From adc36858e83c7e6db3e7309bf6b20d610d622798 Mon Sep 17 00:00:00 2001 From: Erin Young Date: Thu, 14 Mar 2024 18:31:51 +0000 Subject: [PATCH 01/13] adding multiqc 1.21 --- README.md | 2 +- multiqc/1.21/Dockerfile | 59 +++++++++++++++++++++++++++++++++++++++++ multiqc/1.21/README.md | 13 +++++++++ 3 files changed, 73 insertions(+), 1 deletion(-) create mode 100644 multiqc/1.21/Dockerfile create mode 100644 multiqc/1.21/README.md diff --git a/README.md b/README.md index e881cf123..576aceda6 100644 --- a/README.md +++ b/README.md @@ -200,7 +200,7 @@ 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/1.21/Dockerfile b/multiqc/1.21/Dockerfile new file mode 100644 index 000000000..441d8e0ec --- /dev/null +++ b/multiqc/1.21/Dockerfile @@ -0,0 +1,59 @@ +FROM ubuntu:jammy as app + +ARG MULTIQC_VER="1.21" + +# 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/1.21/README.md b/multiqc/1.21/README.md new file mode 100644 index 000000000..879cb9cd8 --- /dev/null +++ b/multiqc/1.21/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" . +``` From c7223da8718187684b8b78448af8fb1f910b4d01 Mon Sep 17 00:00:00 2001 From: Young Date: Wed, 15 May 2024 11:31:19 -0600 Subject: [PATCH 02/13] Update to 1.22 --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 576aceda6..ff08228d0 100644 --- a/README.md +++ b/README.md @@ -200,7 +200,7 @@ 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 | From 5357373856a7dfd32f1cd9bdff59c3b915706f3a Mon Sep 17 00:00:00 2001 From: Young Date: Wed, 15 May 2024 11:31:48 -0600 Subject: [PATCH 03/13] Update to 1.22 --- multiqc/{1.21 => 1.22}/Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) rename multiqc/{1.21 => 1.22}/Dockerfile (98%) diff --git a/multiqc/1.21/Dockerfile b/multiqc/1.22/Dockerfile similarity index 98% rename from multiqc/1.21/Dockerfile rename to multiqc/1.22/Dockerfile index 441d8e0ec..e4bb3c4f7 100644 --- a/multiqc/1.21/Dockerfile +++ b/multiqc/1.22/Dockerfile @@ -1,6 +1,6 @@ FROM ubuntu:jammy as app -ARG MULTIQC_VER="1.21" +ARG MULTIQC_VER="1.22" # metadata LABEL base.image="ubuntu:jammy" From 2c93d4c35e419b45940d7d7873fdcdfc7e88dfd1 Mon Sep 17 00:00:00 2001 From: Young Date: Wed, 15 May 2024 11:32:09 -0600 Subject: [PATCH 04/13] Rename README.md for 1.22 --- multiqc/{1.21 => 1.22}/README.md | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename multiqc/{1.21 => 1.22}/README.md (100%) diff --git a/multiqc/1.21/README.md b/multiqc/1.22/README.md similarity index 100% rename from multiqc/1.21/README.md rename to multiqc/1.22/README.md From dba79839926cbdfaa391a6183f9d403b8293844a Mon Sep 17 00:00:00 2001 From: Young Date: Fri, 17 May 2024 12:00:06 -0600 Subject: [PATCH 05/13] Update README.md for 1.22.1 --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index ff08228d0..f927a4f53 100644 --- a/README.md +++ b/README.md @@ -200,7 +200,7 @@ 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) |
  • 0.1.3
| 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) |
  • 2.16.2
  • 2.17.6
  • 2.19.0
  • 2.22.0
  • 2.22.1
  • 2.23.0
  • [2.23.0-2023-07 (databases updated July 2023)](mlst/2.23.0-2023-07/)
  • [2.23.0-2023-08 (databases updated Aug 2023)](mlst/2.23.0-2023-08/)
  • [2.23.0-2024-01 (databases updated Jan 2024)](mlst/2.23.0-2024-01/)
  • [2.23.0-2024-03 (databases updated March 2024)](mlst/2.23.0-2024-03/)
| 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) |
  • 1r2.3
| 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) |
