Commit a2979e81 authored by Sascha Steinbiss's avatar Sascha Steinbiss
Browse files

New upstream version 2.12.1+ds

parent 0c1eaaa8

Dockerfile

+2 −2
Original line number Diff line number Diff line 
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

+3 −3
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@@ -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...')

setup.py

+1 −1
Original line number Diff line number Diff line
@@ -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/*']},