J35P312/RareDisease_RNA_workflow:latest

$ singularity pull shub://J35P312/RareDisease_RNA_workflow:latest

Singularity Recipe

Bootstrap: docker
From: ubuntu:16.04

%environment
SHELL=/bin/bash
PATH=/opt/anaconda/bin:${PATH}
LC_ALL=C.UTF-8

%runscript
    echo "This is what happens when you run the container..."
    export PATH=/opt/anaconda/bin:${PATH}    

%post
    echo "Hello from inside the container"
    apt-get update
    apt-get -y install wget git bzip2 build-essential gcc zlib1g-dev language-pack-en-base apt-transport-https make cmake unzip python3
    update-locale LC_ALL=en_US.UTF-8 LANG=en_US.UTF-8

    cd /root/ && wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
    cd /root/ && chmod 700 ./Miniconda3-latest-Linux-x86_64.sh
    cd /root/ && bash ./Miniconda3-latest-Linux-x86_64.sh -b -p /opt/anaconda/

    export PATH=/opt/anaconda/bin:${PATH}

    conda config --add channels defaults
    conda config --add channels conda-forge
    conda config --add channels bioconda

    cd /bin/ && git clone https://github.com/J35P312/BootstrapAnn.git

    conda install samtools star=2.7.8a gatk4=4.2.0 pip tabix
    pip install numpy
    pip install scipy

Collection


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Metrics

key value
id /containers/J35P312-RareDisease_RNA_workflow-latest
collection name J35P312/RareDisease_RNA_workflow
branch main
tag latest
commit f2d776902463dc26e39effa6d8c024d60dfe873c
version (container hash) 5617a7beb3927b6715d5f73a12fb780b
build date 2021-03-23T17:26:19.892Z
size (MB) 2188.0
size (bytes) 1407647775
SIF Download URL (please use pull with shub://)
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