Dockerfile

FROM postgres:16

ENV DEBIAN_FRONTEND=noninteractive \
    CHADO_DB_NAME=postgres \
    CHADO_DB_HOST=localhost \
    CHADO_DB_PORT=5432 \
    CHADO_DB_USERNAME=postgres \
    CHADO_DB_PASSWORD=postgres \
    POSTGRES_PASSWORD=postgres \
    GMOD_ROOT=/usr/share/gmod/ \
    PGDATA=/var/lib/postgresql/data/ \
    SCHEMA_URL=https://github.com/galaxy-genome-annotation/chado-schema-builder/releases/download/1.31-build2022-12-03/chado-1.31.sql.gz \
    INSTALL_CHADO_SCHEMA=1 \
    INSTALL_YEAST_DATA=0

# TODO: Pulled from webapollo docker image, some of these may be extraneous (I
# think the heap stuff.) Installed most from apt for ease of installation
RUN apt-get -qq update && \
    apt-get install --no-install-recommends -y build-essential \
    libpng-dev zlib1g zlib1g-dev build-essential make libpq-dev curl \
    xsltproc wget ca-certificates libperlio-gzip-perl \
    libcapture-tiny-perl libtest-differences-perl libperlio-gzip-perl \
    libdevel-size-perl libdbi-perl libjson-perl libjson-xs-perl libheap-perl \
    libhash-merge-perl libdbd-pg-perl libio-string-perl libtest-most-perl \
    libarray-compare-perl libconvert-binary-c-perl libgraph-perl \
    libgraphviz-perl libsoap-lite-perl libsvg-perl libsvg-graph-perl \
    libset-scalar-perl libsort-naturally-perl libxml-sax-perl libxml-twig-perl \
    libxml-writer-perl libyaml-perl perl-doc libgd-dev nano vim-tiny netcat-openbsd && \
    apt-get autoremove -y && apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*

# Some have to be forced.
# But most install just fine
RUN mkdir -p $GMOD_ROOT $PGDATA && \
    curl -L http://cpanmin.us | perl - App::cpanminus && \
    cpanm --force --notest Test::More Heap::Simple Heap::Simple::XS DBIx::DBStag GO::Parser && \
    cpanm --notest DBI Digest::Crc32 Cache::Ref::FIFO URI::Escape HTML::Entities \
    HTML::HeadParser HTML::TableExtract HTTP::Request::Common LWP XML::Parser \
    XML::Parser::PerlSAX XML::SAX::Writer XML::Simple Data::Stag \
    Error PostScript::TextBlock Spreadsheet::ParseExcel Algorithm::Munkres \
    CJFIELDS/BioPerl-1.6.924.tar.gz Bio::GFF3::LowLevel::Parser File::Next CGI DBD::Pg SQL::Translator \
    Digest::MD5 Text::Shellwords Module::Build Class::DBI Class::DBI::Pg \
    Class::DBI::Pager Template Bio::Chado::Schema GD GO::Parser Bio::FeatureIO \
    && wget https://github.com/GMOD/Chado/archive/master.tar.gz -O /tmp/master.tar.gz \
    && cd / && tar xvfz /tmp/master.tar.gz \
    && mv /Chado-master /chado \
    && rm -f /tmp/master.tar.gz

WORKDIR /chado/chado/
# https://github.com/docker-library/postgres/blob/a82c28e1c407ef5ddfc2a6014dac87bcc4955a26/9.4/docker-entrypoint.sh#L85
# This will cause the chado schema to load on boot and be MUCH better behaved.
RUN perl Makefile.PL GMOD_ROOT=/usr/share/gmod/  DEFAULTS=1 RECONFIGURE=1 && \
    make && \
    make install && \
    wget --quiet $SCHEMA_URL -O /chado.sql.gz && gunzip /chado.sql.gz && \
    wget --quiet http://downloads.yeastgenome.org/curation/chromosomal_feature/saccharomyces_cerevisiae.gff.gz -O saccharomyces_cerevisiae.gff.gz && \
    gunzip -c saccharomyces_cerevisiae.gff.gz > saccharomyces_cerevisiae.gff && \
    sed -i s'/%20/ /g' saccharomyces_cerevisiae.gff && \
    chown -R postgres:postgres /chado/chado/ && \
    sed -i -r 's/defined\(@_\)/@_/g' /usr/local/share/perl/*/Bio/GMOD/DB/Adapter.pm && \
    sed -i "s|listen_addresses=''|listen_addresses='localhost'|" /usr/local/bin/docker-entrypoint.sh

# The sed is required because the gmod_add_organism script assumes a network
# connection rather than socke.

COPY load_schema.sh /docker-entrypoint-initdb.d/00-load_schema.sh
COPY load_yeast.sh /docker-entrypoint-initdb.d/01-load_yeast.sh
COPY search.sh /docker-entrypoint-initdb.d/02-search.sh
COPY search.sql /search.sql