diff --git a/Dockerfile b/Dockerfile index 10a2d3dd..8306c229 100644 --- a/Dockerfile +++ b/Dockerfile @@ -15,15 +15,15 @@ RUN sed -i 's/name: artic/name: base/' /tmp/env.yml RUN micromamba install --yes --file /tmp/env.yml && \ micromamba clean --all --yes -RUN pip uninstall -y tensorflow keras pyabpoa \ - && conda install -y -c conda-forge tensorflow~=2.11 keras~=2.11 - ARG MAMBA_DOCKERFILE_ACTIVATE=1 USER root RUN python3 -m pip install ./fieldbioinformatics +RUN pip uninstall -y tensorflow keras pyabpoa \ + && micromamba install -y -c conda-forge tensorflow~=2.11 keras~=2.11 + USER $MAMBA_USER ENTRYPOINT ["/usr/local/bin/_entrypoint.sh"] diff --git a/environment.yml b/environment.yml index 5b247716..6f90fecc 100644 --- a/environment.yml +++ b/environment.yml @@ -4,14 +4,15 @@ channels: - bioconda - defaults dependencies: + - python==3.9 - longshot - bcftools - biopython - bwa + - clair3 - clint - htslib - minimap2 - - clair3 - multiqc - muscle<5.1 - pandas @@ -25,4 +26,4 @@ dependencies: - samtools - tqdm - pip: - - medaka~=1.12.0 + - medaka==1.12.0