Merge pull request #887 from Kincekara/gubbins

adds gubbins

Program_Licenses.md

@@ -59,6 +59,7 @@ The licenses of the open-source software that is contained in these Docker image
 | geNomad | ACADEMIC, INTERNAL, RESEARCH & DEVELOPMENT, NON-COMMERCIAL USE ONLY | https://github.com/apcamargo/genomad/blob/main/LICENSE |
 | GenoVi | BY-NC-SA Creative Commons License | https://github.com/robotoD/GenoVi/blob/main/LICENSE.txt |
 | gfastats | MIT | https://github.com/vgl-hub/gfastats/blob/main/LICENSE |
+| Gubbins | GNU GPLv2 | https://github.com/nickjcroucher/gubbins/blob/master/LICENSE |
 | HeatCluster | GPL-3.0 | https://github.com/DrB-S/heatcluster/blob/main/LICENSE |
 | Hmmer | BSD-3 | http://eddylab.org/software/hmmer/Userguide.pdf |
 | homopolish | GNU GPLv3 | https://github.com/ythuang0522/homopolish/blob/master/LICENSE |

README.md

@@ -163,6 +163,7 @@ To learn more about the docker pull rate limits and the open source software pro
 | [geNomad](https://hub.docker.com/r/staphb/genomad) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/genomad)](https://hub.docker.com/r/staphb/genomad) | <ul><li>[1.7.4](./genomad/1.7.4/)</li></ul> | https://github.com/apcamargo/genomad |
 | [GenoVi](https://hub.docker.com/r/staphb/genovi) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/genovi)](https://hub.docker.com/r/staphb/genovi) | <ul><li>[0.2.16](./genovi/0.2.16/)</li></ul> | https://github.com/robotoD/GenoVi |
 | [gfastats](https://hub.docker.com/r/staphb/gfastats) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/gfastats)](https://hub.docker.com/r/staphb/gfastats) | <ul><li>1.3.6</li></ul> | https://github.com/vgl-hub/gfastats |
+| [Gubbins](https://hub.docker.com/r/staphb/gubbins) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/gubbins)](https://hub.docker.com/r/staphb/gubbins) | <ul><li>[3.3.3](./gubbins/3.3.3/)</li></ul> | https://github.com/nickjcroucher/gubbins |
 | [heatcluster](https://hub.docker.com/r/staphb/heatcluster) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/heatcluster)](https://hub.docker.com/r/staphb/heatcluster) | <ul><li>[1.0.2c](./heatcluster/1.0.2c/)</li></ul> | https://github.com/DrB-S/heatcluster/tree/main |
 | [hmmer](https://hub.docker.com/r/staphb/hmmer) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/hmmer)](https://hub.docker.com/r/staphb/hmmer) | <ul><li>[3.3](hmmer/3.3/)</li><li>[3.3.2](hmmer/3.3.2/)</li><li>[3.4](./hmmer/3.4/)</li></ul> | http://hmmer.org/ |
 | [homopolish](https://hub.docker.com/r/staphb/homopolish) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/homopolish)](https://hub.docker.com/r/staphb/homopolish) | <ul><li>0.4.1</li></ul> | https://github.com/ythuang0522/homopolish/ |

gubbins/3.3.3/Dockerfile

@@ -0,0 +1,43 @@
+FROM mambaorg/micromamba:1.5.6 as app
+
+ARG GUBBINS_VER="3.3.3"
+
+USER root
+
+WORKDIR /
+
+LABEL base.image="mambaorg/micromamba:1.5.6"
+LABEL dockerfile.version="1"
+LABEL software="Gubbins"
+LABEL software.version="${GUBBINS_VER}"
+LABEL description="Genealogies Unbiased By recomBinations In Nucleotide Sequences"
+LABEL website="https://github.com/nickjcroucher/gubbins"
+LABEL license="https://github.com/nickjcroucher/gubbins/blob/master/LICENSE"
+LABEL maintainer="Kutluhan Incekara"
+LABEL maintainer.email="[email protected]"
+
+RUN apt-get update && apt-get install --no-install-recommends -y \
+    procps &&\
+    apt-get autoclean && rm -rf /var/lib/apt/lists/*
+
+RUN micromamba install --name base -c conda-forge -c bioconda gubbins=${GUBBINS_VER} && \
+    micromamba clean -a -y && \
+    mkdir /data
+
+ENV PATH="/opt/conda/bin/:${PATH}" \
+    LC_ALL=C.UTF-8
+
+CMD ["run_gubbins.py", "-h"]
+
+WORKDIR /data
+
+FROM app as test
+
+ENV ENV_NAME="base"
+ARG MAMBA_DOCKERFILE_ACTIVATE=1
+
+WORKDIR /test
+
+RUN curl -LJO https://github.com/nickjcroucher/gubbins/raw/master/tests/data/alignment_file_multiple_lines_per_sequence.aln &&\
+    run_gubbins.py alignment_file_multiple_lines_per_sequence.aln
+

gubbins/3.3.3/README.md

@@ -0,0 +1,26 @@
+# Gubbins container
+
+Main tool: [Gubbins](https://github.com/nickjcroucher/gubbins)
+
+Code repository: https://github.com/nickjcroucher/gubbins
+
+Additional tools:
+- RAxML: 8.2.12
+- FastTree: 2.1.11
+- IQTree: 2.0.3
+- RAxML-NG: 1.0.1
+- Rapidnj: 2.3.2
+
+Basic information on how to use this tool:
+- executable: run_gubbins.py
+- help: -h
+- version: --version
+- description: Gubbins detects recombinations through the locally elevated densities of polymorphisms that arise when sequence segments are acquired from a donor genetically divergent from the set of analyzed sequences.
+
+Full documentation: https://github.com/nickjcroucher/gubbins/blob/master/docs/gubbins_manual.md
+
+## Example Usage
+
+```bash
+run_gubbins.py fasta_alignment.aln
+```