From 10a570aa3e7ebd794af4fc019cdd9693d6d156d6 Mon Sep 17 00:00:00 2001 From: Kate Prussing Date: Tue, 24 Oct 2023 13:24:27 -0400 Subject: [PATCH 1/9] Update README.md --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index e5d6b0f1b..b007977f6 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!
  • 3.1.1b
  • 3.8.4
  • 3.8.28
  • 3.9.3
  • 3.9.8
  • 3.10.1
  • 3.10.5
  • 3.10.16
  • 3.10.20
  • 3.10.24
  • 3.10.30
  • 3.10.36
  • 3.10.42
  • 3.11.2 & 2022-12-19.1
  • [3.11.2 & 2023-02-23.1](ncbi-amrfinderplus/3.11.2-2023-02-23.1/)
  • [3.11.4 & 2023-02-23.1](ncbi-amrfinderplus/3.11.4-2023-02-23.1/)
| [https://github.com/ncbi/amr](https://github.com/ncbi/amr) | From 6286414a3bd360f1440afc3fc0607529ea5e856b Mon Sep 17 00:00:00 2001 From: Kate Prussing Date: Tue, 24 Oct 2023 13:25:15 -0400 Subject: [PATCH 2/9] Update README.md --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index b007977f6..edf44fb0c 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) |
  • 1.7
  • 1.8
| 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) |
  • 4.0.0
  • 4.0.0 + RGDv2
  • 4.0.0 + RGDv2 + gnuplot
| 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) |
  • 0.11.0 (Mykrobe) & 1.9.1 (Genotyphi)
  • 0.12.1 (Mykrobe) & 1.9.1 (Genotyphi) & v20210201 (sonneityping)
  • 0.12.1 (Mykrobe) & 2.0 (Genotyphi) & v20210201 (sonneityping)
| 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) |
  • 1.27.0
  • 1.29.0
  • 1.30.1
  • 1.32.0
  • 1.33.0
  • 1.40.0
  • 1.41.6.0
| 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) |
  • 1.27.0
  • 1.29.0
  • 1.30.1
  • 1.32.0
  • 1.33.0
  • 1.40.0
  • 1.41.6
| 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) |
  • 0.5.8
  • 1.0.0
| 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**
  • 13.31.0
  • 13.35.0
  • 13.43.2
  • 14.0.0
  • 14.3.0
  • 14.7.0
  • 14.13.2
  • 14.20.0
  • [14.27.0](ncbi-datasets/14.27.0/)
  • [15.1.0](ncbi-datasets/15.1.0/)
  • [15.2.0](ncbi-datasets/15.2.0/)
  • [15.11.0](ncbi-datasets/15.11.0/)
| [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!
  • 3.1.1b
  • 3.8.4
  • 3.8.28
  • 3.9.3
  • 3.9.8
  • 3.10.1
  • 3.10.5
  • 3.10.16
  • 3.10.20
  • 3.10.24
  • 3.10.30
  • 3.10.36
  • 3.10.42
  • 3.11.2 & 2022-12-19.1
  • [3.11.2 & 2023-02-23.1](ncbi-amrfinderplus/3.11.2-2023-02-23.1/)
  • [3.11.4 & 2023-02-23.1](ncbi-amrfinderplus/3.11.4-2023-02-23.1/)
  • [3.11.8 & 2023-02-23.1](ncbi-amrfinderplus/3.11.8-2023-02-23.1/)
  • [3.11.11 & 2023-04-17.1](ncbi-amrfinderplus/3.11.11-2023-04-17.1)
  • [3.11.14 & 2023-04-17.1](ncbi-amrfinderplus/3.11.14-2023-04-17.1/)
  • [3.11.17 & 2023-07-13.2](ncbi-amrfinderplus/3.11.17-2023-07-13.2/)
  • [3.11.18 & 2023-08-08.2](ncbi-amrfinderplus/3.11.18-2023-08-08.2/)
  • [3.11.20 & 2023-09-26.1](ncbi-amrfinderplus/3.11.20-2023-09-26.1/)
