v1

.github/workflows/main.yml

+name: ci
+
+on:
+  push:
+    branches:
+      - "main"
+
+jobs:
+  docker:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+      - name: Set up QEMU
+        uses: docker/setup-qemu-action@v3
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v3
+      - name: Login to Docker Hub
+        uses: docker/login-action@v3
+        with:
+          username: ${{ secrets.DOCKERHUB_USERNAME }}
+          password: ${{ secrets.DOCKERHUB_TOKEN }}
+      - name: Build and push
+        uses: docker/build-push-action@v5
+        with:
+          context: .
+          platforms: linux/amd64
+          push: true
+          tags: unigebsp/species_profiler
+    
\ No newline at end of file

.gitignore

+.Rproj.user
+.Rhistory
+.RData
+.Ruserdata
+.DS_Store
\ No newline at end of file

Dockerfile

+FROM python:3.10-slim-bullseye
+
+RUN apt-get update -qq && apt-get install -y -qq \
+    git \
+    build-essential \
+    libz-dev \
+    ncbi-blast+ \
+    && rm -rf /var/cache/apt/* /var/lib/apt/lists/*
+    
+# KMA
+RUN git -C /usr/src/ clone --depth 1 https://bitbucket.org/genomicepidemiology/kma.git \
+    && cd /usr/src/kma \
+    && make \
+    && cp /usr/src/kma/kma /usr/src/kma/kma_index /usr/bin 
+
+# plasmidfinder
+RUN mkdir -p /db \
+    && git -C /db clone --depth 1 https://bitbucket.org/genomicepidemiology/plasmidfinder_db.git \
+    && cd /db/plasmidfinder_db && python3 INSTALL.py
+ENV PLASMID_DB=/db/plasmidfinder_db
+RUN git -C /usr/src/ clone --depth 1 https://bitbucket.org/genomicepidemiology/plasmidfinder/ \
+    && cp /usr/src/plasmidfinder/plasmidfinder.py /usr/bin
+
+
+# mlst
+RUN mkdir -p /db \
+    && git -C /db clone --depth 1 https://bitbucket.org/genomicepidemiology/mlst_db.git \
+    && cd /db/mlst_db && python3 INSTALL.py
+RUN git -C /usr/src/ clone --depth 1 https://bitbucket.org/genomicepidemiology/mlst/ \
+    && cp /usr/src/mlst/mlst.py /usr/bin
+
+
+# resfinder
+RUN mkdir -p /db \
+    && git -C /db clone --depth 1 https://git@bitbucket.org/genomicepidemiology/resfinder_db.git \
+    && git -C /db clone --depth 1 https://git@bitbucket.org/genomicepidemiology/pointfinder_db.git \
+    && git -C /db clone --depth 1 https://git@bitbucket.org/genomicepidemiology/disinfinder_db.git \
+    && cd /db/resfinder_db && python3 INSTALL.py \
+    && cd /db/pointfinder_db && python3 INSTALL.py \
+    && cd /db/disinfinder_db && python3 INSTALL.py
+ENV CGE_RESFINDER_RESGENE_DB=/db/resfinder_db/
+ENV CGE_RESFINDER_RESPOINT_DB=/db/pointfinder_db/
+ENV CGE_DISINFINDER_DB=/db/disinfinder_db/
+RUN pip install -U biopython==1.73 tabulate cgecore \
+    && pip install --no-cache-dir resfinder
+

RStudioProject.Rproj

+Version: 1.0
+
+RestoreWorkspace: Default
+SaveWorkspace: Default
+AlwaysSaveHistory: Default
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: No
+NumSpacesForTab: 2
+Encoding: UTF-8
+
+RnwWeave: Sweave
+LaTeX: pdfLaTeX
+
+BuildType: Makefile

Readme.md

+
+
+# Introduction
+
+`cgetools` is s docker container with an installation of several 
+(CGE)[https://bitbucket.org/genomicepidemiology/] softwares and associated 
+databases (mlst,plasmidfinder,resfinder).
+
+
+
+# Usage
+
+To use the tool, you need to mount the working directory on `/cwd`. Example:
+```bash
+docker run --rm -v .:/cwd unigebsp/cgetools plasmidfinder.py
+docker run --rm -v .:/cwd unigebsp/cgetools mlst.py
+docker run --rm -v .:/cwd unigebsp/cgetools resfinder.py
+```
+
+
+# Building
+
+To build the container, run:
+```bash
+docker build -t unigebsp/cgetools ./
+```
+
+