  • 1.7
  • [1.8](./multiqc/1.8/)
  • [1.18](./multiqc/1.18/)
  • [1.19](./multiqc/1.19/)
  • [1.22](./multiqc/1.22/)
| 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) |
  • 1.7
  • [1.8](./multiqc/1.8/)
  • [1.18](./multiqc/1.18/)
  • [1.19](./multiqc/1.19/)
  • [1.22.1](./multiqc/1.22.1/)
| 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)
  • [0.12.2 (Mykrobe) & 2.0 (Genotyphi) & v20210201 (sonneityping)](mykrobe/0.12.2/)
  • [0.13.0](./mykrobe/0.13.0)
| 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](./nanoplot/1.27.0/)
  • [1.29.0](./nanoplot/1.29.0/)
  • [1.30.1](./nanoplot/1.30.1/)
  • [1.32.0](./nanoplot/1.32.0/)
  • [1.33.0](./nanoplot/1.33.0/)
  • [1.40.0](./nanoplot/1.40.0/)
  • [1.41.6](./nanoplot/1.41.6/)
  • [1.42.0](./nanoplot/1.42.0/)
| https://github.com/wdecoster/NanoPlot | From 98e0fc8abfb5450cb5106f30b3e941588512d1d5 Mon Sep 17 00:00:00 2001 From: Young Date: Fri, 17 May 2024 12:00:31 -0600 Subject: [PATCH 06/13] Update to 1.22.1 --- multiqc/{1.22 => 1.22.1}/Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) rename multiqc/{1.22 => 1.22.1}/Dockerfile (98%) diff --git a/multiqc/1.22/Dockerfile b/multiqc/1.22.1/Dockerfile similarity index 98% rename from multiqc/1.22/Dockerfile rename to multiqc/1.22.1/Dockerfile index e4bb3c4f7..ba14a088e 100644 --- a/multiqc/1.22/Dockerfile +++ b/multiqc/1.22.1/Dockerfile @@ -1,6 +1,6 @@ FROM ubuntu:jammy as app -ARG MULTIQC_VER="1.22" +ARG MULTIQC_VER="1.22.1" # metadata LABEL base.image="ubuntu:jammy" From 80beea0166ebaa6bf3404e07b8a5842ac43d9eb0 Mon Sep 17 00:00:00 2001 From: Young Date: Fri, 17 May 2024 12:00:59 -0600 Subject: [PATCH 07/13] Rename README.md to README.md --- multiqc/{1.22 => 1.22.1}/README.md | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename multiqc/{1.22 => 1.22.1}/README.md (100%) diff --git a/multiqc/1.22/README.md b/multiqc/1.22.1/README.md similarity index 100% rename from multiqc/1.22/README.md rename to multiqc/1.22.1/README.md From d57eb280ed8cff58c71286f1a2fb4656821d7ff2 Mon Sep 17 00:00:00 2001 From: Young Date: Wed, 12 Jun 2024 15:19:00 -0600 Subject: [PATCH 08/13] Update README for multiqc 1.22.2 --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index f927a4f53..0de53f14c 100644 --- a/README.md +++ b/README.md @@ -200,7 +200,7 @@ 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) |
  • 0.1.3
| 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) |
  • 2.16.2
  • 2.17.6
  • 2.19.0
  • 2.22.0
  • 2.22.1
  • 2.23.0
  • [2.23.0-2023-07 (databases updated July 2023)](mlst/2.23.0-2023-07/)
  • [2.23.0-2023-08 (databases updated Aug 2023)](mlst/2.23.0-2023-08/)
  • [2.23.0-2024-01 (databases updated Jan 2024)](mlst/2.23.0-2024-01/)
  • [2.23.0-2024-03 (databases updated March 2024)](mlst/2.23.0-2024-03/)
| 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) |
  • 1r2.3
| 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) |
  • 1.7
  • [1.8](./multiqc/1.8/)
  • [1.18](./multiqc/1.18/)
  • [1.19](./multiqc/1.19/)
  • [1.22.1](./multiqc/1.22.1/)
| 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) |
  • [1.7](./multiqc/1.7/)
  • [1.8](./multiqc/1.8/)
  • [1.18](./multiqc/1.18/)
  • [1.19](./multiqc/1.19/)
  • [1.22.2](./multiqc/1.22.2/)
| 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)
  • [0.12.2 (Mykrobe) & 2.0 (Genotyphi) & v20210201 (sonneityping)](mykrobe/0.12.2/)
  • [0.13.0](./mykrobe/0.13.0)
