From 503836e1ad4cba3290d278535ba81b2fa25432dd Mon Sep 17 00:00:00 2001 From: Erin Young Date: Thu, 26 Dec 2024 19:05:23 +0000 Subject: [PATCH 1/4] adding panaroo version 1.5.1 --- README.md | 2 +- panaroo/1.5.1/Dockerfile | 67 ++++++++++++++++++++++++++++++++++++++++ panaroo/1.5.1/README.md | 18 +++++++++++ 3 files changed, 86 insertions(+), 1 deletion(-) create mode 100644 panaroo/1.5.1/Dockerfile create mode 100644 panaroo/1.5.1/README.md diff --git a/README.md b/README.md index 8be427b5b..8d664c3a2 100644 --- a/README.md +++ b/README.md @@ -233,7 +233,7 @@ To learn more about the docker pull rate limits and the open source software pro | [NCBI table2asn](https://hub.docker.com/r/staphb/ncbi-table2asn)
[![docker pulls](https://badgen.net/docker/pulls/staphb/ncbi-table2asn)](https://hub.docker.com/r/staphb/ncbi-table2asn) | | [https://www.ncbi.nlm.nih.gov/genbank/table2asn/](https://www.ncbi.nlm.nih.gov/genbank/table2asn/)
[https://ftp.ncbi.nlm.nih.gov/asn1-converters/versions/2022-06-14/by_program/table2asn/](https://ftp.ncbi.nlm.nih.gov/asn1-converters/versions/2022-06-14/by_program/table2asn/) | | [ONTime](https://hub.docker.com/r/staphb/ontime)
[![docker pulls](https://badgen.net/docker/pulls/staphb/ontime)](https://hub.docker.com/r/staphb/ontime) | | https://github.com/mbhall88/ontime | | [OrthoFinder](https://hub.docker.com/r/staphb/orthofinder)
[![docker pulls](https://badgen.net/docker/pulls/staphb/orthofinder)](https://hub.docker.com/r/staphb/orthofinder) | | https://github.com/davidemms/OrthoFinder | -| [Panaroo](https://hub.docker.com/r/staphb/panaroo)
[![docker pulls](https://badgen.net/docker/pulls/staphb/panaroo)](https://hub.docker.com/r/staphb/panaroo) | | https://github.com/gtonkinhill/panaroo | +| [Panaroo](https://hub.docker.com/r/staphb/panaroo)
[![docker pulls](https://badgen.net/docker/pulls/staphb/panaroo)](https://hub.docker.com/r/staphb/panaroo) | | https://github.com/gtonkinhill/panaroo | | [pandas](https://hub.docker.com/r/staphb/pandas)
[![docker pulls](https://badgen.net/docker/pulls/staphb/pandas)](https://hub.docker.com/r/staphb/pandas) | | https://github.com/pandas-dev/pandas | | [pango_aliasor](https://hub.docker.com/r/staphb/pango_aliasor)
[![docker pulls](https://badgen.net/docker/pulls/staphb/pango_aliasor)](https://hub.docker.com/r/staphb/pango_aliasor) | | https://github.com/corneliusroemer/pango_aliasor | | [Pangolin](https://hub.docker.com/r/staphb/pangolin)
[![docker pulls](https://badgen.net/docker/pulls/staphb/pangolin)](https://hub.docker.com/r/staphb/pangolin) |
Click to see Pangolin v4.2 and older versions! **Pangolin version & pangoLEARN data release date** **Pangolin version & pangolin-data version**
**Pangolin version & pangolin-data version** | https://github.com/cov-lineages/pangolin
https://github.com/cov-lineages/pangoLEARN
https://github.com/cov-lineages/pango-designation
https://github.com/cov-lineages/scorpio
https://github.com/cov-lineages/constellations
https://github.com/cov-lineages/lineages (archived)
