diff --git a/README.md b/README.md index 66943bd3b..58343ecdf 100644 --- a/README.md +++ b/README.md @@ -155,7 +155,7 @@ To learn more about the docker pull rate limits and the open source software pro | [dragonflye](https://hub.docker.com/r/staphb/dragonflye)
[![docker pulls](https://badgen.net/docker/pulls/staphb/dragonflye)](https://hub.docker.com/r/staphb/dragonflye) | | https://github.com/rpetit3/dragonflye | | [Dr. PRG ](https://hub.docker.com/r/staphb/drprg)
[![docker pulls](https://badgen.net/docker/pulls/staphb/drprg)](https://hub.docker.com/r/staphb/drprg) | | https://mbh.sh/drprg/ | | [DSK](https://hub.docker.com/r/staphb/dsk)
[![docker pulls](https://badgen.net/docker/pulls/staphb/dsk)](https://hub.docker.com/r/staphb/dsk) | | https://gatb.inria.fr/software/dsk/ | -| [el_gato](https://hub.docker.com/r/staphb/elgato)
[![docker pulls](https://badgen.net/docker/pulls/staphb/elgato)](https://hub.docker.com/r/staphb/elgato) | | https://github.com/appliedbinf/el_gato | +| [el_gato](https://hub.docker.com/r/staphb/elgato)
[![docker pulls](https://badgen.net/docker/pulls/staphb/elgato)](https://hub.docker.com/r/staphb/elgato) | | https://github.com/appliedbinf/el_gato | | [emboss](https://hub.docker.com/r/staphb/emboss)
[![docker pulls](https://badgen.net/docker/pulls/staphb/emboss)](https://hub.docker.com/r/staphb/emboss) | | http://emboss.sourceforge.net | | [emmtyper](https://hub.docker.com/r/staphb/emmtyper)
[![docker pulls](https://badgen.net/docker/pulls/staphb/emmtyper)](https://hub.docker.com/r/staphb/emmtyper) | | https://github.com/MDU-PHL/emmtyper | | [emm-typing-tool](https://hub.docker.com/r/staphb/emm-typing-tool)
[![docker pulls](https://badgen.net/docker/pulls/staphb/emm-typing-tool)](https://hub.docker.com/r/staphb/emm-typing-tool) | | https://github.com/phe-bioinformatics/emm-typing-tool | diff --git a/elgato/1.20.1/Dockerfile b/elgato/1.20.1/Dockerfile new file mode 100644 index 000000000..c675a4b43 --- /dev/null +++ b/elgato/1.20.1/Dockerfile @@ -0,0 +1,55 @@ +FROM staphb/ispcr:33 as app + +ARG ELGATO_VER="1.20.1" + +LABEL base.image="ubuntu:jammy" +LABEL dockerfile.version="1" +LABEL software="el_gato" +LABEL software.version="${ELGATO_VER}" +LABEL description="Epidemiology of Legionella : Genome-bAsed Typing" +LABEL website="https://github.com/appliedbinf/el_gato" +LABEL license="https://github.com/appliedbinf/el_gato/blob/main/LICENSE" +LABEL maintainer="Kutluhan Incekara" +LABEL maintainer.email="kutluhan.incekara@ct.gov" + +WORKDIR / + +# dependencies +RUN apt-get update && apt-get install --no-install-recommends -y \ + wget \ + python3-pip \ + minimap2 \ + samtools \ + ncbi-blast+ && \ + apt-get autoclean && rm -rf /var/lib/apt/lists/* + +# install el_gato +RUN wget --no-check-certificate https://github.com/appliedbinf/el_gato/archive/refs/tags/${ELGATO_VER}.tar.gz &&\ + tar -xvf ${ELGATO_VER}.tar.gz && rm ${ELGATO_VER}.tar.gz &&\ + cd el_gato-${ELGATO_VER} &&\ + python3 -m pip install . -vv --no-cache-dir &&\ + mv ./el_gato/db/ /usr/local/bin/db/ + +# install fpd2 for pdf reports +RUN pip install --no-cache-dir fpdf2 packaging + +ENV LC_ALL=C + +CMD el_gato.py -h + +WORKDIR /data + +## Test ## +FROM app as test + +RUN apt-get update && apt-get install unzip + +# download Legionella pneumophila ST62 genome +RUN wget -P /usr/local/bin/ https://ftp.ncbi.nlm.nih.gov/pub/datasets/command-line/v2/linux-amd64/datasets &&\ + chmod 755 /usr/local/bin/datasets &&\ + datasets download genome accession GCF_900119765.1 --include genome &&\ + unzip -j ncbi_dataset.zip ncbi_dataset/data/GCF_900119765.1/GCF_900119765.1_2532STDY5467631_genomic.fna -d . + +# test el_gato +RUN el_gato.py --assembly GCF_900119765.1_2532STDY5467631_genomic.fna --out test/ &&\ + cat test/run.log diff --git a/elgato/1.20.1/README.md b/elgato/1.20.1/README.md new file mode 100644 index 000000000..8a83429f7 --- /dev/null +++ b/elgato/1.20.1/README.md @@ -0,0 +1,33 @@ +# el_gato container + +Main tool: [el_gato](https://github.com/appliedbinf/el_gato) + +Code repository: https://github.com/appliedbinf/el_gato + +Additional tools: +- minimap2: 2.24-r1122 +- samtools: 1.13 +- ncbi-blast+: 2.12.0+ +- isPCR: v33x2 + +Basic information on how to use this tool: +- executable: el_gato.py +- help: -h +- version: -v +- description: Epidemiology of Legionella : Genome-bAsed Typing + +Additional information: + +Container contains necessary database of Legionella sequence types + +Full documentation: https://github.com/appliedbinf/el_gato + +## Example Usage + +```bash +# Paired-end: +el_gato.py --read1 read1.fastq.gz --read2 read2.fastq.gz --out output_folder/ + +# Assembly: +el_gato.py --assembly assembly_file.fna --out output_folder/ +``` \ No newline at end of file