Add camdac dockerfile

Dockerfile

@@ -0,0 +1,40 @@
+# Use a lightweight R base image
+FROM rocker/r-ver:4.3.0
+# Set the working directory
+WORKDIR /app
+
+# Install system dependencies (if needed)
+# For example, if your package needs external libraries, install them here
+RUN chmod 1777 /tmp
+RUN apt-get update \
+    && apt-get install -y --no-install-recommends \
+    && apt-get install -y libxml2 libodbc1 \
+    && apt-get install -y libz-dev libbz2-dev bzip2-doc zlib1g-dev \
+    && apt-get install -y liblzma-dev libcurl4-openssl-dev wget \
+    && apt-get install -y default-jre git curl bzip2
+
+# Install alleleCounter
+RUN git clone https://github.com/cancerit/alleleCount.git \
+    && cd alleleCount && bash ./setup.sh /usr/local
+RUN echo 'export LD_LIBRARY_PATH=/usr/local/lib:$LD_LIBRARY_PATH' >> ~/.bashrc
+RUN echo 'export PATH=/usr/local/bin:$PATH' >> ~/.bashrc
+
+# Install CAMDAC
+RUN R -q -e 'install.packages("remotes")'
+RUN R -q -e 'remotes::install_github("VanLoo-lab/CAMDAC@wgbs", lib="/usr/local/lib/R/site-library")'
+
+# Install CAMDAC References from repository [Deprecated]
+#RUN R -q -e 'library(CAMDAC);CAMDAC::download_pipeline_files(bsseq="wgbs", directory="pipeline_files/")'
+
+# Install CAMDAC references from local WGBS files
+# Copy local WGBS pipeline files and extract for CAMDAC
+RUN mkdir -p /opt/pipeline_files
+COPY ./camdac_wgbs_pipeline_files.tar.gz /opt/camdac_wgbs_pipeline_files.tar.gz
+RUN tar -zxvf /opt/camdac_wgbs_pipeline_files.tar.gz -C /opt/pipeline_files
+RUN rm /opt/camdac_wgbs_pipeline_files.tar.gz
+
+# Set the working directory
+WORKDIR /app
+
+# Set command to be use
+CMD ["/usr/local/bin/Rscript"]