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Moved software version numbers into ARGs
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@@ -4,6 +4,11 @@ ENV DEBIAN_FRONTEND=noninteractive | |
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| MAINTAINER [email protected] | ||
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| # Software version numbers | ||
| ARG BOWTIE2_VERSION=2.2.9 | ||
| ARG SPADES_VERSION=3.13.1 | ||
| ARG ARIBA_VERSION=2.14.2 | ||
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| RUN apt-get -qq update && \ | ||
| apt-get install --no-install-recommends -y \ | ||
| build-essential \ | ||
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@@ -22,24 +27,25 @@ RUN apt-get -qq update && \ | |
| wget \ | ||
| zlib1g-dev | ||
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| 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 -f 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 | ||
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| RUN wget -q https://github.com/ablab/spades/releases/download/v3.13.1/SPAdes-3.13.1-Linux.tar.gz \ | ||
| && tar -zxf SPAdes-3.13.1-Linux.tar.gz \ | ||
| && rm -f SPAdes-3.13.1-Linux.tar.gz | ||
| 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 | ||
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| # 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 PATH=$PATH:$PWD/SPAdes-3.13.1-Linux/bin | ||
| ENV ARIBA_BOWTIE2=$PWD/bowtie2-${BOWTIE2_VERSION}/bowtie2 ARIBA_CDHIT=cdhit-est MPLBACKEND="agg" | ||
| ENV PATH=$PATH:$PWD/SPAdes-${SPADES_VERSION}-Linux/bin | ||
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| RUN cd /usr/local/bin && ln -s /usr/bin/python3 python && cd | ||
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| RUN git clone https://github.com/sanger-pathogens/ariba.git \ | ||
| && cd ariba \ | ||
| && git checkout v2.14.2 \ | ||
| && git checkout v${ARIBA_VERSION} \ | ||
| && rm -rf .git \ | ||
| && python3 setup.py test \ | ||
| && python3 setup.py install | ||
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