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commit 1b8ded512f5c7c9ae229317e66e0c1d5d7ab295f Author: Sascha Steinbiss <[email protected]> Date: Tue Aug 15 10:30:00 2017 +0200 New upstream version 2.10.1+ds --- Dockerfile | 49 +++++++++++++++++++++++++++++++---------------- ariba/mapping.py | 3 ++- ariba/ref_genes_getter.py | 1 + setup.py | 2 +- 4 files changed, 37 insertions(+), 18 deletions(-) diff --git a/Dockerfile b/Dockerfile index 47bfb78..5edfee1 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,19 +1,36 @@ -# -# This container will install ARIBA from master -# -FROM debian:testing +FROM ubuntu:17.04 -# -# Authorship -# -MAINTAINER [email protected] +RUN apt-get update +RUN apt-get install --no-install-recommends -y \ + build-essential \ + cd-hit \ + curl \ + git \ + libbz2-dev \ + liblzma-dev \ + mummer \ + python \ + python3-dev \ + python3-setuptools \ + python3-pip \ + python3-tk \ + python3-matplotlib \ + unzip \ + wget \ + zlib1g-dev -# -# Install the dependancies -# -RUN apt-get update -qq && apt-get install -y git bowtie2 cd-hit fastaq libc6 libfml0 libgcc1 libminimap0 libstdc++6 mummer python3 python3-setuptools python3-dev python3-pysam python3-pymummer python3-dendropy gcc g++ zlib1g-dev +RUN wget -q http://downloads.sourceforge.net/project/bowtie-bio/bowtie2/2.2.9/bowtie2-2.2.9-linux-x86_64.zip \ + && unzip bowtie2-2.2.9-linux-x86_64.zip \ + && rm bowtie2-2.2.9-linux-x86_64.zip -# -# Get the latest code from github and install -# -RUN git clone https://github.com/sanger-pathogens/ariba.git && cd ariba && python3 setup.py install +# Need MPLBACKEND="agg" to make matplotlib work without X11, otherwise get the error +# _tkinter.TclError: no display name and no $DISPLAY environment variable +ENV ARIBA_BOWTIE2=$PWD/bowtie2-2.2.9/bowtie2 ARIBA_CDHIT=cdhit-est MPLBACKEND="agg" + +RUN git clone https://github.com/sanger-pathogens/ariba.git \ + && cd ariba \ + && git checkout v2.10.1 \ + && python3 setup.py test \ + && python3 setup.py install + +CMD ariba diff --git a/ariba/mapping.py b/ariba/mapping.py index 718c2f5..40564ba 100644 --- a/ariba/mapping.py +++ b/ariba/mapping.py @@ -1,5 +1,6 @@ import os import sys +from distutils.version import LooseVersion import pysam import pyfastaq from ariba import common @@ -82,7 +83,7 @@ def run_bowtie2( '-2', reads_rev, ] - if bowtie2_version == '2.3.1': + if LooseVersion(bowtie2_version) >= LooseVersion('2.3.1'): map_cmd.append('--score-min G,1,10') if remove_both_unmapped: diff --git a/ariba/ref_genes_getter.py b/ariba/ref_genes_getter.py index 82dc57f..fc9b859 100644 --- a/ariba/ref_genes_getter.py +++ b/ariba/ref_genes_getter.py @@ -115,6 +115,7 @@ class RefGenesGetter: for gene_key, gene_dict in sorted(json_data.items()): crecord = card_record.CardRecord(gene_dict) data = crecord.get_data() + data['ARO_description'] = data['ARO_description'].encode('utf-8') fasta_name_prefix = '.'.join([ card_record.CardRecord._ARO_name_to_fasta_name(data['ARO_name']), data['ARO_accession'], diff --git a/setup.py b/setup.py index eda17e3..b85411e 100644 --- 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='2.10.0', + version='2.10.1', description='ARIBA: Antibiotic Resistance Identification By Assembly', packages = find_packages(), package_data={'ariba': ['test_run_data/*']}, -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/ariba.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
