Migrating a Pipeline for the C-MA($)over-barIKI gateway from Tapis v2 to Tapis v3

The C-MA ($) over bar IKI science gateway allows researchers to run microbial workflows on a computer cluster with just a click of a button. This is possible because of the Tapis[1] framework developed at the Texas Advanced Computing Center (TACC). Currently, the C-MA ($) over bar IKI gateway uses the v2 version of Tapis, which has been refactored into a new v3 version that is more robust and has added capabilities such as support for containerized apps, a new Streaming Data API, and multi-site security kernel. This project aims to keep the C-MA ($) over bar IKI gateway up-to-date and modern by migrating the gateway from the pre-existing Tapis v2 framework to the new Tapis v3 framework starting with one of the pipelines applications as a pilot which required three major steps: 1) Containerizing an microbiome pipeline. 2) Developing a new app definition for the workflow. 3) Enabling the ability to submit jobs to a SLURM scheduler from inside a singularity container. This initial pilot illustrates that it is possible to run these pipelines as a "container within a container" for parallelization providing the ability to leverage a single application definition in Tapis that can execute across multiple compute infrastructures.