New upstream version 2.14.2+ds

# Distribution / packaging

.Python

env/

venv/

build/

develop-eggs/

dist/

var/

*.egg-info/

.installed.cfg

*.egg

*.egg*

# PyInstaller

#  Usually these files are written by a python script from a template

.tox/

.coverage

.cache

out.card*

nosetests.xml

coverage.xml

# PyBuilder

target/

# PyCharm

.idea

# Mac files

.DS_Store

    - libgfortran3

    - libncurses5-dev

python:

- '3.5'

- '3.6'

sudo: false

install:

- source ./install_dependencies.sh

# Change Log

## [Unreleased](https://github.com/sanger-pathogens/ariba/tree/HEAD)

[v2.14.2](https://github.com/sanger-pathogens/ariba/tree/v2.14.2) (2019-06-18)

[Full Changelog](https://github.com/sanger-pathogens/ariba/compare/v2.14.1...v2.14.2)

[Full Changelog](https://github.com/sanger-pathogens/ariba/compare/v2.13.1...HEAD)

**Fixed bugs:**

- Added Spades assembler into Docker file - RT ticket 660940

- Incremented release number

- Added LICENSE file into release distribution - RT ticket 660890

[v2.14.1](https://github.com/sanger-pathogens/ariba/tree/v2.14.1) (2019-06-13)

[Full Changelog](https://github.com/sanger-pathogens/ariba/compare/v2.14.0...v2.14.1)

**Fixed bugs:**

- Ariba fails to install from PyPI due to missing .h files in distribution. Related to MANIFEST.in change in [\#269](https://github.com/sanger-pathogens/ariba/pull/269)

- Fix for Issue [\#263](https://github.com/sanger-pathogens/ariba/issues/263)

[v2.14.0](https://github.com/sanger-pathogens/ariba/tree/v2.14.0) (2019-06-06)

[Full Changelog](https://github.com/sanger-pathogens/ariba/compare/v2.13.5...v2.14.0)

**Closed issues:**

- Reference dataset of ARG-ANNOT cannot be downloaded [\#265](https://github.com/sanger-pathogens/ariba/issues/265)

- unable to download mlst schemes [\#264](https://github.com/sanger-pathogens/ariba/issues/264)

- Several "At least one cluster failed!Stopping..." errors [\#261](https://github.com/sanger-pathogens/ariba/issues/261)

- Allow increasing cd-hit-est memory allocation [\#255](https://github.com/sanger-pathogens/ariba/issues/255)

- Ariba pubmlstget Error [\#240](https://github.com/sanger-pathogens/ariba/issues/240)

- segmentation fault when I import ariba [\#230](https://github.com/sanger-pathogens/ariba/issues/230)

- How to use spades and set minimum coverage [\#215](https://github.com/sanger-pathogens/ariba/issues/215)

**Merged pull requests:**

- Additional v2.14.0 updates [\#270](https://github.com/sanger-pathogens/ariba/pull/270) ([kpepper](https://github.com/kpepper))

- Added getref feature for NCBI's Bacterial Antimicrobial Resistance Reference Gene Database [\#269](https://github.com/sanger-pathogens/ariba/pull/269) ([schultzm](https://github.com/schultzm))

## [v2.13.5](https://github.com/sanger-pathogens/ariba/tree/v2.13.5) (2019-03-26)

[Full Changelog](https://github.com/sanger-pathogens/ariba/compare/v2.13.4...v2.13.5)

**Fixed bugs:**

- Ariba fails without --noclean depending on database [\#205](https://github.com/sanger-pathogens/ariba/issues/205)

**Closed issues:**

- Installation failed: clang: error: linker command failed with exit code 1 \(use -v to see invocation\) [\#245](https://github.com/sanger-pathogens/ariba/issues/245)

-  virfinddb db not downloading properly [\#229](https://github.com/sanger-pathogens/ariba/issues/229)

- getref error with resfinder db [\#225](https://github.com/sanger-pathogens/ariba/issues/225)

**Merged pull requests:**

- Updated CHANGELOG.md [\#260](https://github.com/sanger-pathogens/ariba/pull/260) ([kpepper](https://github.com/kpepper))

- Bump version to 2.13.5 and fix Spades invocation issue [\#259](https://github.com/sanger-pathogens/ariba/pull/259) ([kpepper](https://github.com/kpepper))

- Minor code change to mitigate issue \#245 \(installation failure\) [\#258](https://github.com/sanger-pathogens/ariba/pull/258) ([kpepper](https://github.com/kpepper))

