Aexbrayat/snakevir:latest

$ singularity pull shub://Aexbrayat/snakevir:latest

Singularity Recipe

Bootstrap: docker
From: continuumio/miniconda3

# sudo singularity build snakemake Singularity

%files
    snakevir.scif
    Snakefile
    config.yaml

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

%post
    mkdir -p /samples /data /snakevirome
    apt-get update && apt-get -y install build-essential valgrind time python-numpy python-dev python-qt4 python-lxml python-six
    /opt/conda/bin/conda config --add channels defaults
    /opt/conda/bin/conda config --add channels conda-forge
    /opt/conda/bin/conda config --add channels bioconda

    # Install scif and scif-apps
    /opt/conda/bin/pip install scif
    /opt/conda/bin/scif install /snakevir.scif

    # Install snakemake
    /opt/conda/bin/pip install snakemake==4.4.0
    /opt/conda/bin/pip install docutils==0.14
    /opt/conda/bin/pip install biopython
    /opt/conda/bin/pip install pandas
    /opt/conda/bin/python - <<EOF
from ete3 import NCBITaxa
ncbi = NCBITaxa()
ncbi.update_taxonomy_database()

%runscript
    PATH=/opt/conda/bin:$PATH
    export PATH
    exec scif "$@"

Collection

• Name: Aexbrayat/snakevir
• License: None

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