bsiranosian/bens_1337_workflows:snippy

$ singularity pull shub://bsiranosian/bens_1337_workflows:snippy

Singularity Recipe

BootStrap: docker
From: ubuntu:16.04


# this command assumes at least singularity 2.3
%environment
    PATH="/usr/local/anaconda/bin:$PATH"

%post 
    apt-get update
    apt-get install -y locales wget build-essential
    # localle update necessary for quast
    locale-gen --purge "en_US.UTF-8"
    update-locale LANG="en_US.UTF-8"

    # install anaconda
    if [ ! -d /usr/local/anaconda ]; then
         wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh \
            -O ~/anaconda.sh && \
         bash ~/anaconda.sh -b -p /usr/local/anaconda && \
         rm ~/anaconda.sh
    fi
        export PATH="/usr/local/anaconda/bin:$PATH"

    conda install -y -c bioconda -c conda-forge python=2.7 snippy vt vcftools bcftools \
    samtools blast bwa pandas snpeff r-ggplot2 r-rafalib

%runscript
   exec /bin/bash

Collection


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Metrics

key value
id /containers/bsiranosian-bens_1337_workflows-snippy
collection name bsiranosian/bens_1337_workflows
branch master
tag snippy
commit c882e6fbd9df8d0a1cab243d6c00960b24fc12a4
version (container hash) 77512c05d6cf7f9242e6649a270d4aeb
build date 2020-03-25T19:41:44.928Z
size (MB) 4520
size (bytes) 2086789151
SIF Download URL (please use pull with shub://)
Datalad URL View on Datalad
Singularity Recipe Singularity Recipe on Datalad
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