add Singularity build file

Singularity

@@ -0,0 +1,172 @@
+BootStrap: docker
+From: nvidia/cuda:12.9.0-cudnn-devel-ubuntu24.04
+
+# labels visible upon inspect
+%labels
+    Maintainer Francois Aguet
+    tensorqtl_version 1.0.10
+    R_Version 4.4.2
+    Ubuntu_version 24.04
+    CUDA_version 12.9.0
+    Image_Version v1.0
+    Repository https://github.com/broadinstitute/tensorqtl
+
+# help message
+%help
+    This will run tensorqtl, use --nv and have nvidia-container-cli available on the host to make sure you can run with GPU acceleration (https://docs.sylabs.io/guides/latest/user-guide/gpu.html)
+
+# run tensorqtl
+%apprun tensorqtl
+    exec python -m tensorqtl "${@}"
+
+# run tensorqtl
+%runscript
+    exec python -m tensorqtl "${@}"
+
+# install instructions
+%post
+    #####################
+    # Software versions #
+    #####################
+    export R_VERSION=4.4.2
+    export HTSLIB_VERSION=1.21
+    export BCFTOOLS_VERSION=1.21
+    export TENSORQTL_VERSION=1.0.10
+    export PGENLIB_COMMIT='cf54067a3a40417125a9d13640d5ea3450d02dc0'
+
+
+    ##############
+    # fix locale #
+    ##############
+    apt-get update
+    # install locales
+    apt-get install -y --no-install-recommends \
+        locales
+    # Configure default locale
+    echo "en_US.UTF-8 UTF-8" >> /etc/locale.gen
+    locale-gen en_US.utf8
+    /usr/sbin/update-locale LANG=en_US.UTF-8
+    export LC_ALL=en_US.UTF-8
+    export LANG=en_US.UTF-8
+
+
+    #####################################
+    # Install R and python dependencies #
+    #####################################
+    apt-get update
+    # install system libraries R and Python will depend on
+    apt-get install -y --no-install-recommends \
+        software-properties-common \
+        dirmngr \
+        wget \
+        apt-transport-https \
+        build-essential \
+        cmake \
+        curl \
+        libboost-all-dev \
+        libbz2-dev \
+        libcurl3-dev \
+        liblzma-dev \
+        libncurses5-dev \
+        libssl-dev \
+        python3 \
+        python3-pip \
+        python3-apt \
+        python3-venv \
+        python3-dev \
+        libssl-dev \
+        sudo \
+        unzip \
+        wget \
+        zlib1g-dev \
+        gcc-11 \
+        gcc-13 \
+        git
+    # get public key for CRAN
+    wget -qO- https://cloud.r-project.org/bin/linux/ubuntu/marutter_pubkey.asc | \
+        tee -a /etc/apt/trusted.gpg.d/cran_ubuntu_key.asc
+    # add R CRAN repository
+    add-apt-repository \
+        "deb https://cloud.r-project.org/bin/linux/ubuntu $(lsb_release -cs)-cran40/"
+    # install R
+    apt-get install -y --no-install-recommends \
+        r-recommended=${R_VERSION}* \
+        r-base=${R_VERSION}* \
+        r-base-core=${R_VERSION}* \
+        r-base-dev=${R_VERSION}*
+
+
+    ################################
+    # Install HTSlib and BCFtools #
+    ###############################
+    # install htslib
+    cd /opt
+    # download from github page
+    wget --no-check-certificate https://github.com/samtools/htslib/releases/download/${HTSLIB_VERSION}/htslib-${HTSLIB_VERSION}.tar.bz2
+    # extract archive
+    tar -xf htslib-${HTSLIB_VERSION}.tar.bz2 && rm htslib-${HTSLIB_VERSION}.tar.bz2 && cd htslib-${HTSLIB_VERSION}
+    # configure before installation
+    ./configure --enable-libcurl --enable-s3 --enable-plugins --enable-gcs
+    # install and clean up
+    make && make install && make clean
+    cd
+
+    # install bcftools
+    cd /opt
+    # download from github page
+    wget --no-check-certificate https://github.com/samtools/bcftools/releases/download/${BCFTOOLS_VERSION}/bcftools-${BCFTOOLS_VERSION}.tar.bz2
+    tar -xf bcftools-${BCFTOOLS_VERSION}.tar.bz2 && rm bcftools-${BCFTOOLS_VERSION}.tar.bz2 && cd bcftools-${BCFTOOLS_VERSION}
+    # configure before installation
+    ./configure --with-htslib=system
+    # install and clean up
+    make && make install && make clean
+    cd
+
+
+    ##################
+    # Install qvalue #
+    ##################
+    Rscript -e 'if (!requireNamespace("BiocManager", quietly = TRUE)) {install.packages("BiocManager")}; BiocManager::install("qvalue");'
+
+
+    #####################
+    # Install tensorqtl #
+    #####################
+    # install tensorqtl dependencies
+    cd /opt
+    python3 -m venv venv
+    . /opt/venv/bin/activate
+    # upgrade setup tools
+    pip install --upgrade pip setuptools
+     # install other libraries
+    pip install numpy==1.26.4 pandas scipy
+    pip install pandas-plink ipython jupyter jupyterlab IProgress matplotlib pyarrow torch rpy2 gcsfs
+    # install dependencies
+    pip install "cython>=0.29.21"
+    # clone pgenlib
+    git clone https://github.com/chrchang/plink-ng
+    # go to python folder of pgenlib
+    cd plink-ng/2.0/Python
+    # load the specific commit
+    git checkout ${PGENLIB_COMMIT}
+    # install pgenlib
+    python setup.py build_clib build_ext -i
+    python setup.py install
+    # back to home
+    cd /opt
+    # finally install tensorqtl version
+    pip install tensorqtl==${TENSORQTL_VERSION}
+    # or install the dev version from the master branch
+    #git clone https://github.com/broadinstitute/tensorqtl.git
+    #cd tensorqtl
+    #pip install .
+    #cd
+    echo '. /opt/venv/bin/activate' >> $SINGULARITY_ENVIRONMENT
+
+    ###########
+    # cleanup #
+    ###########
+    apt-get clean
+    apt-get autoremove -y
+
+