| 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](./nanoplot/1.27.0/)
  • [1.29.0](./nanoplot/1.29.0/)
  • [1.30.1](./nanoplot/1.30.1/)
  • [1.32.0](./nanoplot/1.32.0/)
  • [1.33.0](./nanoplot/1.33.0/)
  • [1.40.0](./nanoplot/1.40.0/)
  • [1.41.6](./nanoplot/1.41.6/)
  • [1.42.0](./nanoplot/1.42.0/)
| https://github.com/wdecoster/NanoPlot | From fb56b4b7b26eb52a3a2e5cbb04589cc21310fe83 Mon Sep 17 00:00:00 2001 From: Young Date: Wed, 12 Jun 2024 15:19:41 -0600 Subject: [PATCH 09/13] Rename README.md to README.md --- multiqc/{1.22.1 => 1.22.2}/README.md | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename multiqc/{1.22.1 => 1.22.2}/README.md (100%) diff --git a/multiqc/1.22.1/README.md b/multiqc/1.22.2/README.md similarity index 100% rename from multiqc/1.22.1/README.md rename to multiqc/1.22.2/README.md From 98d829806e0b9804f5f25048158422bd43ffbb9c Mon Sep 17 00:00:00 2001 From: Young Date: Wed, 12 Jun 2024 15:21:46 -0600 Subject: [PATCH 10/13] Update to 1.22.2 and remove pandoc --- multiqc/{1.22.1 => 1.22.2}/Dockerfile | 10 +++------- 1 file changed, 3 insertions(+), 7 deletions(-) rename multiqc/{1.22.1 => 1.22.2}/Dockerfile (89%) diff --git a/multiqc/1.22.1/Dockerfile b/multiqc/1.22.2/Dockerfile similarity index 89% rename from multiqc/1.22.1/Dockerfile rename to multiqc/1.22.2/Dockerfile index ba14a088e..743772cf2 100644 --- a/multiqc/1.22.1/Dockerfile +++ b/multiqc/1.22.2/Dockerfile @@ -1,6 +1,6 @@ FROM ubuntu:jammy as app -ARG MULTIQC_VER="1.22.1" +ARG MULTIQC_VER="1.22.2" # metadata LABEL base.image="ubuntu:jammy" @@ -21,11 +21,7 @@ RUN apt-get update && apt-get install -y \ git \ python3 \ python3-dev \ - python3-pip \ - locales \ - pandoc \ - texlive-xetex && \ - locale-gen en_US.UTF-8 && \ + python3-pip && \ apt-get clean && apt-get autoclean && rm -rf /var/lib/apt/lists/* # install multiqc @@ -55,5 +51,5 @@ 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 && \ +RUN multiqc /test/MultiQC_TestData/data/modules/BUSCO --filename multiqc_report2.html -o multiqc_data2 && \ ls multiqc_data2/multiqc_report2.html multiqc_data2/multiqc_report2_data From a3271de238451117f91d79024a5ceb18a7c074a7 Mon Sep 17 00:00:00 2001 From: Young Date: Wed, 12 Jun 2024 15:24:59 -0600 Subject: [PATCH 11/13] removing more things from apt-get --- multiqc/1.22.2/Dockerfile | 11 ++++------- 1 file changed, 4 insertions(+), 7 deletions(-) diff --git a/multiqc/1.22.2/Dockerfile b/multiqc/1.22.2/Dockerfile index 743772cf2..1932c4e8d 100644 --- a/multiqc/1.22.2/Dockerfile +++ b/multiqc/1.22.2/Dockerfile @@ -17,10 +17,6 @@ LABEL maintainer.email="eriny@utah.gov" # install remaining dependencies ARG DEBIAN_FRONTEND=noninteractive RUN apt-get update && apt-get install -y \ - wget \ - git \ - python3 \ - python3-dev \ python3-pip && \ apt-get clean && apt-get autoclean && rm -rf /var/lib/apt/lists/* @@ -39,6 +35,9 @@ WORKDIR /data # testing layer starts here FROM app as test +# getting git +RUN apt-get update && apt-get install -y git + # to ensure multiqc is in PATH RUN multiqc --help @@ -46,10 +45,8 @@ RUN multiqc --help RUN mkdir /test WORKDIR /test -# getting multiqc test data and testing pandoc +# getting multiqc test data 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 && \ - ls multiqc_data2/multiqc_report2.html multiqc_data2/multiqc_report2_data From 241e6781b915aad37e83dd4c2a0510153fdc5d3d Mon Sep 17 00:00:00 2001 From: Kutluhan Incekara <46578029+Kincekara@users.noreply.github.com> Date: