mcw-rcc/cadd:1.5

$ singularity pull shub://mcw-rcc/cadd:1.5

Singularity Recipe

Bootstrap: docker
From: ubuntu:16.04

%labels
Maintainer Matthew Flister

%help
This container runs CADD.

%environment
    export PATH=/opt/miniconda2/bin:$PATH

%runscript
    exec /opt/CADD-scripts/CADD.sh "${@}"

%post
    # default mount points
    mkdir -p /scratch/global /scratch/local /rcc/stor1/refdata /rcc/stor1/projects /rcc/stor1/depts
    
    # Install necessary packages
    apt-get update && apt-get install -y --no-install-recommends \
        build-essential \
        gcc-multilib \
        ca-certificates \
        locales \
        git \
        wget
    apt-get clean
    echo "LC_ALL=en_US.UTF-8" >> /etc/environment
    echo "en_US.UTF-8 UTF-8" >> /etc/locale.gen
    echo "LANG=en_US.UTF-8" > /etc/locale.conf
    locale-gen en_US.UTF-8

    # Install miniconda
    wget https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh -O miniconda2.sh
    bash miniconda2.sh -b -p /opt/miniconda2
    rm miniconda2.sh
    export PATH="/opt/miniconda2/bin:$PATH"
    
    # Install CADD
    cd /opt && git clone https://github.com/kircherlab/CADD-scripts.git
    cd CADD-scripts && conda env create -f src/environment_v1.5.yml

    # setup data
    ln -s /rcc/stor1/refdata/cadd/v1.5/data/annotations/GRCh37_v1.4 /opt/CADD-scripts/data/annotations/GRCh37_v1.4
    ln -s /rcc/stor1/refdata/cadd/v1.5/data/prescored /opt/CADD-scripts/data/prescored

Collection


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Metrics

key value
id /containers/mcw-rcc-cadd-1.5
collection name mcw-rcc/cadd
branch master
tag 1.5
commit 5aaafdcc0fb9b92bdd44eef5daa83f85f3e287ec
version (container hash) c02100da201ac1f07fbce76a8fffd4f2
build date 2019-03-29T19:18:16.702Z
size (MB) 2738
size (bytes) 1055682591
SIF Download URL (please use pull with shub://)
Datalad URL View on Datalad
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