Singulariy file for scziDesk

Singularity

BootStrap: debootstrap
OSVersion: trusty
MirrorURL: http://us.archive.ubuntu.com/ubuntu/


%runscript
    echo "This is what happens when you run the container..."

%post
    echo "Hello from inside the container"
    sed -i 's/$/ universe/' /etc/apt/sources.list

    apt-get -y update
    apt-get -y upgrade
    apt-get -y dist-upgrade

    apt-get install cmake -y
    apt-get update; 
    apt-get install -y software-properties-common
    #apt-get install add-apt-repository
    apt-get update
    apt-get install git -y
    apt-get install libboost-all-dev -y 

    apt-get update && apt-get install -y linux-tools-generic
    apt-get install wget curl

    #Python3.6 and pip
    add-apt-repository ppa:deadsnakes/ppa
    apt-get update && apt install python3.6 -y
    curl https://bootstrap.pypa.io/get-pip.py -o get-pip.py
    python3.6 get-pip.py
    
    #scziDesk dependencies
    apt-get update && pip install tensorflow==1.14
    apt-get update && pip install keras==2.2.4
    apt-get update && pip install scikit-learn==0.22.2

    apt-get update && pip install jgraph tqdm scanpy 
    
    apt-get update 
   
    apt-get clean

%environment
    export PATH=$PATH:/usr/local/bin
    export PKG_CONFIG_PATH='/usr/local/lib/pkgconfig'
    export LD_LIBRARY_PATH='/usr/lib:/usr/lib/x86_64-linux-gnu:/usr/local/lib'

    
    #Some basic Singularity commands
    #Creates a sandbox
    #sudo singularity build --sandbox scziDesk Singularity
    #Converts a sandbox to Image
    #sudo singularity build --writable scziDesk.simg scziDesk

    #Directly making an image from Singularity file (due to writable, the size will be bigger but can be modified)
    #sudo singularity build --writable scziDesk.simg Singularity

    #Directly making an image from Singularity file
    #sudo singularity build --writable scziDesk.simg Singularity