https://github.com/hCoV-2019/pangolin (archived) | diff --git a/panaroo/1.5.1/Dockerfile b/panaroo/1.5.1/Dockerfile new file mode 100644 index 000000000..a7615d4d1 --- /dev/null +++ b/panaroo/1.5.1/Dockerfile @@ -0,0 +1,67 @@ +FROM mambaorg/micromamba:1.5.7 AS app + +# Version arguments +# ARG variables only persist during build time +# THIS ARG ONLY USED FOR A LABEL. VERSION SPECIFIED IN PANAROO-ENVIRONMENT.YML +ARG PANAROO_SOFTWARE_VERSION="1.5.1" + +# build and run as root users since micromamba image has 'mambauser' set as the $USER +USER root +# set workdir to default for building; set to /data at the end +WORKDIR / + +LABEL base.image="mambaorg/micromamba:1.5.7" +LABEL dockerfile.version="1" +LABEL software="Panaroo" +LABEL software.version=${PANAROO_SOFTWARE_VERSION} +LABEL description="An updated pipeline for pangenome investigation" +LABEL website="https://github.com/gtonkinhill/panaroo" +LABEL license="https://github.com/gtonkinhill/panaroo/blob/master/LICENSE" +LABEL maintainer="Kevin Libuit" +LABEL maintainer.email="kevin.libuit@theiagen.com" +LABEL maintainer2="Erin Young" +LABEL maintainer2.email="eriny@utah.gov" + +# install dependencies; cleanup apt garbage +RUN apt-get update && apt-get install -y --no-install-recommends \ + wget \ + ca-certificates \ + procps && \ + apt-get autoclean && rm -rf /var/lib/apt/lists/* + +# Install Panaroo conda environment into base environment +# clean up conda garbage +# conda environment includes optional tools prokka, prank, mafft, clustal, and mash +RUN micromamba install -y -n base -c conda-forge -c bioconda -c defaults python=3.9 panaroo=${PANAROO_SOFTWARE_VERSION} && \ + micromamba clean -a -f -y + +# set the environment, put new conda env in PATH by default +ENV PATH="/opt/conda/bin:/opt/conda/envs/base/bin:${PATH}" \ + LC_ALL=C.UTF-8 + +# set working directory to /data +WORKDIR /data + +# set default command +CMD panaroo -h + +# new base for testing +FROM app AS test + +# checks to see if tool is in PATH +RUN panaroo --version && panaroo -h + +WORKDIR /test + +# Grab test data from 1.2.10 +RUN wget -q https://raw.githubusercontent.com/StaPH-B/docker-builds/master/panaroo/1.2.10/tests/ecoli_1.gff && \ + wget -q https://raw.githubusercontent.com/StaPH-B/docker-builds/master/panaroo/1.2.10/tests/ecoli_2.gff && \ + wget -q https://raw.githubusercontent.com/StaPH-B/docker-builds/master/panaroo/1.2.10/tests/gene_data.csv && \ + wget -q https://raw.githubusercontent.com/StaPH-B/docker-builds/master/panaroo/1.2.10/tests/summary_statistics.txt + +# Run Panaroo +RUN panaroo --clean-mode strict -i *.gff -o panaroo_results/ + +RUN head panaroo_results/summary_statistics.txt && \ + head summary_statistics.txt && \ + cmp summary_statistics.txt panaroo_results/summary_statistics.txt diff --git a/panaroo/1.5.1/README.md b/panaroo/1.5.1/README.md new file mode 100644 index 000000000..22ed4b599 --- /dev/null +++ b/panaroo/1.5.1/README.md @@ -0,0 +1,18 @@ +# Panaroo Container + +Main tool : [Panaroo](https://github.com/gtonkinhill/panaroo) + +Full documentation: https://gtonkinhill.github.io/panaroo/#/ + +Panaroo is