diff --git a/README.md b/README.md index bda448883..bd86457ff 100644 --- a/README.md +++ b/README.md @@ -243,7 +243,7 @@ To learn more about the docker pull rate limits and the open source software pro | [polypolish](https://hub.docker.com/r/staphb/polypolish/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/polypolish)](https://hub.docker.com/r/staphb/polypolish) | | https://github.com/rrwick/Polypolish | | [PopPUNK](https://hub.docker.com/r/staphb/poppunk/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/poppunk)](https://hub.docker.com/r/staphb/poppunk) | | https://github.com/bacpop/PopPUNK | | [Porechop](https://hub.docker.com/r/staphb/porechop/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/porechop)](https://hub.docker.com/r/staphb/porechop) | | https://github.com/rrwick/Porechop | -| [PPanGGOLiN](https://hub.docker.com/r/staphb/ppanggolin/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/ppanggolin)](https://hub.docker.com/r/staphb/ppanggolin) | | https://github.com/labgem/PPanGGOLiN | +| [PPanGGOLiN](https://hub.docker.com/r/staphb/ppanggolin/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/ppanggolin)](https://hub.docker.com/r/staphb/ppanggolin) | | https://github.com/labgem/PPanGGOLiN | | [Prokka](https://hub.docker.com/r/staphb/prokka/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/prokka)](https://hub.docker.com/r/staphb/prokka) | | https://github.com/tseemann/prokka | | [pyCirclize](https://hub.docker.com/r/staphb/pycirclize/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/pycirclize)](https://hub.docker.com/r/staphb/pycirclize) | | https://github.com/moshi4/pyCirclize | | [pyGenomeViz](https://hub.docker.com/r/staphb/pygenomeviz/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/pygenomeviz)](https://hub.docker.com/r/staphb/pygenomeviz) | | https://github.com/moshi4/pyGenomeViz | diff --git a/ppanggolin/2.1.2/Dockerfile b/ppanggolin/2.1.2/Dockerfile new file mode 100644 index 000000000..c8a7fe3f8 --- /dev/null +++ b/ppanggolin/2.1.2/Dockerfile @@ -0,0 +1,53 @@ +ARG PPANGGOLIN_VER="2.1.2" + +FROM mambaorg/micromamba:1.5.8 as app + +ARG PPANGGOLIN_VER + +# 'LABEL' instructions tag the image with metadata that might be important to the user +LABEL base.image="mambaorg/micromamba:1.5.8" +LABEL dockerfile.version="1" +LABEL software="PPanGGOLiN" +LABEL software.version="${PPANGGOLIN_VER}" +LABEL description="Depicting microbial species diversity via a Partitioned PanGenome Graph Of Linked Neighbors" +LABEL website="https://github.com/labgem/PPanGGOLiN" +LABEL license="https://github.com/labgem/PPanGGOLiN/blob/master/LICENSE.txt" +LABEL maintainer="Erin Young" +LABEL maintainer.email="eriny@utah.gov" + +USER root + +RUN apt-get update && apt-get install -y --no-install-recommends \ + ca-certificates \ + procps \ + wget && \ + apt-get autoclean && rm -rf /var/lib/apt/lists/* + +ENV PATH="/opt/conda/envs/base/bin/:/opt/conda/bin/:$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 all --fasta genomes.fasta.list --output output diff --git a/ppanggolin/2.1.2/README.md b/ppanggolin/2.1.2/README.md new file mode 100644 index 000000000..ad910731d --- /dev/null +++ b/ppanggolin/2.1.2/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 +```