Dockerfile.walter_update

# Lembrem de criar a imagem no mesmo diretorio em que estiver os arquivos PGAP-1.12.md5 e updatePaths.patch
# Remember to run the image creation in the same directory as the PGAP-1.12.md5 and updatePaths.patch files
# Base image from Ubuntu 22.04
# Imagem base do Ubuntu 22.04
FROM ubuntu:22.04

# Disable interactive prompts during package installation
# Desabilitar prompts interativos durante a instalação de pacotes
ENV DEBIAN_FRONTEND=noninteractive

# Update package list and install system utilities
# Atualizar lista de pacotes e instalar utilitários do sistema
RUN apt-get update && \
    apt-get install -y openjdk-8-jre-headless file gcc make unzip wget patch && \
    apt-get clean

# Install bioinformatics utilities
# Instalar utilitários de bioinformática
RUN apt-get install -y bioperl mcl phylip mafft && \
    apt-get clean

# Set the working directory to root
# Definir o diretório de trabalho para a raiz
WORKDIR /

# Copy the PGAP checksum file into the container
# Copiar o arquivo de checksum do PGAP para o contêiner
COPY PGAP-1.12.md5 /PGAP-1.12.md5

# Download, verify, and extract PGAP
# Baixar, verificar e extrair o PGAP
RUN wget https://downloads.sourceforge.net/project/pgap/PGAP-1.12/PGAP-1.12.tar.gz && \
    md5sum -c PGAP-1.12.md5 && \
    tar xzf PGAP-1.12.tar.gz && \
    mv /PGAP-1.12 /pgap

# Copy the patch file into the container
# Copiar o arquivo de patch para o contêiner
COPY updatePaths.patch /updatePaths.patch

# Apply the patch to PGAP
# Aplicar o patch no PGAP
RUN patch /pgap/PGAP.pl < /updatePaths.patch

# Remove downloaded files to clean up
# Remover arquivos baixados para limpeza
RUN rm /PGAP-1.12.tar.gz /updatePaths.patch

# Install Perl modules needed by PGAP
# Instalar módulos Perl necessários para o PGAP
RUN (echo y; echo o conf prerequisites_policy follow; echo o conf commit) | cpan && \
    cpan Bio::Phylo && \
    cpan Inline::C && \
    cpan Bio::AlignIO && \
    cpan Statistics::LineFit && \
    cpan Statistics::Distributions

# Keep the container running by tailing /dev/null
# Manter o contêiner em execução exibindo /dev/null
CMD ["tail", "-f", "/dev/null"]