Bootstrap: docker
From: ubuntu:22.04

%labels
    Author ATGC
    Tool MOTIF
    Version 1.0

%environment
    export LC_ALL=C.UTF-8
    export LANG=C.UTF-8
    export PATH="/opt/motif/bin:$PATH"

%post
    set -eux
    apt-get update
    apt-get install -y --no-install-recommends \
        ca-certificates \
        git \
        build-essential \
        g++ \
        make \
        zlib1g-dev \
        libgecode-dev \
        python3 \
        python3-pip \
        bash \
        coreutils \
        zip

    # Replace this URL with the public repository you will create for MOTIF runtime.
    MOTIF_REPO_URL="https://gite.lirmm.fr/atgc/atgc_motif.git"
    git clone --depth 1 "${MOTIF_REPO_URL}" /opt/motif

    # Compatibility patch for legacy libSSA code with Gecode >= 6 (Ubuntu 22.04+).
    python3 - <<'PY'
from pathlib import Path

hpp = Path("/opt/motif/libSSA/src/seqGenerator.hpp")
cpp = Path("/opt/motif/libSSA/src/seqGenerator.cpp")
src_makefile = Path("/opt/motif/libSSA/src/Makefile")
ssa_makefile = Path("/opt/motif/libSSA/src/SSA/Makefile")
if not hpp.exists() or not cpp.exists():
    raise SystemExit(0)

hpp_text = hpp.read_text(encoding="utf-8")
cpp_text = cpp.read_text(encoding="utf-8")
original_hpp = hpp_text
original_cpp = cpp_text

hpp_text = hpp_text.replace(
    "    CpSeqGeneratorCore(bool share, CpSeqGeneratorCore& s) ;",
    "    CpSeqGeneratorCore(CpSeqGeneratorCore& s) ;",
)
hpp_text = hpp_text.replace(
    "    copy(bool share) ;",
    "    copy(void) ;",
)

if "default_options()" not in cpp_text:
    cpp_text = cpp_text.replace(
        "#include <memory>\n\n",
        "#include <memory>\n\n"
        "namespace {\n"
        "const Gecode::SizeOptions& default_options() {\n"
        "\tstatic Gecode::SizeOptions options(\"CpSeqGeneratorCore\");\n"
        "\treturn options;\n"
        "}\n"
        "}\n\n",
        1,
    )

cpp_text = cpp_text.replace(
    "CpSeqGeneratorCore::CpSeqGeneratorCore( float const pwm[][4], int const pwmWidth, float const minThreshold ) :\n"
    "\t\tsequence( *this, pwmWidth, 0, 3 ), scores_by_position( *this, pwmWidth )",
    "CpSeqGeneratorCore::CpSeqGeneratorCore( float const pwm[][4], int const pwmWidth, float const minThreshold ) :\n"
    "\t\tScript(default_options()), sequence( *this, pwmWidth, 0, 3 ), scores_by_position( *this, pwmWidth )",
)
cpp_text = cpp_text.replace(
    "CpSeqGeneratorCore::CpSeqGeneratorCore(bool share, CpSeqGeneratorCore& s) : Script(share,s) {\n"
    "\tsequence.update(*this, share, s.sequence);\n"
    "}",
    "CpSeqGeneratorCore::CpSeqGeneratorCore(CpSeqGeneratorCore& s) : Script(s) {\n"
    "\tsequence.update(*this, s.sequence);\n"
    "\tscores_by_position.update(*this, s.scores_by_position);\n"
    "}",
)
cpp_text = cpp_text.replace(
    "CpSeqGeneratorCore::copy(bool share) {\n"
    "\treturn new CpSeqGeneratorCore(share,*this);\n"
    "}",
    "CpSeqGeneratorCore::copy(void) {\n"
    "\treturn new CpSeqGeneratorCore(*this);\n"
    "}",
)

if "CpSeqGeneratorCore(bool share, CpSeqGeneratorCore& s)" in hpp_text:
    raise RuntimeError("Failed to patch seqGenerator.hpp cloning constructor for Gecode >= 6.")
if "copy(bool share)" in hpp_text:
    raise RuntimeError("Failed to patch seqGenerator.hpp copy signature for Gecode >= 6.")
if "Script(share,s)" in cpp_text:
    raise RuntimeError("Failed to patch seqGenerator.cpp Script clone constructor for Gecode >= 6.")
if "copy(bool share)" in cpp_text:
    raise RuntimeError("Failed to patch seqGenerator.cpp copy() signature for Gecode >= 6.")

if hpp_text != original_hpp:
    hpp.write_text(hpp_text, encoding="utf-8")
if cpp_text != original_cpp:
    cpp.write_text(cpp_text, encoding="utf-8")

if src_makefile.exists():
    src_text = src_makefile.read_text(encoding="utf-8")
    original_src = src_text
    src_text = src_text.replace(
        "CFLAGS=-Wall -Wextra -O3 -march=native -I$(CURDIR)",
        "CFLAGS=-std=gnu++14 -Wall -Wextra -O3 -march=native -I$(CURDIR)",
    )
    src_text = src_text.replace(
        "$(CC) $(CFLAGS) $(DIR_GECODE_H) $(DIR_GECODE_LIB) $(GECODE_LINKER) -o $@ $^ -Ikseq -lz -lrt",
        "$(CC) $(CFLAGS) $(DIR_GECODE_H) -o $@ $^ $(DIR_GECODE_LIB) $(GECODE_LINKER) -Ikseq -lz -lrt",
    )
    if "$(DIR_GECODE_LIB) $(GECODE_LINKER) -o $@ $^" in src_text:
        raise RuntimeError("Failed to patch libSSA/src/Makefile link order for Gecode.")
    if src_text != original_src:
        src_makefile.write_text(src_text, encoding="utf-8")

if ssa_makefile.exists():
    ssa_text = ssa_makefile.read_text(encoding="utf-8")
    original_ssa = ssa_text
    ssa_text = ssa_text.replace(
        "CFLAGS=-W -Wall -pedantic -pedantic-errors -O9 -DNDEBUG",
        "CFLAGS=-std=gnu++14 -W -Wall -pedantic -O9 -DNDEBUG",
    )
    ssa_text = ssa_text.replace("-pedantic-errors", "")
    if "CFLAGS=" in ssa_text and "-std=" not in ssa_text:
        ssa_text = ssa_text.replace("CFLAGS=", "CFLAGS=-std=gnu++14 ", 1)
    if "-pedantic-errors" in ssa_text:
        raise RuntimeError("Failed to patch SSA/Makefile pedantic flags for modern compilers.")
    if ssa_text != original_ssa:
        ssa_makefile.write_text(ssa_text, encoding="utf-8")
PY

    if [ -f /opt/motif/requirements.txt ]; then
        python3 -m pip install --no-cache-dir -r /opt/motif/requirements.txt
    fi

    # Build searchMotif if not already provided by the runtime repository.
    if [ ! -x /opt/motif/libSSA/bin/searchMotif ]; then
        mkdir -p /opt/motif/libSSA/bin
        make -C /opt/motif/libSSA/src DIR_GECODE_LIB= DIR_GECODE_H= ../bin/searchMotif
    fi

    test -x /opt/motif/libSSA/bin/searchMotif
    chmod +x /opt/motif/bin/motif-run

    apt-get clean
    rm -rf /var/lib/apt/lists/*

%runscript
    exec /opt/motif/bin/motif-run "$@"

%test
    test -x /opt/motif/bin/motif-run
    test -x /opt/motif/libSSA/bin/searchMotif
    /opt/motif/bin/motif-run --help