for merge

docker-baseimage/Dockerfile

@@ -43,6 +43,7 @@ RUN apt-get update -y && apt-get install -y --no-install-recommends \
     git-lfs \
     smbclient \
     groff \
+    mailutils \
     && apt-get clean all
 
 #set timezone to CDT

docker-bsseq/Dockerfile

@@ -0,0 +1,37 @@
+# Use the Rocker R image
+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 \
+    curl \
+    gzip \
+    lsof \
+    libz-dev \
+    libbz2-dev \
+    liblzma-dev \
+    libxml2 \
+    libxml2-dev \
+    libxt6 \
+    libglpk-dev \
+    libmysqlclient21 \
+    libcurl4-openssl-dev \
+    python3 \
+    python3-pip && \
+    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', 'vcfR')); \
+    BiocManager::install(c('HDF5Array', 'bsseq', 'DSS', 'GenomicRanges', 'IRanges', 'methylKit'))"
+
+# Entry point for the container
+CMD ["bash"]

docker-dorado/Dockerfile

@@ -0,0 +1,8 @@
+FROM ontresearch/dorado@sha256:e70f10b2c11e8b772edf00d07107e8dec8da281a49e90f8908aa68085959a34d
+LABEL description="Image with dorado"
+USER root
+# Install essential packages
+RUN sudo mkdir -p /opt/dorado/models && \
+    dorado download --directory /opt/dorado/models --model all
+
+ENV PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin

docker-modkit/Dockerfile

@@ -0,0 +1,16 @@
+FROM ubuntu:focal-20221130
+
+LABEL description="Basic image with modkit"
+
+# Install essential packages
+RUN apt-get update -y && \
+    apt-get install -y wget
+
+# build modkit
+RUN mkdir /opt/modkit && \
+    wget https://github.com/nanoporetech/modkit/releases/download/v0.3.1rc1/modkit_v0.3.1rc1_centos7_x86_64.tar.gz && \
+    tar -xf modkit_v0.3.1rc1_centos7_x86_64.tar.gz -C /opt/modkit && \
+    chmod +x /opt/modkit/dist/modkit && \
+    ln -s /opt/modkit/dist/modkit /usr/local/bin/modkit
+
+ENV PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin