Merge pull request #825 from Kincekara/elgato

adds el_gato

Program_Licenses.md

@@ -34,6 +34,7 @@ The licenses of the open-source software that is contained in these Docker image
 | dragonflye | GNU GPLv3 | https://github.com/rpetit3/dragonflye/blob/main/LICENSE |
 | drprg | MIT | https://github.com/mbhall88/drprg/blob/main/LICENSE |
 | DSK | GNU Affero GPLv3 | https://github.com/GATB/dsk/blob/master/LICENSE |
+| el_gato | MIT | https://github.com/appliedbinf/el_gato/blob/main/LICENSE |
 | emboss | GNU GPLv3 | http://emboss.sourceforge.net/licence/ |
 | emmtyper | GNU GPLv3 | https://github.com/MDU-PHL/emmtyper/blob/master/LICENSE |
 | emm-typing-tool | GNU GPLv3 | https://github.com/phe-bioinformatics/emm-typing-tool/blob/master/LICENCE |

README.md

@@ -139,6 +139,7 @@ To learn more about the docker pull rate limits and the open source software pro
 | [dragonflye](https://hub.docker.com/r/staphb/dragonflye) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/dragonflye)](https://hub.docker.com/r/staphb/dragonflye) | <ul><li>1.0.14</li><li>[1.1.1](dragonflye/1.1.1/)</li></ul> | https://github.com/rpetit3/dragonflye |
 | [Dr. PRG ](https://hub.docker.com/r/staphb/drprg) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/drprg)](https://hub.docker.com/r/staphb/drprg) | <ul><li>[0.1.1](drprg/0.1.1/)</li></ul> | https://mbh.sh/drprg/ |
 | [DSK](https://hub.docker.com/r/staphb/dsk) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/dsk)](https://hub.docker.com/r/staphb/dsk) | <ul><li>0.0.100</li></ul> | https://gatb.inria.fr/software/dsk/ |
+| [el_gato](https://hub.docker.com/r/staphb/elgato) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/elgato)](https://hub.docker.com/r/staphb/elgato) | <ul><li>[1.15.2](./elgato/1.15.2)</li></ul> | https://github.com/appliedbinf/el_gato |
 | [emboss](https://hub.docker.com/r/staphb/emboss) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/emboss)](https://hub.docker.com/r/staphb/emboss) | <ul><li>6.6.0 (no version)</li></ul> | http://emboss.sourceforge.net |
 | [emmtyper](https://hub.docker.com/r/staphb/emmtyper) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/emmtyper)](https://hub.docker.com/r/staphb/emmtyper) | <ul><li>0.2.0</li></ul> | https://github.com/MDU-PHL/emmtyper |
 | [emm-typing-tool](https://hub.docker.com/r/staphb/emm-typing-tool) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/emm-typing-tool)](https://hub.docker.com/r/staphb/emm-typing-tool) | <ul><li>0.0.1 (no version)</li></ul> | https://github.com/phe-bioinformatics/emm-typing-tool |

elgato/1.15.2/Dockerfile

@@ -0,0 +1,54 @@
+FROM staphb/ispcr:33 as app
+
+ARG ELGATO_VER="1.15.2"
+
+LABEL base.image="ubuntu:jammy"
+LABEL dockerfile.version="1"
+LABEL software="el_gato"
+LABEL software.version="${ELGATO_VER}"
+LABEL description="Epidemiology of Legionella : Genome-bAsed Typing"
+LABEL website="https://github.com/appliedbinf/el_gato"
+LABEL license="https://github.com/appliedbinf/el_gato/blob/main/LICENSE"
+LABEL maintainer="Kutluhan Incekara"
+LABEL maintainer.email="[email protected]"
+
+WORKDIR /
+
+# dependencies
+RUN apt-get update && apt-get install --no-install-recommends -y \
+    wget \
+    python3-pip \
+    minimap2 \
+    samtools \
+    ncbi-blast+ && \
+    apt-get autoclean && rm -rf /var/lib/apt/lists/*
+
+# install el_gato
+RUN wget --no-check-certificate https://github.com/appliedbinf/el_gato/archive/refs/tags/${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 &&\
+    mv ./el_gato/db/ /usr/local/bin/db/
+
+# install fpd2 for pdf reports    
+RUN pip install fpdf2
+
+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/

elgato/1.15.2/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/
+```