Merge pull request #1074 from Kincekara/integron_finder

adds integron finder

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 |

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) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/hmmer)](https://hub.docker.com/r/staphb/hmmer) | <ul><li>[3.3](hmmer/3.3/)</li><li>[3.3.2](hmmer/3.3.2/)</li><li>[3.4](./hmmer/3.4/)</li></ul> | http://hmmer.org/ |
 | [homopolish](https://hub.docker.com/r/staphb/homopolish) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/homopolish)](https://hub.docker.com/r/staphb/homopolish) | <ul><li>0.4.1</li></ul> | https://github.com/ythuang0522/homopolish/ |
 | [htslib](https://hub.docker.com/r/staphb/htslib) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/htslib)](https://hub.docker.com/r/staphb/htslib) | <ul><li>[1.14](./htslib/1.14)</li><li>[1.15](./htslib/1.15)</li><li>[1.16](./htslib/1.16)</li><li>[1.17](./htslib/1.17)</li><li>[1.18](./htslib/1.18/)</li><li>[1.19](./htslib/1.19/)</li><li>[1.20](./htslib/1.20/)</li><li>[1.20.c](./htslib/1.20.c/)</li><li>[1.21](./htslib/1.21/)</li></ul> | https://www.htslib.org/ |
+| [Integron Finder](https://hub.docker.com/r/staphb/integron_finder/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/integron_finder)](https://hub.docker.com/r/staphb/integron_finder) | <ul><li>[2.0.5](./integron_finder/2.0.5/)</li></ul> | https://github.com/gem-pasteur/Integron_Finder |
 | [iqtree](https://hub.docker.com/r/staphb/iqtree/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/iqtree)](https://hub.docker.com/r/staphb/iqtree) | <ul><li>1.6.7</li></ul> | http://www.iqtree.org/ |
 | [iqtree2](https://hub.docker.com/r/staphb/iqtree2/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/iqtree2)](https://hub.docker.com/r/staphb/iqtree2) | <ul><li>2.1.2</li><li>2.2.2.2</li><li>[2.2.2.6](iqtree2/2.2.2.6/)</li><li>[2.2.2.7](iqtree2/2.2.2.7/)</li><li>[2.3.1](iqtree2/2.3.1/)</li><li>[2.3.4](iqtree2/2.3.4/)</li><li>[2.3.6](iqtree2/2.3.6/)</li></ul> | http://www.iqtree.org/ |
 | [IPA](https://hub.docker.com/r/staphb/pbipa) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/pbipa)](https://hub.docker.com/r/staphb/pbipa) | <ul><li>[1.8.0](./pbipa/1.8.0/)</li></ul> | https://github.com/PacificBiosciences/pbipa |

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="${INTEGRON_FINDER_VER}"
+LABEL description="Finds integrons in DNA sequences"
+LABEL website="https://github.com/gem-pasteur/Integron_Finder"
+LABEL license="https://github.com/gem-pasteur/Integron_Finder/blob/master/COPYING"
+LABEL maintainer="Kutluhan Incekara"
+LABEL maintainer.email="[email protected]"
+
+RUN apt-get update && apt-get install --no-install-recommends -y \
+    python3-pip \
+    hmmer \
+    infernal \
+    prodigal && \
+    apt-get autoclean && rm -rf /var/lib/apt/lists/*
+
+RUN pip3 install --no-cache-dir integron_finder==${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
+
+
+

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
+```