Sascha Steinbiss pushed to branch upstream at Debian Med / ariba
Commits: a2979e81 by Sascha Steinbiss at 2018-06-19T17:09:12+02:00 New upstream version 2.12.1+ds - - - - - 3 changed files: - Dockerfile - ariba/ref_genes_getter.py - 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...') ===================================== 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/commit/a2979e81b138866d256554065a0f699c68b50a8f -- View it on GitLab: https://salsa.debian.org/med-team/ariba/commit/a2979e81b138866d256554065a0f699c68b50a8f You're receiving this email because of your account on salsa.debian.org.
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