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Merge pull request #771 from kprus/master
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Update NanoPlot to 1.41.6
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erinyoung authored Oct 25, 2023
2 parents 1a1796b + 3b679e2 commit 4e7064b
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3 changes: 2 additions & 1 deletion README.md
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Expand Up @@ -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) |
Expand Down Expand Up @@ -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)
56 changes: 56 additions & 0 deletions 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]"
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
19 changes: 19 additions & 0 deletions nanoplot/1.41.6/README.md
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# 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
```

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