Merge pull request #771 from kprus/master

Update NanoPlot to 1.41.6

README.md

@@ -182,7 +182,7 @@ To learn more about the docker pull rate limits and the open source software pro
 | [MultiQC](https://hub.docker.com/r/staphb/multiqc) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/multiqc)](https://hub.docker.com/r/staphb/multiqc) | <ul><li>1.7</li><li>1.8</li></ul> | https://github.com/ewels/MultiQC |
 | [Mummer](https://hub.docker.com/r/staphb/mummer) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/mummer)](https://hub.docker.com/r/staphb/mummer) | <ul><li>4.0.0</li><li>4.0.0 + RGDv2</li><li>4.0.0 + RGDv2 + gnuplot</li></ul> | https://github.com/mummer4/mummer |
 | [Mykrobe + Genotyphi + sonneityping](https://hub.docker.com/r/staphb/mykrobe) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/mykrobe)](https://hub.docker.com/r/staphb/mykrobe) | <ul><li>0.11.0 (Mykrobe) & 1.9.1 (Genotyphi) </li><li>0.12.1 (Mykrobe) & 1.9.1 (Genotyphi) & v20210201 (sonneityping) </li><li>0.12.1 (Mykrobe) & 2.0 (Genotyphi) & v20210201 (sonneityping) </li></ul> | https://github.com/Mykrobe-tools/mykrobe <br/> https://github.com/typhoidgenomics/genotyphi <br/> https://github.com/katholt/sonneityping |
-| [NanoPlot](https://hub.docker.com/r/staphb/nanoplot) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/nanoplot)](https://hub.docker.com/r/staphb/nanoplot) | <ul><li>1.27.0</li><li>1.29.0</li><li>1.30.1</li><li>1.32.0</li><li>1.33.0</li><li>1.40.0</li></ul> | https://github.com/wdecoster/NanoPlot |
+| [NanoPlot](https://hub.docker.com/r/staphb/nanoplot) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/nanoplot)](https://hub.docker.com/r/staphb/nanoplot) | <ul><li>1.27.0</li><li>1.29.0</li><li>1.30.1</li><li>1.32.0</li><li>1.33.0</li><li>1.40.0</li><li>[1.41.6](nanoplot/1.41.6/)</li></ul> | https://github.com/wdecoster/NanoPlot |
 | [ngmaster](https://hub.docker.com/r/staphb/ngmaster) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/ngmaster)](https://hub.docker.com/r/staphb/ngmaster) | <ul><li>0.5.8</li><li>1.0.0</li></ul> | https://github.com/MDU-PHL/ngmaster |
 | [NCBI Datasets](https://hub.docker.com/r/staphb/ncbi-datasets) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/ncbi-datasets)](https://hub.docker.com/r/staphb/ncbi-datasets) | <details><summary> Click to see all datasets versions </summary> **datasets versions** <ul><li>13.31.0</li><li>13.35.0</li><li>13.43.2</li><li>14.0.0</li><li>14.3.0</li><li>14.7.0</li><li>14.13.2</li><li>14.20.0</li><li>[14.27.0](ncbi-datasets/14.27.0/)</li><li>[15.1.0](ncbi-datasets/15.1.0/)</li><li>[15.2.0](ncbi-datasets/15.2.0/)</li><li>[15.11.0](ncbi-datasets/15.11.0/)</li></ul> | [https://github.com/ncbi/datasets](https://github.com/ncbi/datasets) <br/>[https://www.ncbi.nlm.nih.gov/datasets/docs/v1/](https://www.ncbi.nlm.nih.gov/datasets/docs/v1/) |
 | [NCBI AMRFinderPlus](https://hub.docker.com/r/staphb/ncbi-amrfinderplus) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/ncbi-amrfinderplus)](https://hub.docker.com/r/staphb/ncbi-amrfinderplus) | **AMRFinderPlus & database verion** <details><summary> Click to see AMRFinderplus v3.11.4 and older versions! </summary> <ul><li>3.1.1b</li><li>3.8.4</li><li>3.8.28</li><li>3.9.3</li><li>3.9.8</li><li>3.10.1</li><li>3.10.5</li><li>3.10.16</li><li>3.10.20</li><li>3.10.24</li><li>3.10.30</li><li>3.10.36</li><li>3.10.42</li><li>3.11.2 & 2022-12-19.1</li><li>[3.11.2 & 2023-02-23.1](ncbi-amrfinderplus/3.11.2-2023-02-23.1/)</li><li>[3.11.4 & 2023-02-23.1](ncbi-amrfinderplus/3.11.4-2023-02-23.1/)</li></ul> </details> <ul><li>[3.11.8 & 2023-02-23.1](ncbi-amrfinderplus/3.11.8-2023-02-23.1/)</li><li>[3.11.11 & 2023-04-17.1](ncbi-amrfinderplus/3.11.11-2023-04-17.1)</li><li>[3.11.14 & 2023-04-17.1](ncbi-amrfinderplus/3.11.14-2023-04-17.1/)</li><li>[3.11.17 & 2023-07-13.2](ncbi-amrfinderplus/3.11.17-2023-07-13.2/)</li><li>[3.11.18 & 2023-08-08.2](ncbi-amrfinderplus/3.11.18-2023-08-08.2/)</li><li>[3.11.20 & 2023-09-26.1](ncbi-amrfinderplus/3.11.20-2023-09-26.1/)</li></ul> | [https://github.com/ncbi/amr](https://github.com/ncbi/amr) |
@@ -313,3 +313,4 @@ Each Dockerfile lists the author(s)/maintainer(s) as a metadata `LABEL`, but the
   * [@cimendes](https://github.com/cimendes)
   * [@golden75](https://github.com/golden75)
   * [@Kincekara](https://github.com/Kincekara)
+  * [@kprus](https://github.com/kprus)