Thu, 13 Jun 2024 09:22:50 -0400 Subject: [PATCH 12/13] Update Dockerfile update website and license remove ARG debian interactive add --no-cache-dir to pip remove redundant PATH=$PATH --- multiqc/1.22.2/Dockerfile | 16 ++++++---------- 1 file changed, 6 insertions(+), 10 deletions(-) diff --git a/multiqc/1.22.2/Dockerfile b/multiqc/1.22.2/Dockerfile index 1932c4e8d..66ac73df8 100644 --- a/multiqc/1.22.2/Dockerfile +++ b/multiqc/1.22.2/Dockerfile @@ -8,24 +8,20 @@ LABEL dockerfile.version="1" LABEL software="MultiQC" LABEL software.version="${MULTIQC_VER}" LABEL description="Aggregate bioinformatics results across many samples into a single report." -LABEL website="https://github.com/ewels/MultiQC" -LABEL license="https://github.com/ewels/MultiQC/blob/master/LICENSE" +LABEL website="https://github.com/MultiQC/MultiQC" +LABEL license="https://github.com/MultiQC/MultiQC/blob/main/LICENSE" LABEL maintainer="Erin Young" LABEL maintainer.email="eriny@utah.gov" -# Although... let's be honest. Most of this is copied and pasted from Abigail Shockey -# install remaining dependencies -ARG DEBIAN_FRONTEND=noninteractive -RUN apt-get update && apt-get install -y \ +RUN apt-get update && apt-get install --no-install-recommends -y \ python3-pip && \ apt-get clean && apt-get autoclean && rm -rf /var/lib/apt/lists/* # install multiqc -RUN pip3 install "multiqc==${MULTIQC_VER}" +RUN pip3 install --no-cache-dir "multiqc==${MULTIQC_VER}" -# add pandoc to path -ENV PATH="${PATH}" \ - LC_ALL='C.UTF-8' LANG='C.UTF-8' +ENV LC_ALL='C.UTF-8' \ + LANG='C.UTF-8' CMD multiqc --help From 99a2e49de4b40efb982fce6e81427c108d1fe5ac Mon Sep 17 00:00:00 2001 From: Kutluhan Incekara <46578029+Kincekara@users.noreply.github.com> Date: Thu, 13 Jun 2024 09:35:24 -0400 Subject: [PATCH 13/13] Update README.md --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 0de53f14c..64b1c6072 100644 --- a/README.md +++ b/README.md @@ -200,7 +200,7 @@ 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) |
  • 0.1.3
| 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) |
  • 2.16.2
  • 2.17.6
  • 2.19.0
  • 2.22.0
  • 2.22.1
  • 2.23.0
  • [2.23.0-2023-07 (databases updated July 2023)](mlst/2.23.0-2023-07/)
  • [2.23.0-2023-08 (databases updated Aug 2023)](mlst/2.23.0-2023-08/)
  • [2.23.0-2024-01 (databases updated Jan 2024)](mlst/2.23.0-2024-01/)
  • [2.23.0-2024-03 (databases updated March 2024)](mlst/2.23.0-2024-03/)
| 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) |
  • 1r2.3
| 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) |
  • [1.7](./multiqc/1.7/)
  • [1.8](./multiqc/1.8/)
  • [1.18](./multiqc/1.18/)
  • [1.19](./multiqc/1.19/)
  • [1.22.2](./multiqc/1.22.2/)
| 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) |
  • [1.7](./multiqc/1.7/)
  • [1.8](./multiqc/1.8/)
  • [1.18](./multiqc/1.18/)
  • [1.19](./multiqc/1.19/)
  • [1.22.2](./multiqc/1.22.2/)
| https://github.com/MultiQC/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)
  • [0.12.2 (Mykrobe) & 2.0 (Genotyphi) & v20210201 (sonneityping)](mykrobe/0.12.2/)
  • [0.13.0](./mykrobe/0.13.0)
| 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](./nanoplot/1.27.0/)
  • [1.29.0](./nanoplot/1.29.0/)
  • [1.30.1](./nanoplot/1.30.1/)
  • [1.32.0](./nanoplot/1.32.0/)
  • [1.33.0](./nanoplot/1.33.0/)
  • [1.40.0](./nanoplot/1.40.0/)
  • [1.41.6](./nanoplot/1.41.6/)
  • [1.42.0](./nanoplot/1.42.0/)
| https://github.com/wdecoster/NanoPlot |