added oxford nanopore basecallers to dockerfiles

base/Dockerfile

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+FROM continuumio/miniconda3:latest
+
+LABEL maintainer "Saad Khan <[email protected]>"
+LABEL maintainer "Ryan Forster <[email protected]>"
+
+RUN apt-get -y update && \
+	apt-get -y upgrade && \
+    apt-get -y install gcc make g++ curl
+
+RUN git clone https://github.com/artic-network/artic-ncov2019.git
+
+# Install Flappie and runnie, the free versions of Oxford Nanopore's basecallers
+RUN curl -s https://packagecloud.io/install/repositories/github/git-lfs/script.deb.sh | bash && \
+    apt-get install git-lfs
+RUN git clone https://github.com/nanoporetech/flappie && \
+    cd flappie && \
+    make flappie && \
+    make runnie
+
+WORKDIR /artic-ncov2019
+
+RUN conda env create -f environment.yml
+
+RUN mkdir analysis
+
+RUN echo "source activate artic-ncov2019" > ~/.bashrc
+ENV PATH /opt/conda/envs/artic-ncov2019/bin:$PATH

base/README.md

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+This Image contains the artic utilities along with the flappie and runnie
+basecallers by Oxford Nanopore.
+
+# Usage
+
+    docker pull skhan8/artic
+    docker run -it skhan8/artic <your command>

medaka/Dockerfile

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+FROM continuumio/miniconda3:latest
+
+LABEL maintainer "Saad Khan <[email protected]>"
+LABEL maintainer "Ryan Forster <[email protected]>"
+
+RUN apt-get -y update && \
+	apt-get -y upgrade && \
+    apt-get -y install gcc make g++ curl
+
+RUN git clone https://github.com/artic-network/artic-ncov2019.git
+
+# Install Flappie and runnie, the free versions of Oxford Nanopore's basecallers
+RUN curl -s https://packagecloud.io/install/repositories/github/git-lfs/script.deb.sh | bash && \
+    apt-get install git-lfs
+RUN git clone https://github.com/nanoporetech/flappie && \
+    cd flappie && \
+    make flappie && \
+    make runnie
+
+WORKDIR /artic-ncov2019
+
+RUN conda env create -f environment-medaka.yml
+
+RUN mkdir analysis
+
+RUN echo "source activate artic-ncov2019" > ~/.bashrc
+ENV PATH /opt/conda/envs/artic-ncov2019/bin:$PATH

medaka/README.md

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+This Image contains the version of the artic utilities which use [medaka](https://github.com/nanoporetech/medaka), a
+sequence correction tool which relies on neural networks.
+In addition, we include the flappie and runnie basecallers by Oxford Nanopore.
+
+# Usage
+
+    docker pull skhan8/artic:medaka
+    docker run -it skhan8/artic:medaka <your command>