add plasmidfinder 3.0.3

README.md

@@ -267,7 +267,7 @@ To learn more about the docker pull rate limits and the open source software pro
 | [Piggy](https://hub.docker.com/r/staphb/piggy) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/piggy)](https://hub.docker.com/r/staphb/piggy) | <details><summary>Click to see all versions</summary> <ul><li>[1.5](./build-files/piggy/1.5/)</li></ul> </details> | https://github.com/harry-thorpe/piggy |
 | [Pilon](https://hub.docker.com/r/staphb/pilon) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/pilon)](https://hub.docker.com/r/staphb/pilon) | <details><summary>Click to see all versions</summary> <ul><li>[1.23.0](./build-files/pilon/1.23.0/)</li><li>[1.24](./build-files/pilon/1.24/)</li></ul> </details> | https://github.com/broadinstitute/pilon |
 | [Piranha](https://hub.docker.com/r/staphb/piranha) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/piranha)](https://hub.docker.com/r/staphb/piranha) | <details><summary>Click to see all versions</summary> <ul><li>[1.0.4](./build-files/piranha/1.0.4/)</li><li>[1.4.2](./build-files/piranha/1.4.2/)</li><li>[1.5.3](./build-files/piranha/1.5.3/)</li></ul> </details> | https://github.com/polio-nanopore/piranha |
-| [PlasmidFinder](https://hub.docker.com/r/staphb/plasmidfinder) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/plasmidfinder)](https://hub.docker.com/r/staphb/plasmidfinder) | <details><summary>Click to see all versions</summary> <ul><li>[2.1.6](./build-files/plasmidfinder/2.1.6/)</li><li>[2.1.6_2024-03-07](./build-files/plasmidfinder/2.1.6_2024-03-07/)</li><li>[2.1.6_2025-02-19](./build-files/plasmidfinder/2.1.6_2025-02-19/)</li><li>[3.0.1](./build-files/plasmidfinder/3.0.1/)</li><li>[3.0.2](./build-files/plasmidfinder/3.0.2/)</li></ul> </details> | https://bitbucket.org/genomicepidemiology/plasmidfinder/src/master/ |
+| [PlasmidFinder](https://hub.docker.com/r/staphb/plasmidfinder) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/plasmidfinder)](https://hub.docker.com/r/staphb/plasmidfinder) | <details><summary>Click to see all versions</summary> <ul><li>[2.1.6](./build-files/plasmidfinder/2.1.6/)</li><li>[2.1.6_2024-03-07](./build-files/plasmidfinder/2.1.6_2024-03-07/)</li><li>[2.1.6_2025-02-19](./build-files/plasmidfinder/2.1.6_2025-02-19/)</li><li>[3.0.1](./build-files/plasmidfinder/3.0.1/)</li><li>[3.0.2](./build-files/plasmidfinder/3.0.2/)</li><li>[3.0.3](./build-files/plasmidfinder/3.0.3)</li></ul> </details> | https://bitbucket.org/genomicepidemiology/plasmidfinder/src/master/ |
 | [PlasmidSeeker](https://hub.docker.com/r/staphb/plasmidseeker) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/plasmidseeker)](https://hub.docker.com/r/staphb/plasmidseeker) | <details><summary>Click to see all versions</summary> <ul><li>[1.0](./build-files/plasmidseeker/1.0/)</li><li>[1.3](./build-files/plasmidseeker/1.3/)</li></ul> </details> | https://github.com/bioinfo-ut/PlasmidSeeker |
 | [plassembler](https://hub.docker.com/r/staphb/plassembler/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/plassembler)](https://hub.docker.com/r/staphb/plassembler) | <details><summary>Click to see all versions</summary> <ul><li>[1.6.2](./build-files/plassembler/1.6.2/)</li><li>[1.8.0](./build-files/plassembler/1.8.0/)</li><li>[1.8.1](./build-files/plassembler/1.8.1/)</li><li>[1.8.2](./build-files/plassembler/1.8.2/)</li></ul> </details> | https://github.com/gbouras13/plassembler |
 | [pling](https://hub.docker.com/r/staphb/pling/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/pling)](https://hub.docker.com/r/staphb/pling) | <details><summary>Click to see all versions</summary> <ul><li>[2.0.0](./build-files/pling/2.0.0)</li><li>[2.0.1](./build-files/pling/2.0.1)</li></ul> </details> | https://github.com/iqbal-lab-org/pling |

