diff --git a/README.md b/README.md index 9542b26c2..ea4f0994a 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) | @@ -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 | @@ -314,3 +314,5 @@ Each Dockerfile lists the author(s)/maintainer(s) as a metadata `LABEL`, but the * [@golden75](https://github.com/golden75) * [@Kincekara](https://github.com/Kincekara) * [@Haikelnb](https://github.com/Haikelnb) + * [@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 +``` 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