Create Dockerfile

nanoplot/1.41.6/Dockerfile

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+FROM ubuntu:focal as app
+
+# for easy upgrade later. ARG variables only persist during image build time.
+ARG NANOPLOT_VER="1.41.6"
+
+LABEL base.image="ubuntu:focal"
+LABEL dockerfile.version="1"
+LABEL software="nanoplot"
+LABEL software.version="${NANOPLOT_VER}"
+LABEL description="Plotting suite for Oxford Nanopore sequencing data and alignments"
+LABEL website="https://github.com/wdecoster/NanoPlot"
+LABEL license="https://github.com/wdecoster/NanoPlot/blob/master/LICENSE"
+LABEL maintainer="Curtis Kapsak"
+LABEL maintainer.email="[email protected]"
+
+# install dependencies via apt; cleanup apt garbage; set locale to en_US.UTF-8
+RUN apt-get update && apt-get install -y zlib1g-dev \
+ bzip2 \
+ libbz2-dev \
+ liblzma-dev \
+ libcurl4-gnutls-dev \
+ libncurses5-dev \
+ libssl-dev \
+ python3 \
+ python3-pip \
+ python3-setuptools \
+ locales && \
+ locale-gen en_US.UTF-8 && \
+ apt-get autoclean && rm -rf /var/lib/apt/lists/*
+
+# for singularity compatibility
+ENV LC_ALL=C
+
+# install NanoPlot via pypi using pip3; make /data directory
+RUN pip3 install matplotlib psutil requests NanoPlot==${NANOPLOT_VER} && \
+ mkdir /data
+
+WORKDIR /data
+
+# testing layer
+FROM app as test
+
+# print help options and version
+RUN NanoPlot --help && NanoPlot --version
+
+# install wget for downloading test data
+RUN apt-get update && apt-get install -y wget
+
+# download ONT data for a Salmonella isolate, run NanoPlot on the FASTQ file
+# Go here for more info: https://www.ebi.ac.uk/ena/browser/view/SRR19787768?show=reads
+RUN wget https://ftp.sra.ebi.ac.uk/vol1/fastq/SRR197/068/SRR19787768/SRR19787768_1.fastq.gz && \
+ NanoPlot --fastq SRR19787768_1.fastq.gz --log --N50 -o /data/nanoplot-test && \
+ ls -lh /data/nanoplot-test && \
+ cat /data/nanoplot-test/NanoStats.txt