run_locally.md

Run locally

This guide provides information needed to run the pipeline in a local linux environment.

0) Install Nextflow, Docker and/or Singularity

0.1) Install Nextflow

wget -qO- https://get.nextflow.io | bash && sudo mv nextflow /usr/bin/

0.1) Install Docker

See https://docs.docker.com/engine/install/ubuntu/

0.2) Install Singularity

See https://sylabs.io/guides/3.8/user-guide/quick_start.html and https://sylabs.io/guides/3.0/user-guide/installation.html

Commands to install on CentOS:

sudo yum update -y && \
sudo yum groupinstall -y 'Development Tools' && \
sudo yum install -y \
    openssl-devel \
    libuuid-devel \
    libseccomp-devel \
    wget \
    squashfs-tools

export VERSION=1.16.6 OS=linux ARCH=amd64 && # adjust this as necessary \
    wget https://dl.google.com/go/go$VERSION.$OS-$ARCH.tar.gz && \
    sudo tar -C /usr/local -xzvf go$VERSION.$OS-$ARCH.tar.gz && \
    rm go$VERSION.$OS-$ARCH.tar.gz

echo 'export GOPATH=${HOME}/go' >> ~/.bashrc && \
    echo 'export PATH=/usr/local/go/bin:${PATH}:${GOPATH}/bin' >> ~/.bashrc && \
    source ~/.bashrc

go get -u github.com/golang/dep/cmd/dep


export VERSION=3.8.0 && # adjust this as necessary \
    wget https://github.com/sylabs/singularity/releases/download/v${VERSION}/singularity-ce-${VERSION}.tar.gz && \
    tar -xzf singularity-ce-${VERSION}.tar.gz && \
    cd singularity-ce-${VERSION}

./mconfig && \
    make -C builddir && \
    sudo make -C builddir install

singularity help

1) Clone the git repository to local machine

git clone https://github.com/TheJacksonLaboratory/splicing-pipelines-nf
cd splicing-pipelines-nf

2) Run the pipeline

2.1) Quick test with Docker container engine

nextflow run . -profile ultra_quick_test,docker --cleanup

2.2) Quick test with Docker container engine

nextflow run . -profile ultra_quick_test,singularity --cleanup