J35P312/TayWhale:latest

$ singularity pull shub://J35P312/TayWhale: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
    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 STAR --yes
	conda install -c bioconda picard --yes	
	conda install -c bioconda samtools --yes
	conda install -c bioconda STAR-Fusion --yes
	conda install -c bioconda stringtie --yes
	conda install -c bioconda salmon --yes
	conda install -c bioconda gffcompare --yes

Collection

• Name: J35P312/TayWhale
• License: None

Metrics

Feedback

Was this page helpful?

Glad to hear it! Please tell us how we can improve.

Sorry to hear that. Please tell us how we can improve.