Commit 4b898686 authored by Sascha Steinbiss's avatar Sascha Steinbiss
Browse files

New upstream version 2.14.4+ds

parent 5aef8353

CHANGELOG.md

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# 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

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@@ -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

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@@ -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/*']},