ci: use mamba env create

docker/carlisle_r/Dockerfile

@@ -9,13 +9,13 @@ ARG REPONAME="000000"
 ENV REPONAME=${REPONAME}
 
 # install conda packages
-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"
+COPY environment.yml /data2/
+ENV CONDA_ENV=carlisle
+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"
 ENV R_LIBS_USER=/opt2/conda/lib/R/library/
+
 # install ELBOW manually, fails with mamba
 RUN wget --no-check-certificate https://bioconductor.riken.jp/packages/3.4/bioc/src/contrib/ELBOW_1.10.0.tar.gz && \
     R -e 'install.packages("ELBOW_1.10.0.tar.gz", repos = NULL, type="source", INSTALL_opts = "--no-lock")'

docker/carlisle_r/environment.yml

@@ -0,0 +1,38 @@
+channels:
+  - bioconda
+  - conda-forge
+  - r
+dependencies:
+  - bioconductor-bsgenome.hsapiens.ncbi.t2t.chm13v2.0
+  - bioconductor-chipenrich
+  - bioconductor-chipseeker
+  - bioconductor-ComplexHeatmap
+  - bioconductor-deseq2
+  - bioconductor-edger
+  - 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
+  - deeptools
+  - r-argparse
+  - r-circlize
+  - r-DT
+  - r-ggfortify
+  - r-ggvenn
+  - r-htmltools
+  - r-latticeextra
+  - r-openxlsx
+  - r-pander
+  - r-pdp
+  - r-plotly
+  - r-plyr
+  - r-rcolorbrewer
+  - r-reshape2
+  - r-tidyverse
+  - r-xfun>=0.43
+  - r-yaml