New upstream version 2.3.4

ltmain.sh linguist-vendored

 No newline at end of file

    - check

    - g++

    - libtool

    - libsubunit-dev

    - pkg-config

    - python3-dev

    - python3-setuptools

v2.3.2 - 12 Jan 2018

-----

Update installation instructions to remove all reference to HomeBrew.

v2.3.1 - 22 Sept 2017

-----

Output a tree with the internal nodes labelled.

#

#  From this base-image / starting-point

#

FROM debian:testing

# Use a LTS Ubuntu version as parent image

FROM ubuntu:16.04

ARG DEBIAN_FRONTEND=noninteractive

ARG PYTHONWARNINGS="ignore:Unverified HTTPS request"

ENV LD_LIBRARY_PATH='/usr/local/lib'

WORKDIR /opt

#

#  Authorship

#

MAINTAINER ap13@sanger.ac.uk

# Install general dependencies

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

	curl \

	make \

	automake \

	gcc \

	pkg-config \

	zlib1g-dev \

	autoconf \

	check \

	libtool \

	libsubunit-dev \

	git \

    python3 \

    python3-dev \

    python3-setuptools \

    python3-pip

#

# Pull in packages from testing

#

RUN apt-get update -qq

# Install python dependencies 

RUN pip3 install --trusted-host pypi.python.org --upgrade pip

RUN pip3 install certifi \

  && pip3 install wheel \

  && pip3 install nose \

  && pip3 install pillow \

  && pip3 install dendropy \

  && pip3 install biopython

#

# Install Roary

#

RUN apt-get install gubbins

# Install RAxML

ARG raxml_version='8.2.12'

RUN curl -L https://github.com/stamatak/standard-RAxML/archive/v${raxml_version}.tar.gz -o standard-RAxML-${raxml_version}.tar.gz \

  && tar xzf standard-RAxML-${raxml_version}.tar.gz \

  && cd standard-RAxML-${raxml_version} \

  && make -f Makefile.gcc \

  && make -f Makefile.PTHREADS.gcc \

  && cp raxmlHPC /usr/local/bin/ \

  && cp raxmlHPC-PTHREADS /usr/local/bin/ \

  && cd .. \

  && rm -rf standard-RAxML-${raxml_version}

# Install FastTree

ARG fasttree_version='2.1.10'

RUN curl http://www.microbesonline.org/fasttree/FastTree-${fasttree_version}.c -o FastTree.c \

  && gcc -O3 -finline-functions -funroll-loops -Wall -o FastTree FastTree.c -lm \

  && mv FastTree /usr/local/bin/ \

  && rm FastTree.c

# Install IQTree

ARG iqtree_version='1.6.6'

RUN curl -L https://github.com/Cibiv/IQ-TREE/releases/download/v${iqtree_version}/iqtree-${iqtree_version}-Linux.tar.gz -o iqtree-${iqtree_version}-Linux.tar.gz \

  && tar xzf iqtree-${iqtree_version}-Linux.tar.gz \

  && cp iqtree-${iqtree_version}-Linux/bin/iqtree /usr/local/bin \

  && rm -rf iqtree-${iqtree_version}-Linux

# Install Gubbins

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

  && cd gubbins \

  && autoreconf -i \

  && ./configure \

  && make \

  && make check \

  && make install \

  && cd python \

  && python3 setup.py install

# Rename executable for backwards compatibility

RUN mv /usr/local/bin/run_gubbins.py /usr/local/bin/run_gubbins