From 30fedfb4c9f0cb5ba1bdc0f799b4820af560b057 Mon Sep 17 00:00:00 2001 From: Kincekara Date: Mon, 30 Sep 2024 19:06:10 +0000 Subject: [PATCH] adds integron finder --- Program_Licenses.md | 1 + README.md | 1 + integron_finder/2.0.5/Dockerfile | 41 ++++++++++++++++++++++++++++++++ integron_finder/2.0.5/README.md | 29 ++++++++++++++++++++++ 4 files changed, 72 insertions(+) create mode 100644 integron_finder/2.0.5/Dockerfile create mode 100644 integron_finder/2.0.5/README.md diff --git a/Program_Licenses.md b/Program_Licenses.md index 398acb32e..84442d2d8 100644 --- a/Program_Licenses.md +++ b/Program_Licenses.md @@ -71,6 +71,7 @@ The licenses of the open-source software that is contained in these Docker image | Hmmer | BSD-3 | http://eddylab.org/software/hmmer/Userguide.pdf | | homopolish | GNU GPLv3 | https://github.com/ythuang0522/homopolish/blob/master/LICENSE | | htslib | MIT | https://github.com/samtools/htslib/blob/develop/LICENSE | +| Integron Finder | GNU GPLv3 | https://github.com/gem-pasteur/Integron_Finder/blob/master/COPYING | | iqtree | GNU GPLv2 | https://github.com/Cibiv/IQ-TREE/blob/master/LICENSE | | iqtree2 | GNU GPLv2 | https://github.com/iqtree/iqtree2/blob/master/LICENSE | | IPA | BSD-3 | https://github.com/PacificBiosciences/pbipa/blob/master/LICENSE.txt | diff --git a/README.md b/README.md index 550af8968..46cbd15a5 100644 --- a/README.md +++ b/README.md @@ -180,6 +180,7 @@ To learn more about the docker pull rate limits and the open source software pro | [hmmer](https://hub.docker.com/r/staphb/hmmer)
[![docker pulls](https://badgen.net/docker/pulls/staphb/hmmer)](https://hub.docker.com/r/staphb/hmmer) | | http://hmmer.org/ | | [homopolish](https://hub.docker.com/r/staphb/homopolish)
[![docker pulls](https://badgen.net/docker/pulls/staphb/homopolish)](https://hub.docker.com/r/staphb/homopolish) | | https://github.com/ythuang0522/homopolish/ | | [htslib](https://hub.docker.com/r/staphb/htslib)
[![docker pulls](https://badgen.net/docker/pulls/staphb/htslib)](https://hub.docker.com/r/staphb/htslib) | | https://www.htslib.org/ | +| [Integron Finder](https://hub.docker.com/r/staphb/integron_finder/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/integron_finder)](https://hub.docker.com/r/staphb/integron_finder) | | https://github.com/gem-pasteur/Integron_Finder | | [iqtree](https://hub.docker.com/r/staphb/iqtree/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/iqtree)](https://hub.docker.com/r/staphb/iqtree) | | http://www.iqtree.org/ | | [iqtree2](https://hub.docker.com/r/staphb/iqtree2/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/iqtree2)](https://hub.docker.com/r/staphb/iqtree2) | | http://www.iqtree.org/ | | [IPA](https://hub.docker.com/r/staphb/pbipa)
[![docker pulls](https://badgen.net/docker/pulls/staphb/pbipa)](https://hub.docker.com/r/staphb/pbipa) | | https://github.com/PacificBiosciences/pbipa | diff --git a/integron_finder/2.0.5/Dockerfile b/integron_finder/2.0.5/Dockerfile new file mode 100644 index 000000000..a2bdfcb51 --- /dev/null +++ b/integron_finder/2.0.5/Dockerfile @@ -0,0 +1,41 @@ +FROM ubuntu:jammy AS app + +ARG INTEGRON_FINDER_VER="2.0.5" + +LABEL base.image="ubuntu:jammy" +LABEL dockerfile.version="1" +LABEL software="Integron Finder" +LABEL software.version="${INTEGRON_FINDER_VER}" +LABEL description="Finds integrons in DNA sequences" +LABEL website="https://github.com/gem-pasteur/Integron_Finder" +LABEL license="https://github.com/gem-pasteur/Integron_Finder/blob/master/COPYING" +LABEL maintainer="Kutluhan Incekara" +LABEL maintainer.email="kutluhan.incekara@ct.gov" + +RUN apt-get update && apt-get install --no-install-recommends -y \ + python3-pip \ + hmmer \ + infernal \ + prodigal && \ + apt-get autoclean && rm -rf /var/lib/apt/lists/* + +RUN pip3 install --no-cache-dir integron_finder==${INTEGRON_FINDER_VER} + +ENV LC_ALL=C + +CMD [ "integron_finder", "--help" ] + +WORKDIR /data + +## Test ## +FROM app AS test + +RUN apt-get update && apt-get install -y wget + +RUN wget -q https://github.com/gem-pasteur/Integron_Finder/raw/master/tests/data/Replicons/NZ_CP016323.fna &&\ + integron_finder --local-max --circ --keep-tmp NZ_CP016323.fna &&\ + cat Results_Integron_Finder_NZ_CP016323/NZ_CP016323.summary &&\ + head Results_Integron_Finder_NZ_CP016323/NZ_CP016323.integrons + + + diff --git a/integron_finder/2.0.5/README.md b/integron_finder/2.0.5/README.md new file mode 100644 index 000000000..63c84cab3 --- /dev/null +++ b/integron_finder/2.0.5/README.md @@ -0,0 +1,29 @@ +# Integron Finder container + +Main tool: [Integron Finder](https://integronfinder.readthedocs.io/en/latest/) + +Code repository: https://github.com/gem-pasteur/Integron_Finder + +Additional tools: + - Python 3.10.12 + - numpy 2.1.1 + - pandas 2.2.3 + - matplolib 3.9.2 + - biopython 1.84 + - Prodigal V2.6.3 + - INFERNAL 1.1.4 + - HMMER 3.3.2 + +Basic information on how to use this tool: +- executable: integron_finder +- help: --help +- version: --version +- description: Finds integrons in DNA sequences + +Full documentation: https://integronfinder.readthedocs.io/en/latest/ + +## Example Usage + +```bash +integron_finder --local-max --circ --keep-tmp genome.fna +```