Updated Poppunk to version 2.7.8

README.md

@@ -272,7 +272,7 @@ To learn more about the docker pull rate limits and the open source software pro
 | [pod5](https://hub.docker.com/r/staphb/pod5/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/pod5)](https://hub.docker.com/r/staphb/pod5) | <details><summary>Click to see all versions</summary> <ul><li>[0.3.23](./build-files/pod5/0.3.23/)</li><li>[0.3.27](./build-files/pod5/0.3.27/)</li><li>[0.3.34](./build-files/pod5/0.3.34/)</li></ul> </details> | https://github.com/nanoporetech/pod5-file-format |
 | [PolkaPox](https://hub.docker.com/r/staphb/polkapox/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/polkapox)](https://hub.docker.com/r/staphb/polkapox) | <details><summary>Click to see all versions</summary> <ul><li>[1.0.0-beta](./build-files/polkapox/1.0.0-beta/)</li></ul> </details> | https://github.com/CDCgov/polkapox |
 | [polypolish](https://hub.docker.com/r/staphb/polypolish/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/polypolish)](https://hub.docker.com/r/staphb/polypolish) | <details><summary>Click to see all versions</summary> <ul><li>[0.5.0](./build-files/polypolish/0.5.0/)</li><li>[0.6.0](./build-files/polypolish/0.6.0/)</li><li>[0.6.0-bwa](./build-files/polypolish/0.6.0-bwa/)</li><li>[0.6.1](./build-files/polypolish/0.6.1/)</li></ul> </details> | https://github.com/rrwick/Polypolish |
-| [PopPUNK](https://hub.docker.com/r/staphb/poppunk/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/poppunk)](https://hub.docker.com/r/staphb/poppunk) | <details><summary>Click to see all versions</summary> <ul><li>[2.4.0](./build-files/poppunk/2.4.0/)</li><li>[2.5.0](./build-files/poppunk/2.5.0/)</li><li>[2.6.0](./build-files/poppunk/2.6.0/)</li><li>[2.6.2](./build-files/poppunk/2.6.2/)</li><li>[2.6.3](./build-files/poppunk/2.6.3/)</li><li>[2.6.5](./build-files/poppunk/2.6.5/)</li><li>[2.7.5](./build-files/poppunk/2.7.5/)</li><li>[2.7.6](./build-files/poppunk/2.7.6/)</li><li>[2.7.7](./build-files/poppunk/2.7.7/)</li></ul> </details> | https://github.com/bacpop/PopPUNK |
+| [PopPUNK](https://hub.docker.com/r/staphb/poppunk/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/poppunk)](https://hub.docker.com/r/staphb/poppunk) | <details><summary>Click to see all versions</summary> <ul><li>[2.4.0](./build-files/poppunk/2.4.0/)</li><li>[2.5.0](./build-files/poppunk/2.5.0/)</li><li>[2.6.0](./build-files/poppunk/2.6.0/)</li><li>[2.6.2](./build-files/poppunk/2.6.2/)</li><li>[2.6.3](./build-files/poppunk/2.6.3/)</li><li>[2.6.5](./build-files/poppunk/2.6.5/)</li><li>[2.7.5](./build-files/poppunk/2.7.5/)</li><li>[2.7.6](./build-files/poppunk/2.7.6/)</li><li>[2.7.7](./build-files/poppunk/2.7.7/)</li><li>[2.7.8](./build-files/poppunk/2.7.8/)</li></ul> </details> | https://github.com/bacpop/PopPUNK |
 | [Porechop](https://hub.docker.com/r/staphb/porechop/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/porechop)](https://hub.docker.com/r/staphb/porechop) | <details><summary>Click to see all versions</summary> <ul><li>[0.2.4](./build-files/porechop/0.2.4/)</li></ul> </details> | https://github.com/rrwick/Porechop |
 | [PPanGGOLiN](https://hub.docker.com/r/staphb/ppanggolin/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/ppanggolin)](https://hub.docker.com/r/staphb/ppanggolin) | <details><summary>Click to see all versions</summary> <ul><li>[1.2.105](./build-files/ppanggolin/1.2.105/)</li><li>[2.0.3](./build-files/ppanggolin/2.0.3/)</li><li>[2.0.5](./build-files/ppanggolin/2.0.5/)</li><li>[2.1.2](./build-files/ppanggolin/2.1.2/)</li><li>[2.2.1](./build-files/ppanggolin/2.2.1/)</li><li>[2.2.4](./build-files/ppanggolin/2.2.4/)</li><li>[2.2.5](./build-files/ppanggolin/2.2.5/)</li><li>[2.2.6](./build-files/ppanggolin/2.2.6/)</li></ul> </details> | https://github.com/labgem/PPanGGOLiN |
 | [Primer3](https://hub.docker.com/r/staphb/primer3/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/primer3)](https://hub.docker.com/r/staphb/primer3) | <details><summary>Click to see all versions</summary> <ul><li>[2.3.4](./build-files/primer3/2.3.4/)</li><li>[2.6.1](./build-files/primer3/2.6.1/)</li></ul> </details> | https://github.com/primer3-org/primer3 |

