Aexbrayat/snakescif:latest

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

Singularity Recipe

Bootstrap: docker
From: continuumio/miniconda3:4.3.27

# sudo singularity build snakemake Singularity

%files
    snakevir.scif
    Snakefile
    config.yaml
    cluster.json
    

%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==5.7.4
    /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


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Metrics

key value
id /containers/Aexbrayat-snakescif-latest
collection name Aexbrayat/snakescif
branch master
tag latest
commit 7c2349ae5306744417cb6464008f29f804156588
version (container hash) 05ffe76063511d067feea53a1cffb154
build date 2020-10-24T18:16:22.555Z
size (MB) 6304.0
size (bytes) 2833498143
SIF Download URL (please use pull with shub://)
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