Singularity.PHI1.0.def

Bootstrap: docker
From: ubuntu:22.04
%help
    Container for PHI v.1.0
    https://github.com/at-cg/PHI

    Includes 
        PHI
        HTSlib
        Samtools
        BCFtools
        sdsl-lite
        libhandlegraph
        gbwt
        gbwtgraph
        gurobi
        vg
        
    Licensed by CC-BY


%labels
    VERSION "PHI v.1.0"
    Maintainer Francois Sabot <francois.sabot@ird.fr>
    March, 2025

%post
    # faster apt downloads
    export DEBIAN_FRONTEND=noninteractive
    export LC_ALL=C
    (
        . /etc/os-release
        cat << _EOF_ > mirror.txt
deb mirror://mirrors.ubuntu.com/mirrors.txt ${UBUNTU_CODENAME} main restricted universe multiverse
deb mirror://mirrors.ubuntu.com/mirrors.txt ${UBUNTU_CODENAME}-updates main restricted universe multiverse
deb mirror://mirrors.ubuntu.com/mirrors.txt ${UBUNTU_CODENAME}-backports main restricted universe multiverse
deb mirror://mirrors.ubuntu.com/mirrors.txt ${UBUNTU_CODENAME}-security main restricted universe multiverse

_EOF_
        mv /etc/apt/sources.list /etc/apt/sources.list.bak
        cat mirror.txt /etc/apt/sources.list.bak > /etc/apt/sources.list
    )

    # apt dependencies
    apt update
    apt install -y \
    	apt-utils \
        autoconf \
        automake \
        gcc \
        build-essential \
        software-properties-common \
        tar \
        unzip \
        wget \
        zlib1g-dev \
        sudo \
        cmake \
        libstdc++-12-dev \
        bzip2 \
        xz-utils \
        lz4 \
        zstd \
        git-all \
        libbz2-dev \
        liblzma-dev \
        libncurses5-dev


       
# Installation based on installdeps file

#Main folder
cd /opt
git clone https://github.com/at-cg/PHI
export PHIDIR=/opt/PHI



#Subfolders
mkdir -p $PHIDIR/extra
mkdir -p $PHIDIR/extra/plugins
mkdir -p $PHIDIR/extra/lib
mkdir -p $PHIDIR/extra/bin
mkdir -p $PHIDIR/extra/include

#Install folder
mkdir -p $PHIDIR/temp_bin
cd $PHIDIR/temp_bin


# htslib
git clone https://github.com/samtools/htslib.git
cd htslib
git submodule update --init --recursive
autoreconf -i
./configure --prefix=$PHIDIR/extra
make -j4
make install
cd ..

# samtools
git clone https://github.com/samtools/samtools.git
cd samtools
autoheader
autoconf -Wno-syntax
./configure --prefix=$PHIDIR/extra
make -j4
make install
cd ..

# bcftools
git clone https://github.com/samtools/bcftools.git
cd bcftools
make -j4
cp bcftools $PHIDIR/extra/bin/
cp -r plugins/* $PHIDIR/extra/plugins/
cd ..

# sdsl-lite
git clone https://github.com/vgteam/sdsl-lite.git
cd sdsl-lite
cd build
cmake ..
make -j4
cp -r lib/* $PHIDIR/extra/lib/.
cp -r external/libdivsufsort/lib/* $PHIDIR/extra/lib/
cd ../..

# libhandlegraph
git clone https://github.com/vgteam/libhandlegraph.git
cd libhandlegraph
mkdir -p build
cd build
cmake .. 
make -j4 CPPFLAGS="-I../../sdsl-lite/include" LDFLAGS="-L../../sdsl-lite/build/lib/ -L../../sdsl-lite/build/external/libdivsufsort/lib/"
#A VERIFIER !!
cp libhandlegraph.a $PHIDIR/extra/lib/
cp libhandlegraph.so $PHIDIR/extra/lib/
cd ../..

# gbwt
git clone https://github.com/jltsiren/gbwt.git
cd gbwt
make -j4 CPPFLAGS="-I../sdsl-lite/include -I../libhandlegraph/src/include/" LDFLAGS="-L../sdsl-lite/build/lib/ -L../sdsl-lite/build/external/libdivsufsort/lib/ -L../libhandlegraph/build/"
cp -r lib/* $PHIDIR/extra/lib/
cd ..

# gbwtgraph
git clone https://github.com/jltsiren/gbwtgraph.git
cd gbwtgraph
make CPPFLAGS="-I../sdsl-lite/include -I../gbwt/include -I../libhandlegraph/src/include/" \
     LDFLAGS="-L../gbwt/lib -L../sdsl-lite/build/lib/ -L../sdsl-lite/build/external/libdivsufsort/lib/ -L../libhandlegraph/build/" -j4
cp bin/gfa2gbwt $PHIDIR/extra/bin/
cp -r lib/* $PHIDIR/extra/lib/
cd ..

# zlib
wget --no-check-certificate https://zlib.net/current/zlib.tar.gz
tar -xvf zlib.tar.gz
cd zlib-*
./configure --prefix=$PHIDIR/extra
make -j4
make install
cd ..

# vg
wget https://github.com/vgteam/vg/releases/download/v1.60.0/vg -O $PHIDIR/extra/bin/vg
chmod +x $PHIDIR/extra/bin/vg



# gurobi
wget --no-check-certificate https://packages.gurobi.com/11.0/gurobi11.0.2_linux64.tar.gz
tar -xvf gurobi11.0.2_linux64.tar.gz
cd gurobi1102/linux64
cp -r lib/* $PHIDIR/extra/lib/.
cp -r include/* $PHIDIR/extra/include/.
cd $PHIDIR/temp_bin

# Cleaning
rm -rf $PHIDIR/temp_bin

#Install PHI itself
cd /opt/PHI
export PATH=/opt/PHI/extra/bin:/opt/PHI/extra/include:$PATH
export LD_LIBRARY_PATH=/opt/PHI/extra/lib:$LD_LIBRARY_PATH
make -j4
    
%environment
	export PATH=/opt/PHI/extra/bin:/opt/PHI:$PATH
	export LD_LIBRARY_PATH=/opt/PHI/extra/lib:$LD_LIBRARY_PATH

	
%runscript
    exec "$@"