updated rbio

docker-rbioconductor/Dockerfile

@@ -4,9 +4,6 @@ FROM rocker/r-ver:4.4.0
 # Copy installBioc.r script
 RUN cp /usr/local/lib/R/site-library/littler/examples/installBioc.r /usr/local/bin/installBioc.r
 
-# Install BiocManager
-RUN Rscript -e "install.packages('BiocManager')"
-
 # Install system dependencies
 RUN apt-get update && apt-get -y install \
     less \
@@ -21,17 +18,25 @@ RUN apt-get update && apt-get -y install \
     libxt6 \
     libglpk-dev \
     libmysqlclient21 \
-    libcurl4-openssl-dev \
-    python3 \
-    python3-pip && \
+    libcurl4-openssl-dev && \
     apt-get clean
 
 # Install Bioconductor packages
 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', 'dplyr','vcfR')); \
-    BiocManager::install(c('HDF5Array', 'bsseq', 'DSS', 'GenomicRanges', 'IRanges', 'methylKit'))"
+RUN R -e "install.packages(c('argparse', 'data.table', 'dplyr', 'tidyverse', 'vcfR'))"
+RUN R -e "BiocManager::install(c('HDF5Array', 'bsseq', 'DSS', 'GenomicRanges', 'IRanges', 'methylKit'))"
+
+ARG MAMBA_VERSION="24.3.0-0"
+
+ENV CONDA_DIR /opt/conda
+COPY env/*.yml /tmp/
+RUN curl -L -O "https://github.com/conda-forge/miniforge/releases/download/${MAMBA_VERSION}/Miniforge3-$(uname)-$(uname -m).sh" && \
+    bash Miniforge3-$(uname)-$(uname -m).sh -f -b -p /opt/conda && \
+    rm -f Miniforge3-$(uname)-$(uname -m).sh && \
+    $CONDA_DIR/bin/mamba install -y -f /tmp/basic-tools.yml && \
+    $CONDA_DIR/bin/conda clean -y --all
 
 # Entry point for the container
 CMD ["bash"]

docker-rbioconductor/env/basic-tools.yml

@@ -0,0 +1,41 @@
+name: basic-tools
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - python
+  - ipykernel
+  - pandas
+  - numpy
+  - matplotlib
+  - seaborn
+  - pybedtools
+  - bedtools
+  - bcftools
+  - htslib
+  - samtools
+  - tabulate
+  - deeptools
+  - pip
+  - adjustText
+  - Jinja2
+  - openpyxl
+  - scikit-misc
+  - scikit-learn
+  - zlib
+  - pip:
+    - polars
+    - pyranges
+    - diptest
+    - gtfparse
+    - lets-plot
+    - openai
+    - langchain-openai
+    - jupyter-ai[all]
+    - python-docx
+    - shiny
+    - figeno
+    - pypandoc_binary 
+    - cairosvg
+    - rpy2

docker-rbioconductor/scripts/conda_soft_links.sh

@@ -0,0 +1,10 @@
+# this loop to avoid overiding any existing soft-linked binary
+link_path=$1
+for file in `ls $link_path` ; do 
+    if [ -f /usr/local/bin/$file ] 
+    then 
+        :
+    else 
+        ln -s ${link_path}/$file /usr/local/bin/$file
+    fi 
+done