an updated pipeline for pangenome investigation. + +[Tonkin-Hill G, MacAlasdair N, Ruis C, Weimann A, Horesh G, Lees JA, Gladstone RA, Lo S, Beaudoin C, Floto RA, Frost SDW, Corander J, Bentley SD, Parkhill J. 2020. Producing polished prokaryotic pangenomes with the Panaroo pipeline. Genome Biol 21:180.](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-020-02090-4) + + +## Example Usage + +```bash +# Using GFFs in the same format as output by Prokka run: +mkdir results +panaroo -i *.gff -o results --clean-mode strict +``` From 79299ebbb2e05a78b256d51204e574c42e8a80d7 Mon Sep 17 00:00:00 2001 From: Young Date: Fri, 27 Dec 2024 12:34:03 -0700 Subject: [PATCH 2/4] adjusted hyperlink path --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 8d664c3a2..10096e138 100644 --- a/README.md +++ b/README.md @@ -233,7 +233,7 @@ To learn more about the docker pull rate limits and the open source software pro | [NCBI table2asn](https://hub.docker.com/r/staphb/ncbi-table2asn)
[![docker pulls](https://badgen.net/docker/pulls/staphb/ncbi-table2asn)](https://hub.docker.com/r/staphb/ncbi-table2asn) | | [https://www.ncbi.nlm.nih.gov/genbank/table2asn/](https://www.ncbi.nlm.nih.gov/genbank/table2asn/)
[https://ftp.ncbi.nlm.nih.gov/asn1-converters/versions/2022-06-14/by_program/table2asn/](https://ftp.ncbi.nlm.nih.gov/asn1-converters/versions/2022-06-14/by_program/table2asn/) | | [ONTime](https://hub.docker.com/r/staphb/ontime)
[![docker pulls](https://badgen.net/docker/pulls/staphb/ontime)](https://hub.docker.com/r/staphb/ontime) | | https://github.com/mbhall88/ontime | | [OrthoFinder](https://hub.docker.com/r/staphb/orthofinder)
[![docker pulls](https://badgen.net/docker/pulls/staphb/orthofinder)](https://hub.docker.com/r/staphb/orthofinder) | | https://github.com/davidemms/OrthoFinder | -| [Panaroo](https://hub.docker.com/r/staphb/panaroo)
[![docker pulls](https://badgen.net/docker/pulls/staphb/panaroo)](https://hub.docker.com/r/staphb/panaroo) | | https://github.com/gtonkinhill/panaroo | +| [Panaroo](https://hub.docker.com/r/staphb/panaroo)
[![docker pulls](https://badgen.net/docker/pulls/staphb/panaroo)](https://hub.docker.com/r/staphb/panaroo) | | https://github.com/gtonkinhill/panaroo | | [pandas](https://hub.docker.com/r/staphb/pandas)
[![docker pulls](https://badgen.net/docker/pulls/staphb/pandas)](https://hub.docker.com/r/staphb/pandas) | | https://github.com/pandas-dev/pandas | | [pango_aliasor](https://hub.docker.com/r/staphb/pango_aliasor)
[![docker pulls](https://badgen.net/docker/pulls/staphb/pango_aliasor)](https://hub.docker.com/r/staphb/pango_aliasor) | | https://github.com/corneliusroemer/pango_aliasor | | [Pangolin](https://hub.docker.com/r/staphb/pangolin)
[![docker pulls](https://badgen.net/docker/pulls/staphb/pangolin)](https://hub.docker.com/r/staphb/pangolin) |
Click to see Pangolin v4.2 and older versions! **Pangolin version & pangoLEARN data release date**
  • 1.1.14
  • 2.0.4 & 2020-07-20
  • 2.0.5 & 2020-07-20
  • 2.1.1 & 2020-12-17
  • 2.1.3 & 2020-12-17
  • 2.1.6 & 2021-01-06
  • 2.1.7 & 2021-01-11
