sonicparanoid.def

Bootstrap: library
From: godloved/secure/ubuntu-bionic

%labels
    Author: davidgodlove@gmail.com

%pre
    # this is going to delete your cache to make sure you are getting a minty
    # fresh image from the library
    singularity cache clean --force

%setup
    # insert the fingerprint here
    KEY_FP=B7761495F83E6BF7686CA5F0C1A7D02200787921
    MESSG="Container verified"
    singularity verify /root/.singularity/cache/library/sha256* | \
    grep -q $KEY_FP
    singularity verify /root/.singularity/cache/library/sha256* | \
    grep -q "$MESSG"

%post
    apt-get update
    apt-get -y install python3 python3-pip python3-venv python3-biopython \
        build-essential python3-testresources cmake zlib1g-dev
    cd /usr/bin
    python3 -m pip install -U pip setuptools cython pandas biopython sh \
        scikit-learn scipy mypy psutil
    pip3 install sonicparanoid

    # it looks like it will try to install more software "on demand" or
    # something when you run a test.  maybe because it is trying to optimize
    # for arch or available instruction sets or something? unclear. but it 
    # barfs if you try to do this at runtime b/c read only file system.
    cd /tmp
    sonicparanoid-get-test-data -o .
    cd sonicparanoid_test
    sonicparanoid -i ./test_input -o ./test_output -m fast -t 4

    # make nih hpc specific links
    mkdir -p /vf /gpfs /spin1 /data /scratch /fdb /lscratch
    for i in $(seq 1 30); do
        ln -s /gpfs/gsfs${i} /gs${i};
    done