dpmerrell/pynbs-singularity:latest

$ singularity pull shub://dpmerrell/pynbs-singularity:latest

Singularity Recipe

Bootstrap: docker
From: continuumio/miniconda

%labels
AUTHOR dmerrell@cs.wisc.edu 

# I took some inspiration from this webpage:
# https://reproducibility.sschmeier.com/container/index.html#building-your-own-singularity-container-locally

############################################
%files
    run_pyNBS.py /run_pyNBS.py

############################################
%environment
# This sets global environment variables for anything run within the container
export PATH="/opt/conda/bin:/usr/local/bin:/usr/bin:/bin:"
export MKL_NUM_THREADS=4
export NUMEXPR_NUM_THREADS=4
export OMP_NUM_THREADS=4

unset CONDA_DEFAULT_ENV
export ANACONDA_HOME=/opt/conda


############################################
%post
# This is going to be executed after the base container has been downloaded
export PATH=/opt/conda/bin:$PATH
conda config --add channels defaults
conda config --add channels conda-forge
conda config --add channels bioconda

# Install dependencies (OLD versions of packages)
conda install --yes -c anaconda mkl-service=1.1.2
conda install --yes networkx=2.0
conda install --yes numpy=1.11.0
conda install --yes scipy=0.17.1
conda install --yes pandas=0.19.0
conda install --yes scikit-learn=0.17.1
conda install --yes seaborn=0.7.1
conda install --yes -c conda-forge lifelines

# Get the pyNBS source code
git clone https://github.com/idekerlab/pyNBS
cd pyNBS

# Install PyNBS
python setup.py install

conda clean --index-cache --tarballs --packages --yes

############################################
%runscript
    exec python /run_pyNBS.py "$@"

Collection

• Name: dpmerrell/pynbs-singularity
• License: MIT License

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