nanoplot/1.41.6/Dockerfile

@@ -0,0 +1,56 @@
+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="${NANOPLOT_VER}"
+LABEL description="Plotting suite for Oxford Nanopore sequencing data and alignments"
+LABEL website="https://github.com/wdecoster/NanoPlot"
+LABEL license="https://github.com/wdecoster/NanoPlot/blob/master/LICENSE"
+LABEL maintainer="Curtis Kapsak"
+LABEL maintainer.email="[email protected]"
+LABEL maintainer2="Kate Prussing"
+LABEL maintainer2.email="[email protected]"
+
+# install dependencies via apt; cleanup apt garbage; set locale to en_US.UTF-8
+RUN apt-get update && apt-get install -y zlib1g-dev \
+ bzip2 \
+ libbz2-dev \
+ liblzma-dev \
+ libcurl4-gnutls-dev \
+ libncurses5-dev \
+ libssl-dev \
+ python3 \
+ python3-pip \
+ python3-setuptools \
+ locales && \
+ locale-gen en_US.UTF-8 && \
+ apt-get autoclean && rm -rf /var/lib/apt/lists/*
+
+# for singularity compatibility
+ENV LC_ALL=C
+
+# install NanoPlot via pypi using pip3; make /data directory
+RUN pip3 install matplotlib psutil requests NanoPlot==${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

nanoplot/1.41.6/README.md

@@ -0,0 +1,19 @@
+# NanoPlot container
+
+Main tool : [NanoPlot](https://github.com/wdecoster/NanoPlot)
+
+Additional tools:
+
+- nanomath 1.3.0
+- nanoget 1.19.3
+
+Full documentation: [https://github.com/wdecoster/NanoPlot](https://github.com/wdecoster/NanoPlot)
+
+Plotting tool for long read sequencing data and alignments.
+
+## Example Usage
+
+```bash
+# pass in the sequencing_summary.txt file produced by Guppy/Dorado basecaller
+NanoPlot --summary sequencing_summary.txt --N50 --loglength -t 4 -o nanoplot-out
+```