From c8db6af6107f9ec8289efd4e3752a2d3521fecea Mon Sep 17 00:00:00 2001 From: Kincekara Date: Tue, 24 Oct 2023 13:32:08 +0000 Subject: [PATCH 01/11] add quast 5.2.0 --- README.md | 2 +- quast/5.2.0/Dockerfile | 110 +++++++++++++++++++++++++++++++++++++++++ quast/5.2.0/README.md | 36 ++++++++++++++ 3 files changed, 147 insertions(+), 1 deletion(-) create mode 100644 quast/5.2.0/Dockerfile create mode 100644 quast/5.2.0/README.md diff --git a/README.md b/README.md index e5d6b0f1b..ebb1c43b8 100644 --- a/README.md +++ b/README.md @@ -205,7 +205,7 @@ To learn more about the docker pull rate limits and the open source software pro | [Porechop](https://hub.docker.com/r/staphb/porechop/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/porechop)](https://hub.docker.com/r/staphb/porechop) | | https://github.com/rrwick/Porechop | | [Prokka](https://hub.docker.com/r/staphb/prokka/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/prokka)](https://hub.docker.com/r/staphb/prokka) | | https://github.com/tseemann/prokka | | [pyGenomeViz](https://hub.docker.com/r/staphb/pygenomeviz/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/pygenomeviz)](https://hub.docker.com/r/staphb/pygenomeviz) | | https://github.com/moshi4/pyGenomeViz | -| [QUAST](https://hub.docker.com/r/staphb/quast/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/quast)](https://hub.docker.com/r/staphb/quast) | | https://github.com/ablab/quast | +| [QUAST](https://hub.docker.com/r/staphb/quast/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/quast)](https://hub.docker.com/r/staphb/quast) | | https://github.com/ablab/quast | | [QuickSNP](https://hub.docker.com/r/staphb/quicksnp/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/quicksnp)](https://hub.docker.com/r/staphb/quicksnp) | | https://github.com/k-florek/QuickSNP | | [racon](https://hub.docker.com/r/staphb/racon)
[![docker pulls](https://badgen.net/docker/pulls/staphb/racon)](https://hub.docker.com/r/staphb/racon)| | https://github.com/lbcb-sci/racon
https://github.com/isovic/racon (ARCHIVED) | | [rasusa](https://hub.docker.com/r/staphb/rasusa/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/rasusa)](https://hub.docker.com/r/staphb/rasusa) | | https://github.com/mbhall88/rasusa | diff --git a/quast/5.2.0/Dockerfile b/quast/5.2.0/Dockerfile new file mode 100644 index 000000000..9147b5ed4 --- /dev/null +++ b/quast/5.2.0/Dockerfile @@ -0,0 +1,110 @@ +ARG QUAST_VER="5.2.0" + +## Builder ## +FROM ubuntu:focal as builder + +ARG QUAST_VER + +# define timezone to avoid build stalls +ENV TZ=America/New_York +RUN ln -snf /usr/share/zoneinfo/$TZ /etc/localtime && echo $TZ > /etc/timezone + +RUN apt-get update && apt-get install --no-install-recommends -y \ + wget \ + python2 \ + perl \ + cpanminus \ + g++ \ + make \ + openjdk-8-jre-headless \ + r-base \ + pkg-config \ + libfreetype6-dev \ + libpng-dev \ + libboost-all-dev \ + locales &&\ + locale-gen en_US.UTF-8 &&\ + cpanm Time::HiRes &&\ + apt-get autoclean &&\ + rm -rf /var/lib/apt/lists/* + +# python dependencies +RUN update-alternatives --install /usr/bin/python python /usr/bin/python2 1 &&\ + wget https://bootstrap.pypa.io/pip/2.7/get-pip.py && python get-pip.py &&\ + pip install --no-cache matplotlib simplejson