dominik-handler/AP_singu:pomoxis

$ singularity pull shub://dominik-handler/AP_singu:pomoxis

Singularity Recipe

Bootstrap: docker
From: ubuntu:16.04

%labels
  maintainer Dominik Handler <Dominik Handler@imba.oeaw.ac.at  
  pomoxis v0.2.2 

%post
    apt-get update
    apt-get -y install wget git build-essential zlib1g-dev libbz2-dev liblzma-dev


  #fix locales
    apt-get clean && apt-get update && apt-get install -y \
       locales \
       language-pack-en && \
       export LANGUAGE=en_US.UTF-8 && \
       export LANG=en_US.UTF-8 && \
       export LC_ALL=en_US.UTF-8 && \
       locale-gen en_US.UTF-8 && \
       dpkg-reconfigure --frontend noninteractive locales

  #install miniconda
    apt-get update
    apt-get -y install bzip2 python3-setuptools python3.5 
    
    #update to version 1.19.0
    wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh && \
    bash Miniconda3-latest-Linux-x86_64.sh -b -p /Software/anaconda3 && \
    rm Miniconda3-latest-Linux-x86_64.sh
    PATH="/Software/anaconda3/bin:$PATH"

  #insatall conda packages  
    conda config --add channels defaults
    conda config --add channels conda-forge
    conda config --add channels bioconda

    git clone --recursive https://github.com/nanoporetech/pomoxis
    cd pomoxis

    CONDA=/Software/anaconda3/ make conda
    
%environment
    PATH="PATH=/Software/anaconda3/bin:${PATH}"
    export $PATH
    export LD_LIBRARY_PATH=/cm/local/apps/cuda-driver/libs/390.12/lib64:/cm/local/apps/cuda-driver/libs/390.12/lib:/software/171020/software/cuda/9.0.176/extras/CUPTI/lib64:/software/171020/software/cuda/9.0.176/lib64:/cm/local/apps/cuda-driver/libs/390.12/lib64:/cm/local/apps/cuda-driver/libs/390.12/lib:$LD_LIBRARY_PATH
    export PATH=/cm/local/apps/cuda-driver/libs/390.12/bin:/software/171020/software/cuda/9.0.176:/software/171020/software/cuda/9.0.176/bin:$PATH

%runscript
  $@

Collection


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Metrics

key value
id /containers/dominik-handler-AP_singu-pomoxis
collection name dominik-handler/AP_singu
branch master
tag pomoxis
commit 7276d9f79e254f090a89495100afdfe489138b6e
version (container hash) cca21733530577d5e56ac683545c56dc
build date 2019-04-26T18:57:08.095Z
size (MB) 1493
size (bytes) 661401631
SIF Download URL (please use pull with shub://)
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