[med-svn] [ariba] 01/03: New upstream version 2.10.1+ds

[Sascha Steinbiss]

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satta pushed a commit to branch master
in repository ariba.

commit 1b8ded512f5c7c9ae229317e66e0c1d5d7ab295f
Author: Sascha Steinbiss <satta at debian.org>
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 ap13 at sanger.ac.uk
+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/*']},

-- 
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