joblib + +# install quast +RUN wget https://github.com/ablab/quast/releases/download/quast_${QUAST_VER}/quast-${QUAST_VER}.tar.gz && \ + tar -xzf quast-${QUAST_VER}.tar.gz && \ + rm -rf quast-${QUAST_VER}.tar.gz && \ + cd /quast-${QUAST_VER} && \ + /quast-${QUAST_VER}/setup.py install + +# add GRIDSS for SV detection +ADD https://github.com/ablab/quast/raw/master/external_tools/gridss/gridss-1.4.1.jar /quast-${QUAST_VER}/quast_libs/gridss/ + +## App ## +FROM ubuntu:focal as app + +ARG QUAST_VER + +LABEL base.image="ubuntu:focal" +LABEL dockerfile.version="1" +LABEL software="QUAST" +LABEL software.version=${QUAST_VER} +LABEL description="Genome assembly evaluation tool" +LABEL website="https://github.com/ablab/quast" +LABEL license="https://github.com/ablab/quast/blob/master/LICENSE.txt" +LABEL maintainer="Curtis Kapsak" +LABEL maintainer.email="pjx8@cdc.gov" +LABEL maintainer2="Kutluhan Incekara" +LABEL maintainer2.email="kutluhan.incekara@ct.gov" + +# define timezone to avoid build stalls +ENV TZ=America/New_York +RUN ln -snf /usr/share/zoneinfo/$TZ /etc/localtime && echo $TZ > /etc/timezone + +# install only necessary programs and libraries to run quast +RUN apt-get update && apt-get install --no-install-recommends -y \ + wget \ + python2 \ + perl \ + openjdk-8-jre-headless \ + r-base \ + libidn11 \ + locales &&\ + locale-gen en_US.UTF-8 &&\ + apt-get autoclean &&\ + rm -rf /var/lib/apt/lists/* + +# python dependencies +RUN update-alternatives --install /usr/bin/python python /usr/bin/python2 1 &&\ + wget https://bootstrap.pypa.io/pip/2.7/get-pip.py && python get-pip.py &&\ + pip install --no-cache matplotlib simplejson joblib +# copy quast and compiled tools +COPY --from=builder /quast-${QUAST_VER} /quast-${QUAST_VER} +# copy compiled Time::HiRes perl module +COPY --from=builder /usr/local/lib/x86_64-linux-gnu/perl/5.30.0/Time/ /usr/local/lib/x86_64-linux-gnu/perl/5.30.0/Time/ + +ENV LC_ALL=C +ENV PATH=$PATH:/quast-${QUAST_VER} + +CMD quast.py --help && quast-lg.py --help && metaquast.py --help + +WORKDIR /data + +## Test ## +FROM app as test +# test quast +RUN quast.py --test-sv && mv ./quast_test_output/ ./quast_test_sv_output/ +# test quast-lg +RUN quast-lg.py --test && mv ./quast_test_output/ ./quast_test_lg_output/ +# test metaquast +RUN metaquast.py --test +# check logs +RUN tail -n5 ./quast_test_sv_output/quast.log &&\ + tail -n5 ./quast_test_lg_output/quast.log &&\ + tail -n5 ./quast_test_output/metaquast.log + +# Note 1: "Warnings are GenMark license related. They disappear when a valid licence is provided." +# Note 2: "metaquast.py --test-no-ref" throws error related Krona plot (known bug of Quast 5.2.0) diff --git a/quast/5.2.0/README.md b/quast/5.2.0/README.md new file mode 100644 index 000000000..160c6f3e4 --- /dev/null +++ b/quast/5.2.0/README.md @@ -0,0 +1,36 @@ +# QUAST container + +Main tool: [QUAST](https://github.com/ablab/quast) + +Code repository: https://github.com/ablab/quast + +Additional tools: +- gridss: 1.4.1 + + +Basic information on how to use this tool: +- executable: quast.py +- help: --help +- version: --version +- description: Genome assembly evaluation tool + +Additional information: + +You need a license key if you want to use GeneMark with Quast!
