fixed rbio

docker-bsseq/Dockerfile

@@ -30,7 +30,7 @@ RUN apt-get update && apt-get -y install \
 RUN R -e "install.packages('BiocManager'); BiocManager::install(version = '3.19')"
 
 # Install required R and Bioconductor packages
-RUN R -e "install.packages(c('argparse', 'data.table', 'tidyverse', 'vcfR')); \
+RUN R -e "install.packages(c('argparse', 'data.table', 'dplyr' 'tidyverse', 'vcfR')); \
     BiocManager::install(c('HDF5Array', 'bsseq', 'DSS', 'GenomicRanges', 'IRanges', 'methylKit'))"
 
 # Entry point for the container

docker-rbioconductor/Dockerfile

@@ -8,6 +8,7 @@ RUN cp /usr/local/lib/R/site-library/littler/examples/installBioc.r /usr/local/b
 RUN apt-get update && apt-get -y install \
     less \
     curl \
+    wget \
     gzip \
     lsof \
     libz-dev \
@@ -17,18 +18,28 @@ RUN apt-get update && apt-get -y install \
     libxml2-dev \
     libxt6 \
     libglpk-dev \
+    libpcre2-dev \
+    libdeflate-dev \
     libmysqlclient21 \
-    libcurl4-openssl-dev \
-    python3 \
-    python3-pip && \
+    libcurl4-openssl-dev && \
     apt-get clean
 
 # Install basic  R packages
 RUN R -e "install.packages(c('argparse', 'data.table', 'dplyr', 'tidyverse', 'tidyr', 'stringr', 'purrr', 'readr', 'vcfR'))"
 
 # Install Bioconductor and packages
 RUN R -e "install.packages('BiocManager'); BiocManager::install(version = '3.19')"
-RUN R -e "BiocManager::install(c('HDF5Array', 'bsseq', 'DSS', 'GenomicRanges', 'IRanges', 'methylKit'))"
+RUN R -e "BiocManager::install(c('HDF5Array', 'bsseq', 'DSS', 'GenomicRanges', 'IRanges', 'methylKit','rtracklayer'))"
+
+ENV CONDA_DIR /opt/conda
+RUN cd /tmp && mkdir -p $CONDA_DIR && \
+    wget "https://github.com/conda-forge/miniforge/releases/download/24.3.0-0/Mambaforge-24.3.0-0-Linux-x86_64.sh" && \
+    bash Mambaforge-24.3.0-0-Linux-x86_64.sh -f -b -p $CONDA_DIR && \
+    rm -f Mambaforge-24.3.0-0-Linux-x86_64.sh && \
+    $CONDA_DIR/bin/mamba install -y --channel conda-forge --channel bioconda bcftools==1.20 htslib==1.20 samtools==1.20 bedtools=2.31 pandas==2.0.2 pybedtools==0.9.0 openpyxl==3.1.2 scipy==1.11.4 cython cyvcf2==0.30.28 pysam==0.22.1 statsmodels pyranges==0.0.129 pybigwig biotite && \
+    $CONDA_DIR/bin/conda clean -y --all && \
+    ln -s /opt/conda/bin/* /usr/local/bin/
+
 
 # Entry point for the container
 CMD ["bash"]