J35P312/PileupPipe:latest

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

Singularity Recipe

Bootstrap: docker
From: ubuntu:16.04

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


%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 libncurses5-dev libncursesw5-dev
    update-locale LC_ALL=en_US.UTF-8 LANG=en_US.UTF-8

    cd /root/ && wget https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh
    cd /root/ && chmod 700 ./Miniconda2-latest-Linux-x86_64.sh
    cd /root/ && bash ./Miniconda2-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

    conda install -c bioconda samtools vt tabix gatk4

Collection


View on Datalad

Metrics

key value
id /containers/J35P312-PileupPipe-latest
collection name J35P312/PileupPipe
branch master
tag latest
commit a7bd1b77888916bd1dbf1b8363b73d95ce9532c2
version (container hash) b2610238b07e67f9d9451124da047bc2
build date 2019-10-31T14:05:16.194Z
size (MB) 1678
size (bytes) 1040302111
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.