New upstream version 2.12.1+ds
Sascha Steinbiss
5 years ago
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FROM ubuntu:17.04
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FROM ubuntu:17.10
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RUN apt-get update
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RUN apt-get install --no-install-recommends -y \
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RUN git clone https://github.com/sanger-pathogens/ariba.git \
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&& cd ariba \
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&& git checkout v2.10.1 \
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&& git checkout v2.12.0 \
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&& python3 setup.py test \
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&& python3 setup.py install
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@classmethod
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def _get_genetic_epi_database_from_bitbucket(cls, db_name, outdir, git_commit=None):
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assert db_name in {'plasmidfinder', 'resfinder', 'virulence_finder'}
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assert db_name in {'plasmidfinder', 'resfinder', 'virulencefinder'}
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cmd = 'git clone ' + 'https://bitbucket.org/genomicepidemiology/' + db_name + '_db.git ' + outdir
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common.syscall(cmd)
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except:
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raise Error('Error mkdir/chdir ' + tmpdir)
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zipfile = 'plasmidfinder.zip'
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zipfile = 'virulencefinder.zip'
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cmd = 'curl -X POST --data "folder=virulencefinder&filename=virulencefinder.zip" -o ' + zipfile + ' https://cge.cbs.dtu.dk/cge/download_data.php'
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print('Downloading data with:', cmd, sep='\n')
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common.syscall(cmd)
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common.syscall('unzip ' + zipfile)
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else:
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RefGenesGetter._get_genetic_epi_database_from_bitbucket('plasmidfinder', tmpdir, git_commit=self.version)
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RefGenesGetter._get_genetic_epi_database_from_bitbucket('virulencefinder', tmpdir, git_commit=self.version)
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os.chdir(tmpdir)
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print('Combining downloaded fasta files...')
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setup(
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ext_modules=[minimap_mod, fermilite_mod, vcfcall_mod],
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name='ariba',
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version='2.12.0',
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version='2.12.1',
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description='ARIBA: Antibiotic Resistance Identification By Assembly',
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packages = find_packages(),
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package_data={'ariba': ['test_run_data/*']},
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