StaPH-B · erinyoung · Dec 26, 2024 · Dec 27, 2024 · Dec 27, 2024 · Dec 27, 2024
diff --git 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) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/ncbi-table2asn)](https://hub.docker.com/r/staphb/ncbi-table2asn) | <ul><li>[1.26.678](./ncbi-table2asn/1.26.678/)</li><li>[1.28.943](./ncbi-table2asn/1.28.943/)</li><li>[1.28.1021](./ncbi-table2asn/1021/)</li></ul> | [https://www.ncbi.nlm.nih.gov/genbank/table2asn/](https://www.ncbi.nlm.nih.gov/genbank/table2asn/) <br/>[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) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/ontime)](https://hub.docker.com/r/staphb/ontime) | <ul><li>[0.2.3](ontime/0.2.3/)</li><li>[0.3.1](ontime/0.3.1/)</li></ul> | https://github.com/mbhall88/ontime |
 | [OrthoFinder](https://hub.docker.com/r/staphb/orthofinder) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/orthofinder)](https://hub.docker.com/r/staphb/orthofinder) | <ul><li>2.17</li></ul> | https://github.com/davidemms/OrthoFinder |
-| [Panaroo](https://hub.docker.com/r/staphb/panaroo)  <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/panaroo)](https://hub.docker.com/r/staphb/panaroo) | <ul><li>[1.2.10](panaroo/1.2.10/)</li><li>[1.3.4](panaroo/1.3.4/)</li><li>[1.5.0](./panaroo/1.5.0/)</li></ul>| https://github.com/gtonkinhill/panaroo |
+| [Panaroo](https://hub.docker.com/r/staphb/panaroo)  <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/panaroo)](https://hub.docker.com/r/staphb/panaroo) | <ul><li>[1.2.10](./build-files/panaroo/1.2.10/)</li><li>[1.3.4](./build-files/panaroo/1.3.4/)</li><li>[1.5.0](./build-files/panaroo/1.5.0/)</li><li>[1.5.1](./build-files/panaroo/1.5.1/)</li></ul>| https://github.com/gtonkinhill/panaroo |
 | [pandas](https://hub.docker.com/r/staphb/pandas)  <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/pandas)](https://hub.docker.com/r/staphb/pandas) | <ul><li>[2.2.3](pandas/2.2.3/)</li></ul>| https://github.com/pandas-dev/pandas |
 | [pango_aliasor](https://hub.docker.com/r/staphb/pango_aliasor)  <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/pango_aliasor)](https://hub.docker.com/r/staphb/pango_aliasor) | <ul><li>[0.3.0](./pango_aliasor/0.3.0/)</li></ul>| https://github.com/corneliusroemer/pango_aliasor |
 | [Pangolin](https://hub.docker.com/r/staphb/pangolin) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/pangolin)](https://hub.docker.com/r/staphb/pangolin) | <details><summary> Click to see Pangolin v4.2 and older versions! </summary> **Pangolin version & pangoLEARN data release date** <ul><li>1.1.14</li><li>2.0.4 & 2020-07-20</li><li>2.0.5 & 2020-07-20</li><li>2.1.1 & 2020-12-17</li><li>2.1.3 & 2020-12-17</li><li>2.1.6 & 2021-01-06</li><li>2.1.7 & 2021-01-11</li><li>2.1.7 & 2021-01-20</li><li>2.1.8 & 2021-01-22</li><li>2.1.10 & 2021-02-01</li><li>2.1.11 & 2021-02-01</li><li>2.1.11 & 2021-02-05</li><li>2.2.1 & 2021-02-06</li><li>2.2.2 & 2021-02-06</li><li>2.2.2 & 2021-02-11</li><li>2.2.2 & 2021-02-12</li><li>2.3.0 & 2021-02-12</li><li>2.3.0 & 2021-02-18</li><li>2.3.0 & 2021-02-21</li><li>2.3.2 & 2021-02-21</li><li>2.3.3 & 2021-03-16</li><li>2.3.4 & 2021-03-16</li><li>2.3.5 & 2021-03-16</li><li>2.3.6 & 2021-03-16</li><li>2.3.6 & 2021-03-29</li><li>2.3.8 & 2021-04-01</li><li>2.3.8 & 2021-04-14</li><li>2.3.8 & 2021-04-21</li><li>2.3.8 & 2021-04-23</li><li>2.4 & 2021-04-28</li><li>2.4.1 & 2021-04-28</li><li>2.4.2 & 2021-04-28</li><li>2.4.2 & 2021-05-10</li><li>2.4.2 & 2021-05-11</li><li>2.4.2 & 2021-05-19</li><li>3.0.5 & 2021-06-05</li><li>3.1.3 & 2021-06-15</li><li>3.1.5 & 2021-06-15</li><li>3.1.5 & 2021-07-07-2</li><li>3.1.7 & 2021-07-09</li><li>3.1.8 & 2021-07-28</li><li>3.1.10 & 2021-07-28</li><li>3.1.11 & 2021-08-09</li><li>3.1.11 & 2021-08-24</li><li>3.1.11 & 2021-09-17</li><li>3.1.14 & 2021-09-28</li><li>3.1.14 & 2021-10-13</li><li>3.1.16 & 2021-10-18</li><li>3.1.16 & 2021-11-04</li><li>3.1.16 & 2021-11-09</li><li>3.1.16 & 2021-11-18</li><li>3.1.16 & 2021-11-25</li><li>3.1.17 & 2021-11-25</li><li>3.1.17 & 2021-12-06</li><li>3.1.17 & 2022-01-05</li><li>3.1.18 & 2022-01-20</li><li>3.1.19 & 2022-01-20</li><li>3.1.20 & 2022-02-02</li><li>3.1.20 & 2022-02-28</li></ul> **Pangolin version & pangolin-data version** <ul><li>4.0 & 1.2.133</li><li>4.0.1 & 1.2.133</li><li>4.0.2 & 1.2.133</li><li>4.0.3 & 1.2.133</li><li>4.0.4 & 1.2.133</li><li>4.0.5 & 1.3</li><li>4.0.6 & 1.6</li><li>4.0.6 & 1.8</li><li>4.0.6 & 1.9</li><li>4.1.1 & 1.11</li><li>4.1.2 & 1.12</li><li>4.1.2 & 1.13</li><li>4.1.2 & 1.14</li><li>4.1.3 & 1.15.1</li><li>4.1.3 & 1.16</li><li>4.1.3 & 1.17</li><li>4.2 & 1.18</li><li>4.2 & 1.18.1</li><li>4.2 & 1.18.1.1</li><li>4.2 & 1.19</li></ul> </details> **Pangolin version & pangolin-data version** <ul><li>[4.3 & 1.20](pangolin/4.3-pdata-1.20/)</li><li>[4.3 & 1.21](pangolin/4.3-pdata-1.21/)</li><li>[4.3.1 & 1.22](pangolin/4.3.1-pdata-1.22/)</li><li>[4.3.1 & 1.23](pangolin/4.3.1-pdata-1.23/)</li><li>[4.3.1 & 1.23.1](pangolin/4.3.1-pdata-1.23.1/)</li><li>[4.3.1 & 1.23.1 with XDG_CACHE_HOME=/tmp](pangolin/4.3.1-pdata-1.23.1-1/)</li><li>[4.3.1 & 1.24](pangolin/4.3.1-pdata-1.24/)</li><li>[4.3.1 & 1.25.1](pangolin/4.3.1-pdata-1.25.1/)</li><li>[4.3.1 & 1.26](pangolin/4.3.1-pdata-1.26/)</li><li>[4.3.1 & 1.27](pangolin/4.3.1-pdata-1.27/)</li><li>[4.3.1 & 1.28](pangolin/4.3.1-pdata-1.28/)</li><li>[4.3.1 & 1.28.1](pangolin/4.3.1-pdata-1.28.1/)</li><li>[4.3.1 & 1.29](pangolin/4.3.1-pdata-1.29/)</li><li>[4.3.1 & 1.30](pangolin/4.3.1-pdata-1.30/)</li><li>[4.3.1 & 1.31](pangolin/4.3.1-pdata-1.31/)</li></ul> |  https://github.com/cov-lineages/pangolin<br/>https://github.com/cov-lineages/pangoLEARN<br/>https://github.com/cov-lineages/pango-designation<br/>https://github.com/cov-lineages/scorpio<br/>https://github.com/cov-lineages/constellations<br/>https://github.com/cov-lineages/lineages (archived)<br/>https://github.com/hCoV-2019/pangolin (archived) |

diff --git a/build-files/panaroo/1.5.1/Dockerfile b/build-files/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="[email protected]"
+LABEL maintainer2="Erin Young"
+LABEL maintainer2.email="[email protected]"
+
+# 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/build-files/panaroo/1.5.1/README.md b/build-files/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
+```