  • 2.1.7 & 2021-01-20
  • 2.1.8 & 2021-01-22
  • 2.1.10 & 2021-02-01
  • 2.1.11 & 2021-02-01
  • 2.1.11 & 2021-02-05
  • 2.2.1 & 2021-02-06
  • 2.2.2 & 2021-02-06
  • 2.2.2 & 2021-02-11
  • 2.2.2 & 2021-02-12
  • 2.3.0 & 2021-02-12
  • 2.3.0 & 2021-02-18
  • 2.3.0 & 2021-02-21
  • 2.3.2 & 2021-02-21
  • 2.3.3 & 2021-03-16
  • 2.3.4 & 2021-03-16
  • 2.3.5 & 2021-03-16
  • 2.3.6 & 2021-03-16
  • 2.3.6 & 2021-03-29
  • 2.3.8 & 2021-04-01
  • 2.3.8 & 2021-04-14
  • 2.3.8 & 2021-04-21
  • 2.3.8 & 2021-04-23
  • 2.4 & 2021-04-28
  • 2.4.1 & 2021-04-28
  • 2.4.2 & 2021-04-28
  • 2.4.2 & 2021-05-10
  • 2.4.2 & 2021-05-11
  • 2.4.2 & 2021-05-19
  • 3.0.5 & 2021-06-05
  • 3.1.3 & 2021-06-15
  • 3.1.5 & 2021-06-15
  • 3.1.5 & 2021-07-07-2
  • 3.1.7 & 2021-07-09
  • 3.1.8 & 2021-07-28
  • 3.1.10 & 2021-07-28
  • 3.1.11 & 2021-08-09
  • 3.1.11 & 2021-08-24
  • 3.1.11 & 2021-09-17
  • 3.1.14 & 2021-09-28
  • 3.1.14 & 2021-10-13
  • 3.1.16 & 2021-10-18
  • 3.1.16 & 2021-11-04
  • 3.1.16 & 2021-11-09
  • 3.1.16 & 2021-11-18
  • 3.1.16 & 2021-11-25
  • 3.1.17 & 2021-11-25
  • 3.1.17 & 2021-12-06
  • 3.1.17 & 2022-01-05
  • 3.1.18 & 2022-01-20
  • 3.1.19 & 2022-01-20
  • 3.1.20 & 2022-02-02
  • 3.1.20 & 2022-02-28
**Pangolin version & pangolin-data version**
  • 4.0 & 1.2.133
  • 4.0.1 & 1.2.133
  • 4.0.2 & 1.2.133
  • 4.0.3 & 1.2.133
  • 4.0.4 & 1.2.133
  • 4.0.5 & 1.3
  • 4.0.6 & 1.6
  • 4.0.6 & 1.8
  • 4.0.6 & 1.9
  • 4.1.1 & 1.11
  • 4.1.2 & 1.12
  • 4.1.2 & 1.13
  • 4.1.2 & 1.14
  • 4.1.3 & 1.15.1
  • 4.1.3 & 1.16
  • 4.1.3 & 1.17
  • 4.2 & 1.18
  • 4.2 & 1.18.1
  • 4.2 & 1.18.1.1
  • 4.2 & 1.19
**Pangolin version & pangolin-data version** | https://github.com/cov-lineages/pangolin
https://github.com/cov-lineages/pangoLEARN
https://github.com/cov-lineages/pango-designation
https://github.com/cov-lineages/scorpio
https://github.com/cov-lineages/constellations
https://github.com/cov-lineages/lineages (archived)
https://github.com/hCoV-2019/pangolin (archived) | From 83729fccb2456ed7e5ec7ba4b0cda58a639f7d36 Mon Sep 17 00:00:00 2001 From: Young Date: Fri, 27 Dec 2024 12:34:40 -0700 Subject: [PATCH 3/4] move to build-files --- {panaroo => build-files/panaroo}/1.5.1/Dockerfile | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename {panaroo => build-files/panaroo}/1.5.1/Dockerfile (100%) diff --git a/panaroo/1.5.1/Dockerfile b/build-files/panaroo/1.5.1/Dockerfile similarity index 100% rename from panaroo/1.5.1/Dockerfile rename to build-files/panaroo/1.5.1/Dockerfile From 129ba5bd32cbe7a688a28e601cbf96b48c316a0d Mon Sep 17 00:00:00 2001 From: Young Date: Fri, 27 Dec 2024 12:35:29 -0700 Subject: [PATCH 4/4] Rename panaroo/1.5.1/README.md to build-files/panaroo/1.5.1/README.md --- {panaroo => build-files/panaroo}/1.5.1/README.md | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename {panaroo => build-files/panaroo}/1.5.1/README.md (100%) diff --git a/panaroo/1.5.1/README.md b/build-files/panaroo/1.5.1/README.md similarity index 100% rename from panaroo/1.5.1/README.md rename to build-files/panaroo/1.5.1/README.md