build-files/plasmidfinder/3.0.3/Dockerfile

@@ -0,0 +1,68 @@
+FROM staphb/kma:1.6.4 AS kma
+
+FROM ubuntu:noble AS app
+
+# set env to avoid /.gitconfig permission error on AWS
+ENV HOME=/root
+
+ARG PLASMIDFINDER_VER="3.0.3"
+
+LABEL base.image="ubuntu:noble"
+LABEL dockerfile.version="1"
+LABEL software="plasmidfinder"
+LABEL software.version="${PLASMIDFINDER_VER}"
+LABEL description="Identifies plasmids in total or partial sequenced isolates of bacteria."
+LABEL website="https://bitbucket.org/genomicepidemiology/plasmidfinder"
+LABEL license="https://bitbucket.org/genomicepidemiology/plasmidfinder/src/master/README.md"
+LABEL maintainer="Kutluhan Incekara"
+LABEL maintainer.email="kutluinct@gmail.com"
+LABEL maintainer2="Erin Young"
+LABEL maintainer2.email="eriny@utah.gov"
+
+# install dependencies; cleanup apt garbage 
+# ncbi-blast+ v2.12.0 (ubuntu:jammy), min required version is 2.8.1
+# python3 v3.10.12, min required version is 3.10
+RUN apt-get update && apt-get install -y --no-install-recommends \
+    wget \
+    ca-certificates \
+    procps \
+    ncbi-blast+ \
+    python3-pip \
+    git \
+    python-is-python3 && \
+    apt-get autoclean && rm -rf /var/lib/apt/lists/* && \
+    update-alternatives --install /usr/bin/python python /usr/bin/python3 10
+
+COPY --from=kma /usr/local/bin/*    /usr/local/bin/
+
+# download plasmindfinder database
+RUN git clone -b plasmidfinder-${PLASMIDFINDER_VER} --depth 1 https://bitbucket.org/genomicepidemiology/plasmidfinder_db.git &&\
+    cd plasmidfinder_db &&\
+    python INSTALL.py &&\
+    rm -rf .git
+
+# install plasmidfinder to specific tag/version; make /data
+RUN pip3 install --no-cache-dir --break-system-packages PlasmidFinder==${PLASMIDFINDER_VER} && \
+    mkdir /data
+
+# set $PATH and locale settings for singularity compatibility
+ENV PATH="${PATH}" \
+    LC_ALL=C.UTF-8 \
+    CGE_BLASTN=/usr/bin/blastn \
+    CGE_PLASMIDFINDER_DB=/plasmidfinder_db \
+    PLASMID_DB=/plasmidfinder_db
+
+# set final working directory for production docker image (app layer only)
+WORKDIR /data
+
+# default command is to pull up help options for virulencefinder
+CMD ["python", "-m", "plasmidfinder", "-h"]
+
+### START OF TEST STAGE ###
+FROM app AS test
+
+RUN python -m plasmidfinder -h
+
+RUN wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR193/000/ERR1937840/ERR1937840.fastq.gz && \
+    gzip -d ERR1937840.fastq.gz && mkdir test && \
+    python -m plasmidfinder -i ERR1937840.fastq -o test

build-files/plasmidfinder/3.0.3/README.md

@@ -0,0 +1,17 @@
+# Plasmidfinder Container
+
+Main tool: [Plasmidfinder](https://bitbucket.org/genomicepidemiology/plasmidfinder/src/master/)
+
+Additional tools:
+- kma : 1.6.4
+- blast : 2.12.0
+- plasmidfinder_db : plasmidfinder-3.0.3 (2.2.0)
+
+The PlasmidFinder service contains one python script plasmidfinder.py which is the script of the latest version of the PlasmidFinder service. The service identifies plasmids in total or partial sequenced isolates of bacteria.
+
+# Example Usage
+```{bash}
+python -m plasmidfinder -i ERR1937840.fastq -o test
+```
+
+Better documentation can be found at [Plasmidfinder](https://bitbucket.org/genomicepidemiology/plasmidfinder/src/master/)