diff --git a/README.md b/README.md index dcb5c7be1..3a419526f 100644 --- a/README.md +++ b/README.md @@ -187,7 +187,7 @@ To learn more about the docker pull rate limits and the open source software pro | [minipolish](https://hub.docker.com/r/staphb/minipolish)
[![docker pulls](https://badgen.net/docker/pulls/staphb/minipolish)](https://hub.docker.com/r/staphb/minipolish) | | https://github.com/rrwick/Minipolish | | [mlst](https://hub.docker.com/r/staphb/mlst)
[![docker pulls](https://badgen.net/docker/pulls/staphb/mlst)](https://hub.docker.com/r/staphb/mlst) | | https://github.com/tseemann/mlst | | [Mugsy](https://hub.docker.com/r/staphb/mugsy)
[![docker pulls](https://badgen.net/docker/pulls/staphb/mugsy)](https://hub.docker.com/r/staphb/mugsy) | | http://mugsy.sourceforge.net/ | -| [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 | +| [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 | diff --git a/multiqc/1.18/Dockerfile b/multiqc/1.18/Dockerfile new file mode 100644 index 000000000..68d8d0955 --- /dev/null +++ b/multiqc/1.18/Dockerfile @@ -0,0 +1,60 @@ +FROM ubuntu:jammy as app + +ARG MULTIQC_VER="1.18" + +# metadata +LABEL base.image="ubuntu:jammy" +LABEL dockerfile.version="1" +LABEL software="MultiQC" +LABEL software.version="${MULTIQC_VER}" +LABEL description="Aggregate bioinformatics results across many samples into a single report." +LABEL website="https://github.com/ewels/MultiQC" +LABEL license="https://github.com/ewels/MultiQC/blob/master/LICENSE" +LABEL maintainer="Erin Young" +LABEL maintainer.email="eriny@utah.gov" +# Although... let's be honest. Most of this is copied and pasted from Abigail Shockey + +# install remaining dependencies +ARG DEBIAN_FRONTEND=noninteractive +RUN apt-get update && apt-get install -y \ + wget \ + git \ + python3 \ + python3-dev \ + python3-pip \ + locales \ + pandoc \ + texlive-xetex && \ + locale-gen en_US.UTF-8 && \ + apt-get clean && apt-get autoclean && rm -rf /var/lib/apt/lists/* + +# install multiqc +RUN pip3 install "multiqc==${MULTIQC_VER}" + + +# add pandoc to path +ENV PATH="${PATH}" \ + LC_ALL='C.UTF-8' LANG='C.UTF-8' + +CMD multiqc --help + +RUN mkdir /data +WORKDIR /data + +# testing layer starts here +FROM app as test + +# to ensure multiqc is in PATH +RUN multiqc --help + +# set working directory so that all test inputs & outputs are kept in /test +RUN mkdir /test +WORKDIR /test + +# getting multiqc test data and testing pandoc +RUN git clone https://github.com/ewels/MultiQC_TestData && \ + multiqc . && \ + ls multiqc_report.html + +RUN multiqc /test/MultiQC_TestData/data/modules/BUSCO --filename multiqc_report2.html -o multiqc_data2 --pdf && \ + ls multiqc_data2/multiqc_report2.html multiqc_data2/multiqc_report2_data diff --git a/multiqc/1.18/README.md b/multiqc/1.18/README.md new file mode 100644 index 000000000..879cb9cd8 --- /dev/null +++ b/multiqc/1.18/README.md @@ -0,0 +1,13 @@ +# MultiQC container + +Main tool : [MultiQC](https://multiqc.info/) + +Aggregate results from bioinformatics analyses across many samples into a single report. + +Full documentation: [Docs] (https://multiqc.info/docs/) + +# Example Usage + +``` +multiqc -f --cl_config "prokka_fn_snames: True" . +```