| [https://github.com/ncbi/amr](https://github.com/ncbi/amr) | From 68f42b14691db847dd196f69a5d17936a7d011e7 Mon Sep 17 00:00:00 2001 From: Kate Prussing Date: Tue, 24 Oct 2023 13:28:02 -0400 Subject: [PATCH 3/9] Create Dockerfile --- nanoplot/1.41.6/Dockerfile | 54 ++++++++++++++++++++++++++++++++++++++ 1 file changed, 54 insertions(+) create mode 100644 nanoplot/1.41.6/Dockerfile diff --git a/nanoplot/1.41.6/Dockerfile b/nanoplot/1.41.6/Dockerfile new file mode 100644 index 000000000..aff09156a --- /dev/null +++ b/nanoplot/1.41.6/Dockerfile @@ -0,0 +1,54 @@ +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="${NANOPLOT_VER}" +LABEL description="Plotting suite for Oxford Nanopore sequencing data and alignments" +LABEL website="https://github.com/wdecoster/NanoPlot" +LABEL license="https://github.com/wdecoster/NanoPlot/blob/master/LICENSE" +LABEL maintainer="Curtis Kapsak" +LABEL maintainer.email="kapsakcj@gmail.com" + +# install dependencies via apt; cleanup apt garbage; set locale to en_US.UTF-8 +RUN apt-get update && apt-get install -y zlib1g-dev \ + bzip2 \ + libbz2-dev \ + liblzma-dev \ + libcurl4-gnutls-dev \ + libncurses5-dev \ + libssl-dev \ + python3 \ + python3-pip \ + python3-setuptools \ + locales && \ + locale-gen en_US.UTF-8 && \ + apt-get autoclean && rm -rf /var/lib/apt/lists/* + +# for singularity compatibility +ENV LC_ALL=C + +# install NanoPlot via pypi using pip3; make /data directory +RUN pip3 install matplotlib psutil requests NanoPlot==${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 From 82ea63610eab15f47d0e0bdf33a316914cb03c4b Mon Sep 17 00:00:00 2001 From: Kate Prussing Date: Tue, 24 Oct 2023 13:42:30 -0400 Subject: [PATCH 4/9] Update Dockerfile --- nanoplot/1.41.6/Dockerfile | 2 ++ 1 file changed, 2 insertions(+) diff --git a/nanoplot/1.41.6/Dockerfile b/nanoplot/1.41.6/Dockerfile index aff09156a..ad1e0de8d 100644 --- a/nanoplot/1.41.6/Dockerfile +++ b/nanoplot/1.41.6/Dockerfile @@ -12,6 +12,8 @@ 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 maintainer="Kate Prussing" +LABEL maintainer.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 \ From 1a2302358a2db840ed86b4a897871f047c959724 Mon Sep 17 00:00:00 2001 From: Kate Prussing Date: Tue, 24 Oct 2023 13:44:06 -0400 Subject: [PATCH 5/9] Create README.md --- nanoplot/1.41.6/README.md | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) create mode 100644 nanoplot/1.41.6/README.md diff --git a/nanoplot/1.41.6/README.md b/nanoplot/1.41.6/README.md new file mode 100644 index 000000000..c37f9f1a4 --- /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 1.2.1 +- nanoget 1.16.1 + +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 +``` From 71416f2a3b72b4fc9f915de68c839c9f1762fef4 Mon Sep 17 00:00:00 2001 From: Kate Prussing Date: Tue, 24 Oct 2023 13:46:41 -0400 Subject: [PATCH 6/9] Update README.md --- nanoplot/1.41.6/README.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/nanoplot/1.41.6/README.md b/nanoplot/1.41.6/README.md index c37f9f1a4..110b10c2e 100644 --- a/nanoplot/1.41.6/README.md +++ b/nanoplot/1.41.6/README.md @@ -4,8 +4,8 @@ Main tool : [NanoPlot](https://github.com/wdecoster/NanoPlot) Additional tools: -- nanomath 1.2.1 -- nanoget 1.16.1 +- nanomath 1.3.0 +- nanoget 1.19.3 Full documentation: [https://github.com/wdecoster/NanoPlot](https://github.com/wdecoster/NanoPlot) From d1290cd047c11ea5164ca7db39cdf5ec7152e2f0 Mon Sep 17 00:00:00 2001 From: