ORFLine-singularity

Repo for making smORF discovery pipeline ORFLine singularity image. Image was automatically build by Singularity Hub. During image build, all orf-discovery pipeline dependencies were installed, specifically, bioinformatics tools were installed via Miniconda to /opt/miniconda/bin and pipeline source code was pulled to ~/project/.

Usage

Install singularity via conda:

# Assuming Linux and root privilige
curl -fsSL https://repo.anaconda.com/miniconda/Miniconda2-latest-Linux-x86_64.sh -o miniconda2.sh

# Install miniconda to user home directory
bash miniconda2.sh -b -p ~/miniconda2

# Add conda bin to $PATH
export PATH=~/miniconda2/bin:$PATH

# Install singularity
conda install -y -c bioconda singularity

Pull the container to your machine:

singularity pull shub://boboppie/ORFLine-singularity
# the default name of the image is ORFLine-singularity_latest.sif

Shell into the container:

singularity shell ORFLine-singularity_latest.sif

Run the container:

singularity run ORFLine-singularity_latest.sif

Need more help? Please read Singularity Hub usage guide.