change registry to gitlab

Dockerfile

@@ -42,19 +42,9 @@ RUN mkdir -p /db \
 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 \
-    && curl -sSL https://pdm-project.org/install-pdm.py | python3 - \
-    && git -C /usr/src/ clone --depth 1 https://bitbucket.org/genomicepidemiology/cgecore.git \
-    && cd /usr/src/cgecore && python3 setup.py install \
-    && git -C /usr/src/ clone --depth 1 https://bitbucket.org/genomicepidemiology/cgelib.git \
-    && cd /usr/src/cgelib && python3 setup.py install \
+RUN curl -sSL https://pdm-project.org/install-pdm.py | python3 - --path /usr/local \
     && git -C /usr/src/ clone --depth 1 https://bitbucket.org/genomicepidemiology/resfinder.git \
-    && cd /usr/src/resfinder && /root/.local/bin/pdm build && pip3 install dist/*.whl
-
-#RUN pip install -U biopython==1.73 tabulate cgecore \
-#    && pip install --no-cache-dir resfinder
-
-
+    && cd /usr/src/resfinder && pdm build && pip3 install dist/*.whl
 
 
 

Readme.md

@@ -12,9 +12,9 @@ databases (mlst,plasmidfinder,resfinder).
 
 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 python3 -m resfinder
+docker run --rm -v .:/cwd registry.gitlab.unige.ch/amr-genomics/cgetools plasmidfinder.py
+docker run --rm -v .:/cwd registry.gitlab.unige.ch/amr-genomics/cgetools mlst.py
+docker run --rm -v .:/cwd registry.gitlab.unige.ch/amr-genomics/cgetools python3 -m resfinder
 ```
 
 
@@ -22,7 +22,7 @@ docker run --rm -v .:/cwd unigebsp/cgetools python3 -m resfinder
 
 To build the container, run:
 ```bash
-docker build -t unigebsp/cgetools ./
+docker build --platform linux/amd64 -t registry.gitlab.unige.ch/amr-genomics/cgetools ./
 ```