Use yml for conda dependencies in Docker

Dockerfile

@@ -1,38 +1,15 @@
 FROM continuumio/miniconda3
 
-RUN conda config --add channels conda-forge \
-    && conda config --add channels bioconda \
-    && conda config --add channels defaults
+ENV PATH=/opt/conda/envs/bact_seq-1.0.0/bin:$PATH
+ENV LC_ALL=C.UTF-8
+ENV LANG=C.UTF-8
 
-RUN conda install -y \
-    numpy>=1.21 \
-    python>=3.7,<3.9 \
-    gawk>=5.1 \
-    pigz>=2.3 \
-    pandas>=1.4 \
-    r-base>=3.6 \
-    r-optparse>=1.7 \
-    r-rcolorbrewer>=1 \
-    r-reshape2>=1.4 \
-    r-pheatmap>=1.0 \
-    r-matrixstats>=0.6 \
-    r-ape>=5.0 \
-    r-xtable>=1.8 \
-    r-rsqlite>=2.2 \
-    r-plyr>=1.8 \
-    r-fastmap>=1.1 \
-    r-devtools>=2.4 \
-    r-scales>=1.1 \
-    r-tidyverse>=1.9 \
-    fastqc>=0.11 \
-    trim-galore>=0.6 \
-    bwa>=0.7 \
-    samtools>=1.15 \
-    bioconductor-edger>=3.36 \
-    bioconductor-deseq2>=1.34 \
-    bioconductor-topgo>=2.00 \
-    bioconductor-go.db>=3.00 \
-    bioconductor-rsubread>=2.00 \
-    bioconductor-enhancedvolcano>=1.00
+RUN echo ". /opt/conda/etc/profile.d/conda.sh" >> ~/.bashrc && \
+    echo "source activate bact_seq-1.0.0" >> ~/.bashrc && \
+    git clone https://github.com/adamd3/BactSeq.git && \
+    /opt/conda/bin/conda env create -f BactSeq/environment.yml && \
+    rm -rf BactSeq
 
-WORKDIR /data/
+ENTRYPOINT ["bash", "-c"]
+
+CMD ["exec \"$@\""]