corrected Dockerfile

Author: VictorDidier

Dockerfile

@@ -2,25 +2,36 @@
 FROM mambaorg/micromamba:latest
 LABEL maintainer="Victor Perez"
 
-# Set the base layer for micromamba and copy the environment file
-COPY --chown=$MAMBA_USER:$MAMBA_USER environment.yml /tmp/env.yaml
+# Set the base layer for micromamba
+USER root
+COPY environment.yml .
 
+# Update package manager and install essential build tools
 RUN apt-get update -qq && apt-get install -y \
     build-essential \
     ffmpeg \
     libsm6 \
     libxext6 \
     procps
 
-RUN micromamba install -y -n base -f /tmp/env.yaml && \
-    micromamba clean --all --yes
+# Set the environment variable for the root prefix
+ARG MAMBA_ROOT_PREFIX=/opt/conda
 
-ENV PATH="${PATH}:/opt/conda/bin"
+# Add /opt/conda/bin to the PATH
+ENV PATH $MAMBA_ROOT_PREFIX/bin:$PATH
 
+# Install dependencies with micromamba, clean afterwards
+RUN micromamba env create -f environment.yml \
+    && micromamba clean --all --yes
+
+# Add environment to PATH
+ENV PATH="/opt/conda/envs/staging_env/bin:$PATH"
+
+# Set the working directory
 WORKDIR /staging
 
+# Copy contents of the folder to the working directory
 COPY . .
-# Update package manager and install essential build tools procps is required for Nextflow/nf-core