PSA: GAPIT Containerization for HPC
I ran into a thorny problem running GWAS on an HPC in December so I’m sending out this PSA to hopefully prevent someone else running into the same issue.
In brief, if you follow GAPIT’s standard install instructions it’s possible to produce a container that runs perfectly on a local machine and fails on the HPC. Why this happens is a little messy but the solution is simple: manually build the GAPIT and install that version along with its dependencies.
In your singularity def file, instead of specifying the package installation as Rscript -e 'install.packages(GAPIT)' you’ll use a tar of the package that’s been copied into the container like so R CMD INSTALL /app/GAPIT_3.4.0.tar.gz
With the below definition file downloaded you can either use the makefile or run the below to build the container.
wget https://cran.r-project.org/src/contrib/Archive/multtest/multtest_2.8.0.tar.gz
git clone https://github.com/jiabowang/GAPIT
R CMD build GAPIT
rm -r ./GAPIT/
sudo singularity build gapit.sif gapit.def