diff --git a/README.md b/README.md index c1f19bcfd..3e11280ed 100644 --- a/README.md +++ b/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)
[![docker pulls](https://badgen.net/docker/pulls/staphb/multiqc)](https://hub.docker.com/r/staphb/multiqc) | | https://github.com/ewels/MultiQC | | [Mummer](https://hub.docker.com/r/staphb/mummer)
[![docker pulls](https://badgen.net/docker/pulls/staphb/mummer)](https://hub.docker.com/r/staphb/mummer) | | https://github.com/mummer4/mummer | | [Mykrobe + Genotyphi + sonneityping](https://hub.docker.com/r/staphb/mykrobe)
[![docker pulls](https://badgen.net/docker/pulls/staphb/mykrobe)](https://hub.docker.com/r/staphb/mykrobe) | | https://github.com/Mykrobe-tools/mykrobe
https://github.com/typhoidgenomics/genotyphi
https://github.com/katholt/sonneityping | -| [NanoPlot](https://hub.docker.com/r/staphb/nanoplot)
[![docker pulls](https://badgen.net/docker/pulls/staphb/nanoplot)](https://hub.docker.com/r/staphb/nanoplot) | | https://github.com/wdecoster/NanoPlot | +| [NanoPlot](https://hub.docker.com/r/staphb/nanoplot)
[![docker pulls](https://badgen.net/docker/pulls/staphb/nanoplot)](https://hub.docker.com/r/staphb/nanoplot) | | https://github.com/wdecoster/NanoPlot | | [ngmaster](https://hub.docker.com/r/staphb/ngmaster)
[![docker pulls](https://badgen.net/docker/pulls/staphb/ngmaster)](https://hub.docker.com/r/staphb/ngmaster) | | https://github.com/MDU-PHL/ngmaster | | [NCBI Datasets](https://hub.docker.com/r/staphb/ncbi-datasets)
[![docker pulls](https://badgen.net/docker/pulls/staphb/ncbi-datasets)](https://hub.docker.com/r/staphb/ncbi-datasets) |
Click to see all datasets versions **datasets versions** | [https://github.com/ncbi/datasets](https://github.com/ncbi/datasets)
[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)
[![docker pulls](https://badgen.net/docker/pulls/staphb/ncbi-amrfinderplus)](https://hub.docker.com/r/staphb/ncbi-amrfinderplus) | **AMRFinderPlus & database verion**
Click to see AMRFinderplus v3.11.4 and older versions!
| [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) diff --git a/nanoplot/1.41.6/Dockerfile b/nanoplot/1.41.6/Dockerfile new file mode 100644 index 000000000..f4de5929f --- /dev/null +++ b/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="${NANOPLOT_VER}" +LABEL description="Plotting suite for Oxford Nanopore sequencing data and alignments" +LABEL website="https://github.com/wdecoster/NanoPlot" +LABEL license="https://github.com/wdecoster/NanoPlot/blob/master/LICENSE" +LABEL maintainer="Curtis Kapsak" +LABEL maintainer.email="kapsakcj@gmail.com" +LABEL maintainer2="Kate Prussing" +LABEL maintainer2.email="catharine.prussing@health.ny.gov" + +# install dependencies via apt; cleanup apt garbage; set locale to en_US.UTF-8 +RUN apt-get update && apt-get install -y zlib1g-dev \ + bzip2 \ + libbz2-dev \ + liblzma-dev \ + libcurl4-gnutls-dev \ + libncurses5-dev \ + libssl-dev \ + python3 \ + python3-pip \ + python3-setuptools \ + locales && \ + locale-gen en_US.UTF-8 && \ + apt-get autoclean && rm -rf /var/lib/apt/lists/* + +# for singularity compatibility +ENV LC_ALL=C + +# install NanoPlot via pypi using pip3; make /data directory +RUN pip3 install matplotlib psutil requests NanoPlot==${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 diff --git a/nanoplot/1.41.6/README.md b/nanoplot/1.41.6/README.md new file mode 100644 index 000000000..110b10c2e --- /dev/null +++ b/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 +```