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PracticalHaplotypeGraph / UserInstructions / CreatePHG_step0_singularity

Use Singularity to run PHG

Quick Start

  1. Follow the Quick Start installation steps to install Singularity on your machine.
  2. Run the following commands to download the PHG and PHG liquibase docker images.
singularity pull docker://maizegenetics/phg
singularity pull docker://maizegenetics/phg_liquibase

Details

You can use Singularity containers to run docker containers without installing Docker. The benefit of using Singularity is that it does not require root access on your machine.

Singularity and Docker work well together, and you can run the PHG Docker container through singularity without needing Docker installed.

Singularity communicates with Docker Hub to pull a Docker image into the Singularity Docker Registry.

As with Docker, Singularity containers give users the ability to work in a uniform and consistent computing environment which facilitates reproducible science.

Here are example Singularity PHG commands that work on a TACC machine. Note the "export PATH=${PATH}:/sbin" command may not be needed. At the time of this writing, there was a singularity issue on TACC machines that required this step.

Also note: "/scratch1/07005/lynnjo" should be replaced by your own scratch directory path, which can be found by doing a "cds" followed by "pwd".

For long singularity runs (e.g. loading haplotypes to the db, or imputing values) a slurm job should be executed. See TACC instructions for further details.

> cds
> mkdir -p phg_scratch/phg_run1
> export PATH=${PATH}:/sbin
> module load tacc-singularity
> cd phg_scratch
> singularity build phg_22.simg docker://maizegenetics/phg:0.0.22
> 
> singularity exec -B /scratch1/07005/lynnjo/phg_scratch/phg_run1/:/phg/ /scratch1/07005/lynnjo/phg_scratch/phg_22.simg /tassel-5-standalone/run_pipeline.pl -debug -Xmx1G -MakeDefaultDirectoryPlugin -workingDir /phg/ -endPlugin

Troubleshooting

  1. If you are having trouble downloading the Docker image with Singularity, check the Singularity troubleshooting guide.

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