parers.def

Bootstrap: docker
From: rocker/tidyverse:4.4.2
# NOTE: base image includes Ubuntu, R, tidyverse
# https://hub.docker.com/r/rocker/tidyverse/
# Ubuntu 24.04.1 LTS
# R version 4.4.2
# Python 3.12.3

%files
    parers.py /parers/parers.py
    R_for_cmd/bargraphs_cmd_compatible.R /parers/R_for_cmd/bargraphs_cmd_compatible.R
    R_for_cmd/bubble_plots_cmd_compatible.R /parers/R_for_cmd/bubble_plots_cmd_compatible.R
    R_for_cmd/difference_plot_cmd_compatible.R /parers/R_for_cmd/difference_plot_cmd_compatible.R
    R_for_cmd/editing_event_comparison_cmd_compatible.R /parers/R_for_cmd/editing_event_comparison_cmd_compatible.R
    R_for_cmd/editing_extent_plot_cmd_compatible.R /parers/R_for_cmd/editing_extent_plot_cmd_compatible.R

%post -c /bin/bash
    # update package list
    apt-get update

    # install python packages for all users of the container
    apt install -y python3-pandas
    apt install -y python3-python-docx
    apt install -y python3-biopython
    apt install -y python3-xlsxwriter

    # since there are Ubuntu packages for bbmap and muscle, 
    # use those for easier container management

    # install bbmap https://sourceforge.net/projects/bbmap/
    apt install -y bbmap  # BBMap version 39.06

    # install muscle https://github.com/rcedgar/muscle
    apt install -y muscle # muscle 5.2.linux64

%environment
    # add a new line to the standard Ubuntu terminal prompt
    # but still prefix with Apptainer so user knows they are in a container
    export PS1='\[\]Apptainer: \[\]\[\033[01;32m\]\u@\h\[\033[00m\]:\[\033[01;34m\]\w\[\033[00m\]\n\$ '

%labels
    Authors: Glenn Morton
    Version v0.0.1

%help
    This container is intended to run the Pipeline for Analysis of RNA Editing in RNA Sequences (PARERS) 
    developed by Ken Stuart's Lab at Seattle Childrens Hospital