traitar3.def

# Singularity definition file for traitar

bootstrap: docker
from: ubuntu:16.04

# To Build: sudo /opt/ohpc/pub/libs/singularity/3.2.1/bin/singularity build traitar.sif traitar.def 
# singularity build --fakeroot traitar3.sif traitar3.def
%help
    A simple container to run traitar

%environment
    PATH="$PATH:/usr/local/anaconda/bin/"
    LC_ALL=C
%post
    apt-get update
    apt-get install -y eatmydata wget curl sudo nano perl elfutils build-essential
    apt-get install -y gfortran emboss
    eatmydata apt-get install -y bzip2
    sudo apt-get install -y libdatetime-perl libxml-simple-perl libdigest-md5-perl git default-jre bioperl
    apt-get clean
    #install anaconda
    wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O ./anaconda.sh && \
    bash ./anaconda.sh -b -p /usr/local/anaconda ; rm ./anaconda.sh
    # set anaconda path
    export PATH="$PATH:/usr/local/anaconda/bin/"
    #configure conda
    conda config --set always_yes yes --set changeps1 no
    conda update -y -q conda
    conda config --add channels defaults
    conda config --add channels conda-forge
    conda config --add channels bioconda
    #install dependencies
    conda install python=3.7
    # conda env setup
    conda install bioconda::hmmer scipy pandas numpy matplotlib pytest
    pip3 install setuptools
    PATH="$PATH:/usr/local/anaconda/lib/python3.7/site-packages/"
    # install parallel
    sudo apt-get install -y parallel
    # traitar install
    git clone https://github.com/nick-youngblut/traitar3.git
    cd traitar3
    python3 setup.py build
    python3 setup.py install
    cd ../
    conda install -c bioconda prodigal
    #House Keeping
    conda clean --tarballs
    #install db
    traitar pfam db

%runscript
    echo "Traitar Singularity"