Adding ppanggolin

Program_Licenses.md

@@ -109,6 +109,7 @@ The licenses of the open-source software that is contained in these Docker image
 | polypolish | GNU GPLv3 | https://github.com/rrwick/Polypolish/blob/main/LICENSE |
 | PopPUNK | Apache 2.0 | https://github.com/bacpop/PopPUNK/blob/master/LICENSE |
 | Porechop | GNU GPLv3 | https://github.com/rrwick/Porechop/blob/master/LICENSE |
+| PPanGGOLiN | CeCILL 2.1 | https://github.com/labgem/PPanGGOLiN/blob/master/LICENSE.txt |
 | Prokka | GNU GPLv3 | https://raw.githubusercontent.com/tseemann/prokka/master/doc/LICENSE.Prokka |
 | pyCirclize | MIT | https://github.com/moshi4/pyCirclize/blob/main/LICENSE |
 | pyGenomeViz | MIT | https://github.com/moshi4/pyGenomeViz/blob/main/LICENSE |

README.md

@@ -214,6 +214,7 @@ To learn more about the docker pull rate limits and the open source software pro
 | [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) | <ul><li>0.5.0</li></ul> | 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) | <ul><li>[2.4.0](./poppunk/2.4.0/)</li><li>[2.5.0](./poppunk/2.5.0/)</li><li>[2.6.0](./poppunk/2.6.0/)</li><li>[2.6.2](./poppunk/2.6.2/)</li></ul> | 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) | <ul><li>0.2.4</li></ul> | 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) | <ul><li>0.2.4</li></ul> | https://github.com/labgem/PPanGGOLiN |
 | [Prokka](https://hub.docker.com/r/staphb/prokka/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/prokka)](https://hub.docker.com/r/staphb/prokka) | <ul><li>1.13.4</li><li>1.14.0</li><li>1.14.5</li><li>1.14.6</li></ul> | https://github.com/tseemann/prokka |
 | [pyCirclize](https://hub.docker.com/r/staphb/pycirclize/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/pycirclize)](https://hub.docker.com/r/staphb/pycirclize) | <ul><li>[1.0.0](pycirclize/1.0.0/)</li></ul> | https://github.com/moshi4/pyCirclize |
 | [pyGenomeViz](https://hub.docker.com/r/staphb/pygenomeviz/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/pygenomeviz)](https://hub.docker.com/r/staphb/pygenomeviz) | <ul><li>0.2.2</li><li>0.3.2</li><li>[0.4.2](pygenomeviz/0.4.2/)</li><li>[0.4.3](pygenomeviz/0.4.3/)</li></ul> | https://github.com/moshi4/pyGenomeViz |

ppanggolin/1.2.105/Dockerfile

@@ -0,0 +1,61 @@
+ARG PPANGGOLIN_VER="1.2.105"
+
+FROM mambaorg/micromamba:1.4.9 as app
+
+ARG PPANGGOLIN_VER
+
+# 'LABEL' instructions tag the image with metadata that might be important to the user
+LABEL base.image="mambaorg/micromamba:1.4.9"
+LABEL dockerfile.version="1"
+LABEL software="PPanGGOLiN"
+LABEL software.version="${PPANGGOLIN_VER}"
+LABEL description="Depicting microbial species diversity via a Partitioned PanGenome Graph Of Linked Neighbors"
+LABEL website="https://github.com/labgem/PPanGGOLiN"
+LABEL license="https://github.com/labgem/PPanGGOLiN/blob/master/LICENSE.txt"
+LABEL maintainer="Erin Young"
+LABEL maintainer.email="[email protected]"
+
+USER root
+
+RUN apt-get update && apt-get install -y --no-install-recommends \
+    ca-certificates \
+    procps \
+    wget && \
+    apt-get autoclean && rm -rf /var/lib/apt/lists/*
+
+ENV PATH="/opt/conda/envs/base/bin/:/opt/conda/bin/:$PATH" LC_ALL=C
+
+RUN micromamba install --name base -c conda-forge -c bioconda -c defaults ppanggolin=${PPANGGOLIN_VER} && \
+    micromamba clean -a -y && \
+    ppanggolin -h && \
+    mkdir /data
+
+# 'CMD' instructions set a default command when the container is run. This is typically 'tool --help.'
+CMD ppanggolin -h
+
+# 'WORKDIR' sets working directory
+WORKDIR /data
+
+FROM app as test
+
+ARG PPANGGOLIN_VER
+
+WORKDIR /test
+
+RUN ppanggolin --help && \
+    ppanggolin --version
+
+# getting test files from github repo
+RUN wget -q https://github.com/labgem/PPanGGOLiN/archive/refs/tags/${PPANGGOLIN_VER}.tar.gz && \
+    tar -xvf ${PPANGGOLIN_VER}.tar.gz
+
+RUN cd PPanGGOLiN-${PPANGGOLIN_VER}/testingDataset && \
+    ppanggolin annotate --fasta organisms.fasta.list --output output && cp output/pangenome.h5 output/pangenome.1.h5 && \
+    ppanggolin cluster   -p output/pangenome.h5                      && cp output/pangenome.h5 output/pangenome.2.h5 && \
+    ppanggolin graph     -p output/pangenome.h5                      && cp output/pangenome.h5 output/pangenome.3.h5 && \
+    ppanggolin partition -p output/pangenome.h5                      && cp output/pangenome.h5 output/pangenome.4.h5 && \
+    ppanggolin draw      -p output/pangenome.h5 --ucurve             && \
+    ppanggolin write     -p output/pangenome.h5 --stats --output output_stats && \
+    md5sum output/pangenome*.h5 && \
+    head output_stats/*
+

ppanggolin/1.2.105/README.md

@@ -0,0 +1,33 @@
+# PPanGGOLiN container
+
+Main tool: [PPanGGOLiN](https://github.com/labgem/PPanGGOLiN)
+
+Code repository: https://github.com/labgem/PPanGGOLiN
+
+Basic information on how to use this tool:
+- executable: ppanggolin
+- help: --help
+- version: --version
+- description: |
+> PPanGGOLiN builds pangenomes through a graphical model and a statistical method to partition gene families in persistent, shell and cloud genomes.
+
+Additional information:
+
+PPanGGOLiN only creates the pangenome graphs. It is recommended to use another tool to visualize them. Please read https://github.com/labgem/PPanGGOLiN/wiki for more information.
+
+Full documentation: https://github.com/labgem/PPanGGOLiN/wiki
+
+## Example Usage
+
+```bash
+ppanggolin annotate --fasta organisms.fasta.list --output output 
+
+# many of the commands manipulate the 'pangenome.h5' file in place
+ppanggolin cluster -p pangenome.h5
+ppanggolin graph -p pangenome.h5 
+ppanggolin partition -p pangenome.h5
+ppanggolin draw -p pangenome.h5 --ucurve   
+
+# there are some human-readable files that can be generated as well
+ppanggolin write -p pangenome.h5 --stats --output stats
+```