From d1fcf6c29e4f70193dd5f37cc23a35d1bf452da1 Mon Sep 17 00:00:00 2001 From: Kincekara Date: Fri, 26 Jul 2024 14:21:12 +0000 Subject: [PATCH 1/3] adds el_gato 1.18.0 --- README.md | 2 +- elgato/1.18.0/Dockerfile | 55 ++++++++++++++++++++++++++++++++++++++++ elgato/1.18.0/README.md | 33 ++++++++++++++++++++++++ 3 files changed, 89 insertions(+), 1 deletion(-) create mode 100644 elgato/1.18.0/Dockerfile create mode 100644 elgato/1.18.0/README.md diff --git a/README.md b/README.md index 5a3d42885..c03429fd0 100644 --- a/README.md +++ b/README.md @@ -146,7 +146,7 @@ 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/1.18.0/Dockerfile b/elgato/1.18.0/Dockerfile new file mode 100644 index 000000000..04989ddb6 --- /dev/null +++ b/elgato/1.18.0/Dockerfile @@ -0,0 +1,55 @@ +FROM staphb/ispcr:33 as app + +ARG ELGATO_VER="1.18.0" + +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/1.18.0/README.md b/elgato/1.18.0/README.md new file mode 100644 index 000000000..8a83429f7 --- /dev/null +++ b/elgato/1.18.0/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 From 52693d186ad2387a161d99293c3d08a92ba61a8a Mon Sep 17 00:00:00 2001 From: Kincekara Date: Tue, 30 Jul 2024 15:26:38 +0000 Subject: [PATCH 2/3] adds elgato 1.18.2 --- README.md | 2 +- elgato/1.18.2/Dockerfile | 55 ++++++++++++++++++++++++++++++++++++++++ elgato/1.18.2/README.md | 33 ++++++++++++++++++++++++ 3 files changed, 89 insertions(+), 1 deletion(-) create mode 100644 elgato/1.18.2/Dockerfile create mode 100644 elgato/1.18.2/README.md diff --git a/README.md b/README.md index c03429fd0..8cb880d11 100644 --- a/README.md +++ b/README.md @@ -146,7 +146,7 @@ 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/1.18.2/Dockerfile b/elgato/1.18.2/Dockerfile new file mode 100644 index 000000000..c7f947d7d --- /dev/null +++ b/elgato/1.18.2/Dockerfile @@ -0,0 +1,55 @@ +FROM staphb/ispcr:33 as app + +ARG ELGATO_VER="1.18.2" + +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/1.18.2/README.md b/elgato/1.18.2/README.md new file mode 100644 index 000000000..8a83429f7 --- /dev/null +++ b/elgato/1.18.2/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 From 2022fc3518176d2b57321f8b97604726d7b2bad0 Mon Sep 17 00:00:00 2001 From: Kincekara Date: Tue, 30 Jul 2024 15:28:44 +0000 Subject: [PATCH 3/3] remove 1.18.0 --- elgato/1.18.0/Dockerfile | 55 ---------------------------------------- elgato/1.18.0/README.md | 33 ------------------------ 2 files changed, 88 deletions(-) delete mode 100644 elgato/1.18.0/Dockerfile delete mode 100644 elgato/1.18.0/README.md diff --git a/elgato/1.18.0/Dockerfile b/elgato/1.18.0/Dockerfile deleted file mode 100644 index 04989ddb6..000000000 --- a/elgato/1.18.0/Dockerfile +++ /dev/null @@ -1,55 +0,0 @@ -FROM staphb/ispcr:33 as app - -ARG ELGATO_VER="1.18.0" - -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/1.18.0/README.md b/elgato/1.18.0/README.md deleted file mode 100644 index 8a83429f7..000000000 --- a/elgato/1.18.0/README.md +++ /dev/null @@ -1,33 +0,0 @@ -# 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