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MGP1000

Deploying the Pipeline

The pipeline was developed to be run on various HPCs without concern of environment incompatibilities, version issues, or missing dependencies. None of the commands require admin access or sudo to be completed. However, there are a few assumptions regarding initial setup of the pipeline but the required software should be readily available on nearly all HPC systems.

  • git
  • make, wget, tar, zip
  • java -version (11 or later)
  • singularity (confirmed usage on v3.1, v3.5.2, v3.7.1, v3.9.8)
  • nextflow (>=20.01.0)

Clone GitHub Repository

git clone https://github.com/pblaney/mgp1000.git

Prep the Pipeline for Usage

Unzip some reference files and create some additional directories for input files and logs.

make prep-pipeline

Having Trouble?

Need to install git-lfs ...
In an effort to containerize the pipeline further, all the necessary reference files and Singularity container images are maintained in the repository using Git's Large File Storage (LFS) extension.

First, a quick test …

git-lfs version

Install git-lfs Linux AMD64 binary executible file (v3.2.0). Other binary files available here

make install-gitlfs-linuxamd64

Move the git-lfs binary to a location on $PATH

mv git-lfs $HOME/bin

Complete the install and configuration

git-lfs install

Use git-lfs to complete the clone

git-lfs pull
Need to install Nextflow ...
It is always preferred to use your HPC's installed module of Nextflow. However, follow below for installation of the Nextflow binary. The most current version of Nextflow requires Java 11 or later. Therefore, the user may need to load this version of Java to complete the install. 
make install-nextflow

Move the nextflow binary to a location on $PATH

mv nextflow $HOME/bin