LPMX: a pure rootless composable container system

BACKGROUND: Delivering tools for genome analysis to users is often difficult given the complex dependencies and conflicts of such tools. Container virtualization systems (such as Singularity) isolate environments, thereby helping developers package tools. However, these systems lack mutual composability, i.e., an easy way to integrate multiple tools in different containers and/or on the host. Another issue is that one may be unable to use a single container system of the same version at all the sites being used, thus discouraging the use of container systems. RESULTS: We developed LPMX, an open-source pure rootless composable container system that provides composability; i.e., the system allows users to easily integrate tools from different containers or even from the host. LPMX accelerates science by letting researchers compose existing containers and containerize tools/pipelines that are difficult to package/containerize using Conda or Singularity, thereby saving researchers’ precious time. The technique used in LPMX allows LPMX to run purely in userspace without root privileges even during installation, thus ensuring that we can use LPMX at any Linux clusters with major distributions. The lowest overhead for launching containers with LPMX gives us courage to isolate tools as much as possible into small containers, thereby minimizing the chance of conflicts. The support for the layered file system keeps the total size of container images for a single genomic pipeline modest, as opposed to Singularity, which uses mostly a flat single-layer image. CONCLUSIONS: LPMX is pure rootless container engine with mutual composability, thus saving researchers’ time, and accelerating science.