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Update docker build for mamba/conflict resolution
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FROM continuumio/miniconda3:4.10.3 | ||
FROM condaforge/mambaforge:4.10.3-5 | ||
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# Install system dependencies | ||
# # Install system dependencies | ||
RUN apt-get update && \ | ||
apt-get install -y build-essential && \ | ||
apt-get clean && \ | ||
rm -rf /var/lib/apt/lists/* | ||
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LABEL org.opencontainers.image.source="https://github.com/usda-ars-gbru/itsxpress" | ||
# Install conda dependencies | ||
RUN conda install -c bioconda vsearch=2.22.1 hmmer=3.1b2 | ||
RUN conda update mamba -c conda-forge | ||
RUN mamba install -c conda-forge python=3.8.16 | ||
RUN mamba install -c bioconda vsearch=2.22.1 hmmer=3.1b2 | ||
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# Copy the itsxpress package files and install dependencies | ||
COPY . /app | ||
WORKDIR /app | ||
RUN pip install --no-cache-dir . | ||
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# Set the default command to run itsxpress | ||
CMD ["itsxpress"] | ||
CMD ["itsxpress"] |