)
+
+**Fixed bugs:**
+
+- ARGannot download fails [\#281](https://github.com/sanger-pathogens/ariba/issues/281)
+
 [v2.14.3](https://github.com/sanger-pathogens/ariba/tree/v2.14.3) (2019-08-23)
 [Full Changelog](https://github.com/sanger-pathogens/ariba/compare/v2.14.2...v2.14.3)
 


=====================================
ariba/ref_genes_getter.py
=====================================
@@ -277,13 +277,12 @@ class RefGenesGetter:
         except:
             raise Error('Error mkdir/chdir ' + tmpdir)
 
-        zipfile = 'arg-annot-database_doc.zip'
-        common.download_file('http://www.mediterranee-infection.com/arkotheque/client/ihumed/_depot_arko/articles/304/arg-annot-database_doc.zip', zipfile, max_attempts=self.max_download_attempts, sleep_time=self.sleep_time, verbose=True)
-        common.syscall('unzip ' + zipfile)
+        downloadfile = 'arg-annot-database_doc'
+        common.download_file('https://www.mediterranee-infection.com/wp-content/uploads/2019/09/ARG-ANNOT_NT_V6_July2019.txt', downloadfile, max_attempts=self.max_download_attempts, sleep_time=self.sleep_time, verbose=True)
         os.chdir(current_dir)
         print('Extracted files.')
 
-        genes_file = os.path.join(tmpdir, 'Database Nt Sequences File.txt')
+        genes_file = os.path.join(tmpdir, downloadfile)
         final_fasta = outprefix + '.fa'
         final_tsv = outprefix + '.tsv'
 


=====================================
setup.py
=====================================
@@ -55,7 +55,7 @@ vcfcall_mod = Extension(
 setup(
     ext_modules=[minimap_mod, fermilite_mod, vcfcall_mod],
     name='ariba',
-    version='2.14.3',
+    version='2.14.4',
     description='ARIBA: Antibiotic Resistance Identification By Assembly',
     packages = find_packages(),
     package_data={'ariba': ['test_run_data/*', 'tb_data/*']},



View it on GitLab: https://salsa.debian.org/med-team/ariba/commit/4b89868644b290acd169790a617663f6f3d88479

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View it on GitLab: https://salsa.debian.org/med-team/ariba/commit/4b89868644b290acd169790a617663f6f3d88479
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