Kate Prussing Date: Tue, 24 Oct 2023 14:10:35 -0400 Subject: [PATCH 7/9] Update Dockerfile --- nanoplot/1.41.6/Dockerfile | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/nanoplot/1.41.6/Dockerfile b/nanoplot/1.41.6/Dockerfile index ad1e0de8d..f4de5929f 100644 --- a/nanoplot/1.41.6/Dockerfile +++ b/nanoplot/1.41.6/Dockerfile @@ -12,8 +12,8 @@ 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 maintainer="Kate Prussing" -LABEL maintainer.email="catharine.prussing@health.ny.gov" +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 \ From bcb44e822224b89bcf379096257d5983f75fde9f Mon Sep 17 00:00:00 2001 From: Young Date: Tue, 24 Oct 2023 14:00:46 -0600 Subject: [PATCH 8/9] Added hyperlink --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index edf44fb0c..dfae39975 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) |
  • 1.7
  • 1.8
| 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) |
  • 4.0.0
  • 4.0.0 + RGDv2
  • 4.0.0 + RGDv2 + gnuplot
| 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) |
  • 0.11.0 (Mykrobe) & 1.9.1 (Genotyphi)
  • 0.12.1 (Mykrobe) & 1.9.1 (Genotyphi) & v20210201 (sonneityping)
  • 0.12.1 (Mykrobe) & 2.0 (Genotyphi) & v20210201 (sonneityping)
| 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) |
  • 1.27.0
  • 1.29.0
  • 1.30.1
  • 1.32.0
  • 1.33.0
  • 1.40.0
  • 1.41.6
| 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) |
  • 1.27.0
  • 1.29.0
  • 1.30.1
  • 1.32.0
  • 1.33.0
  • 1.40.0
  • [1.41.6](nanoplot/1.41.6/)
| 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) |
  • 0.5.8
  • 1.0.0
| 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**
  • 13.31.0
  • 13.35.0
  • 13.43.2
  • 14.0.0
  • 14.3.0
  • 14.7.0
  • 14.13.2
  • 14.20.0
  • [14.27.0](ncbi-datasets/14.27.0/)
  • [15.1.0](ncbi-datasets/15.1.0/)
  • [15.2.0](ncbi-datasets/15.2.0/)
  • [15.11.0](ncbi-datasets/15.11.0/)
| [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!
  • 3.1.1b
  • 3.8.4
  • 3.8.28
  • 3.9.3
  • 3.9.8
  • 3.10.1
  • 3.10.5
  • 3.10.16
  • 3.10.20
  • 3.10.24
  • 3.10.30
  • 3.10.36
  • 3.10.42
  • 3.11.2 & 2022-12-19.1
  • [3.11.2 & 2023-02-23.1](ncbi-amrfinderplus/3.11.2-2023-02-23.1/)
  • [3.11.4 & 2023-02-23.1](ncbi-amrfinderplus/3.11.4-2023-02-23.1/)
  • [3.11.8 & 2023-02-23.1](ncbi-amrfinderplus/3.11.8-2023-02-23.1/)
  • [3.11.11 & 2023-04-17.1](ncbi-amrfinderplus/3.11.11-2023-04-17.1)
  • [3.11.14 & 2023-04-17.1](ncbi-amrfinderplus/3.11.14-2023-04-17.1/)
  • [3.11.17 & 2023-07-13.2](ncbi-amrfinderplus/3.11.17-2023-07-13.2/)
  • [3.11.18 & 2023-08-08.2](ncbi-amrfinderplus/3.11.18-2023-08-08.2/)
  • [3.11.20 & 2023-09-26.1](ncbi-amrfinderplus/3.11.20-2023-09-26.1/)
| [https://github.com/ncbi/amr](https://github.com/ncbi/amr) | From 3b679e2023c76f92bd9d4a2eafb13382d2210132 Mon Sep 17 00:00:00 2001 From: Kate Prussing Date: Wed, 25 Oct 2023 08:25:19 -0400 Subject: [PATCH 9/9] Update README.md --- README.md | 1 + 1 file changed, 1 insertion(+) diff --git a/README.md b/README.md index dfae39975..895c4b086 100644 --- a/README.md +++ b/README.md @@ -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)