build-files/poppunk/2.7.8/Dockerfile

@@ -0,0 +1,67 @@
+FROM mambaorg/micromamba:2.5.0-ubuntu24.04 AS app
+
+# Version arguments
+# ARG variables only persist during build time
+ARG POPPUNK_VERSION="2.7.8"
+
+# build and run as root users since micromamba image has 'mambauser' set as the $USER
+USER root
+# set workdir to default for building; set to /data at the end
+WORKDIR /
+
+LABEL base.image="mambaorg/micromamba:2.5.0-ubuntu24.04"
+LABEL dockerfile.version="1"
+LABEL software="PopPUNK"
+LABEL software.version=${POPPUNK_VERSION}
+LABEL description="POPulation Partitioning Using Nucleotide Kmers"
+LABEL website="https://github.com/bacpop/PopPUNK"
+LABEL license="https://github.com/bacpop/PopPUNK/blob/master/LICENSE"
+LABEL maintainer="Curtis Kapsak"
+LABEL maintainer.email="curtis.kapsak@theiagen.com"
+LABEL maintainer2="Harry Hung"
+LABEL maintainer2.email="ch31@sanger.ac.uk"
+
+# 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/*
+
+# Using an older version of setuptools. Current throws an error in the docker (Feb 2026)
+RUN micromamba create -n poppunk-env -c conda-forge -c bioconda \
+    poppunk=${POPPUNK_VERSION} \
+    setuptools=81.0.0 && \
+    micromamba clean -a -f -y
+
+# set the environment, put new conda env in PATH by default; set locales to UTF-8
+ENV PATH="/opt/conda/envs/poppunk-env/bin:${PATH}" \
+    LC_ALL=C.UTF-8
+
+# set working directory to /data
+WORKDIR /data
+
+CMD ["poppunk", "--help"]
+
+# new base for testing
+FROM app AS test
+
+# print out various help options and version
+RUN poppunk --help && \
+    poppunk_assign --help && \
+    poppunk_visualise --help && \
+    poppunk_mst --help && \
+    poppunk_references --help && \
+    poppunk_info --help && \
+    poppunk_mandrake --help && \
+    poppunk --version
+
+# Download 100 S. Pneumo assemblies from GPS Public Data on ENA
+# Build PopPUNK database from the assemblies
+# Assign clusters on the same assemblies using the built database
+# Compare the database clusters and assigned clusters of the assemblies
+RUN wget https://raw.githubusercontent.com/StaPH-B/docker-builds/refs/heads/master/build-files/poppunk/2.7.5/ftps.txt && \
+    wget https://raw.githubusercontent.com/StaPH-B/docker-builds/refs/heads/master/build-files/poppunk/2.7.5/test.sh && \
+    bash test.sh && cmp assigned.csv database.csv
+
+RUN micromamba list -n poppunk-env