chore: use mamba install instead of mamba env install

because mamba env install just uses conda

related to https://www.github.com/mamba-org/mamba/issues/633

docker/carlisle_r/Dockerfile

@@ -9,11 +9,12 @@ ARG REPONAME="000000"
 ENV REPONAME=${REPONAME}
 
 # install conda packages
-COPY environment.yml /data2/
-ENV CONDA_ENV=carlisle_r
-RUN mamba env create -n ${CONDA_ENV} -f /data2/environment.yml && \
-    echo "conda activate ${CONDA_ENV}" > ~/.bashrc
-ENV PATH="/opt2/conda/envs/${CONDA_ENV}/bin:$PATH"
+COPY packages.txt /data2/
+RUN mamba install \
+    --no-channel-priority \
+    -c bioconda -c conda-forge -c r \
+    --file /data2/packages.txt
+ENV PATH="/opt2/conda/bin:$PATH"
 ENV R_LIBS_USER=/opt2/conda/lib/R/library/
 
 # Save Dockerfile in the docker

docker/carlisle_r/packages.txt

@@ -0,0 +1,28 @@
+bioconductor-bsgenome.hsapiens.ncbi.t2t.chm13v2.0
+bioconductor-chipenrich
+bioconductor-chipseeker
+bioconductor-deseq2
+bioconductor-edger
+bioconductor-elbow
+bioconductor-enhancedvolcano
+bioconductor-genomicfeatures
+bioconductor-htsfilter
+bioconductor-org.Hs.eg.db
+bioconductor-org.Mm.eg.db
+bioconductor-rtracklayer
+bioconductor-txdb.hsapiens.ucsc.hg19.knowngene
+bioconductor-TxDb.Hsapiens.UCSC.hg38.knownGene
+bioconductor-TxDb.Mmusculus.UCSC.mm10.knownGene
+r-argparse
+r-DT
+r-ggfortify
+r-ggvenn
+r-htmltools
+r-latticeextra
+r-pander
+r-pdp
+r-plotly
+r-rcolorbrewer
+r-reshape2
+r-tidyverse
+r-yaml