+The key can be downloaded from http://exon.gatech.edu/GeneMark/license_download.cgi page (GeneMark is free for non-commercial use). +You should choose GeneMarkS-T LINUX 64. Download your license key and add it to your data folder or another folder you will bind to the container. Inside the container, copy the key to your home folder. +``` +cp /data/gm_key_64 ~/.gm_key +``` +Full documentation: https://quast.sourceforge.net/docs/manual.html + +## Example Usage + +```bash +# basic statistics without reference +quast.py contigs.fasta +# genome evaluation with reference +quast.py contigs.fasta -r reference.fasta.gz -g genes.gff +# metagenomic assemblies +metaquast.py contigs_1 contigs_2 ... -r reference_1,reference_2,reference_3,... +``` \ No newline at end of file From 10a570aa3e7ebd794af4fc019cdd9693d6d156d6 Mon Sep 17 00:00:00 2001 From: Kate Prussing Date: Tue, 24 Oct 2023 13:24:27 -0400 Subject: [PATCH 02/11] 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**
  • 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 6286414a3bd360f1440afc3fc0607529ea5e856b Mon Sep 17 00:00:00 2001 From: Kate Prussing Date: Tue, 24 Oct 2023 13:25:15 -0400 Subject: [PATCH 03/11] 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 04/11] 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 05/11] 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 06/11] 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 07/11] 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 08/11] 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 09/11] 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 8782c9fcd2011e16c389c8f2f7ea7258ec6c88a7 Mon Sep 17 00:00:00 2001 From: Young Date: Tue, 24 Oct 2023 14:04:24 -0600 Subject: [PATCH 10/11] Added hyperlink --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index ebb1c43b8..c1f19bcfd 100644 --- a/README.md +++ b/README.md @@ -205,7 +205,7 @@ To learn more about the docker pull rate limits and the open source software pro | [Porechop](https://hub.docker.com/r/staphb/porechop/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/porechop)](https://hub.docker.com/r/staphb/porechop) |
  • 0.2.4
| https://github.com/rrwick/Porechop | | [Prokka](https://hub.docker.com/r/staphb/prokka/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/prokka)](https://hub.docker.com/r/staphb/prokka) |
  • 1.13.4
  • 1.14.0
  • 1.14.5
  • 1.14.6
| https://github.com/tseemann/prokka | | [pyGenomeViz](https://hub.docker.com/r/staphb/pygenomeviz/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/pygenomeviz)](https://hub.docker.com/r/staphb/pygenomeviz) |
  • 0.2.2
  • 0.3.2
  • [0.4.2](pygenomeviz/0.4.2/)
| https://github.com/moshi4/pyGenomeViz | -| [QUAST](https://hub.docker.com/r/staphb/quast/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/quast)](https://hub.docker.com/r/staphb/quast) |
  • 5.0.0
  • 5.0.2
  • 5.2.0
| https://github.com/ablab/quast | +| [QUAST](https://hub.docker.com/r/staphb/quast/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/quast)](https://hub.docker.com/r/staphb/quast) |
  • 5.0.0
  • 5.0.2
  • [5.2.0](./quast/5.2.0)
| https://github.com/ablab/quast | | [QuickSNP](https://hub.docker.com/r/staphb/quicksnp/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/quicksnp)](https://hub.docker.com/r/staphb/quicksnp) |
  • 1.0.1
| https://github.com/k-florek/QuickSNP | | [racon](https://hub.docker.com/r/staphb/racon)
[![docker pulls](https://badgen.net/docker/pulls/staphb/racon)](https://hub.docker.com/r/staphb/racon)|
  • 1.4.3
  • 1.4.20
| https://github.com/lbcb-sci/racon
https://github.com/isovic/racon (ARCHIVED) | | [rasusa](https://hub.docker.com/r/staphb/rasusa/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/rasusa)](https://hub.docker.com/r/staphb/rasusa) |
  • 0.1.0
  • 0.2.0
  • 0.3.0
  • 0.6.0
  • 0.7.0
| https://github.com/mbhall88/rasusa | From 3b679e2023c76f92bd9d4a2eafb13382d2210132 Mon Sep 17 00:00:00 2001 From: Kate Prussing Date: Wed, 25 Oct 2023 08:25:19 -0400 Subject: [PATCH 11/11] 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)