dominik-handler/AP_singu:oligominer

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

Singularity Recipe

#OligoMiner in singularity

Bootstrap: docker
From: ubuntu:16.04

%runscript
    cd /OligoMiner
    python "$@"

%post
    apt-get update
    apt-get -y install wget sudo 

    apt-get update
    apt-get -y install python python-setuptools git-core bzip2

    
    #update to version 1.19.0
    wget https://repo.anaconda.com/miniconda/Miniconda2-latest-Linux-x86_64.sh && \
    bash Miniconda2-latest-Linux-x86_64.sh -b -p /Software/anaconda && \
    rm Miniconda2-latest-Linux-x86_64.sh
    PATH="/Software/anaconda/bin:$PATH"
    
    conda config --add channels r
    conda config --add channels defaults
    conda config --add channels conda-forge
    conda config --add channels bioconda    
    conda install numpy 
    conda install scipy biopython scikit-learn bowtie2 jellyfish

    cd /
    git clone https://github.com/brianbeliveau/OligoMiner
  
    mkdir /groups
    mkdir /scratch
    mkdir /scratch-ii2

%environment
    PATH="PATH=/Software/anaconda/bin:${PATH}"
    export $PATH

%test

Collection


View on Datalad

Metrics

key value
id /containers/dominik-handler-AP_singu-oligominer
collection name dominik-handler/AP_singu
branch master
tag oligominer
commit f9ab8bc372994f187d0f0f2850ca78b934eb6354
version (container hash) effa157c39f7ba0f5dfcf302f3ab8571
build date 2021-03-22T12:04:22.565Z
size (MB) 1263
size (bytes) 497197087
SIF Download URL (please use pull with shub://)
Datalad URL View on Datalad
Singularity Recipe Singularity Recipe on Datalad
We cannot guarantee that all containers will still exist on GitHub.