Merge pull request #27 from CCBR/chipseeker

feat: create docker for ChIPseeker processes

common/ccbr_chipseeker/Dockerfile

@@ -0,0 +1,25 @@
+FROM nciccbr/ccbr_ubuntu_base_20.04:v6.1
+
+# build time variables
+ARG BUILD_DATE="000000"
+ENV BUILD_DATE=${BUILD_DATE}
+ARG BUILD_TAG="000000"
+ENV BUILD_TAG=${BUILD_TAG}
+ARG REPONAME="000000"
+ENV REPONAME=${REPONAME}
+
+# install R packages with conda
+COPY environment.txt /data2/
+RUN mamba install -c bioconda -c conda-forge --file /data2/environment.txt
+ENV R_LIBS_USER=/opt2/conda/lib/R/library/
+
+# cleanup etc
+# Save Dockerfile in the docker
+COPY Dockerfile /opt2/Dockerfile_${REPONAME}.${BUILD_TAG}
+RUN chmod a+r /opt2/Dockerfile_${REPONAME}.${BUILD_TAG}
+ENV PATH="/opt2/:$PATH"
+RUN apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* && \
+    apt-get autoclean && \
+    apt-get autoremove -y && \
+    rm -rf /var/lib/{apt,dpkg,cache,log}/
+WORKDIR /data2

common/ccbr_chipseeker/environment.txt

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+r-base=4.3.1
+r-argparse
+r-BiocManager
+r-dplyr
+r-ggplot2
+r-glue
+bioconductor-ChIPseeker
+bioconductor-org.Bt.eg.db
+bioconductor-org.Hs.eg.db
+bioconductor-org.Mm.eg.db 
+bioconductor-org.Mmu.eg.db 
+bioconductor-TxDb.Btaurus.UCSC.bosTau9.refGene 
+bioconductor-TxDb.Hsapiens.UCSC.hg19.knownGene
+bioconductor-TxDb.Hsapiens.UCSC.hg38.knownGene
+bioconductor-TxDb.Mmulatta.UCSC.rheMac10.refGene
+bioconductor-TxDb.Mmusculus.UCSC.mm9.knownGene
+bioconductor-TxDb.Mmusculus.UCSC.mm10.knownGene