## [v2.13.4](https://github.com/sanger-pathogens/ariba/tree/v2.13.4) (2019-03-15)

[Full Changelog](https://github.com/sanger-pathogens/ariba/compare/v2.13.3...v2.13.4)

**Closed issues:**

- Ariba run signal 28 [\#252](https://github.com/sanger-pathogens/ariba/issues/252)

- NCBI database. [\#241](https://github.com/sanger-pathogens/ariba/issues/241)

**Merged pull requests:**

- Rebuilt CHANGELOG for v2.13.4 [\#257](https://github.com/sanger-pathogens/ariba/pull/257) ([kpepper](https://github.com/kpepper))

- Allow increasing cd-hit-est memory allocation \#255 [\#256](https://github.com/sanger-pathogens/ariba/pull/256) ([kpepper](https://github.com/kpepper))

## [v2.13.3](https://github.com/sanger-pathogens/ariba/tree/v2.13.3) (2019-01-02)

[Full Changelog](https://github.com/sanger-pathogens/ariba/compare/v2.13.2...v2.13.3)

**Merged pull requests:**

- TB D94A fix [\#251](https://github.com/sanger-pathogens/ariba/pull/251) ([martinghunt](https://github.com/martinghunt))

## [v2.13.2](https://github.com/sanger-pathogens/ariba/tree/v2.13.2) (2018-12-21)

[Full Changelog](https://github.com/sanger-pathogens/ariba/compare/v2.13.1...v2.13.2)

**Merged pull requests:**

- Update tb panel [\#250](https://github.com/sanger-pathogens/ariba/pull/250) ([martinghunt](https://github.com/martinghunt))

- Added changelog [\#248](https://github.com/sanger-pathogens/ariba/pull/248) ([ssjunnebo](https://github.com/ssjunnebo))

- Update python min version [\#247](https://github.com/sanger-pathogens/ariba/pull/247) ([ssjunnebo](https://github.com/ssjunnebo))

## [v2.13.1](https://github.com/sanger-pathogens/ariba/tree/v2.13.1) (2018-11-16)

- Initial working version [\#1](https://github.com/sanger-pathogens/ariba/pull/1) ([martinghunt](https://github.com/martinghunt))

\* *This Change Log was automatically generated by [github_changelog_generator](https://github.com/skywinder/Github-Changelog-Generator)*

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FROM ubuntu:17.10

FROM ubuntu:18.04

RUN apt-get update

RUN apt-get install --no-install-recommends -y \

ENV DEBIAN_FRONTEND=noninteractive

MAINTAINER ariba-help@sanger.ac.uk

# Software version numbers

ARG BOWTIE2_VERSION=2.2.9

ARG SPADES_VERSION=3.13.1

ARG ARIBA_VERSION=2.14.2

RUN apt-get -qq update && \

    apt-get install --no-install-recommends -y \

  build-essential \

  cd-hit \

  curl \

  libbz2-dev \

  liblzma-dev \

  mummer \

  python \

  python3-dev \

  python3-setuptools \

  python3-pip \

  wget \

  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

RUN wget -q http://downloads.sourceforge.net/project/bowtie-bio/bowtie2/${BOWTIE2_VERSION}/bowtie2-${BOWTIE2_VERSION}-linux-x86_64.zip \

  && unzip bowtie2-${BOWTIE2_VERSION}-linux-x86_64.zip \

  && rm -f bowtie2-${BOWTIE2_VERSION}-linux-x86_64.zip

RUN wget -q https://github.com/ablab/spades/releases/download/v${SPADES_VERSION}/SPAdes-${SPADES_VERSION}-Linux.tar.gz \

  && tar -zxf SPAdes-${SPADES_VERSION}-Linux.tar.gz \

  && rm -f SPAdes-${SPADES_VERSION}-Linux.tar.gz

# 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"

ENV ARIBA_BOWTIE2=$PWD/bowtie2-${BOWTIE2_VERSION}/bowtie2 ARIBA_CDHIT=cdhit-est MPLBACKEND="agg"

ENV PATH=$PATH:$PWD/SPAdes-${SPADES_VERSION}-Linux/bin

RUN cd /usr/local/bin && ln -s /usr/bin/python3 python && cd

RUN git clone https://github.com/sanger-pathogens/ariba.git \

  && cd ariba \

  && git checkout v2.12.0 \

  && git checkout v${ARIBA_VERSION} \

  && rm -rf .git \

  && python3 setup.py test \

  && python3 setup.py install

recursive-include third_party *.h

include LICENSE

include AUTHORS

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