PT  - JOURNAL ARTICLE
AU  - Xu Yang
AU  - Masahiro Kasahara
TI  - LPMX: A pure rootless composable container system
AID  - 10.1101/2021.06.04.445363
DP  - 2021 Jan 01
TA  - bioRxiv
PG  - 2021.06.04.445363
4099  - http://biorxiv.org/content/early/2021/06/07/2021.06.04.445363.short
4100  - http://biorxiv.org/content/early/2021/06/07/2021.06.04.445363.full
AB  - Summary Delivering tools for genome analysis to users is often difficult given their complex dependencies and conflicts. Container virtualization systems such as Singularity isolate environments, helping developers avoid conflicts between tools. However, they lack composability, an easy way to integrate multiple tools in different containers or multiple tools both in a container and a host, which compromises the use of container systems in genome research. Another issue is that one may not be able to use a single container system of the same version at all sites they use, which discourages the use of container systems. To this end, we present a pure rootless composable container system, LPMX, that provides composability for letting developers easily integrate tools in different existing containers or on host, allowing researchers to compose existing containers. LPMX is pure rootless, so it does not require root privilege neither during installation nor at runtime, allowing researchers to use LPMX across sites without asking permissions from administrators. LPMX provides a pure userspace layered filesystem with at least an order of magnitude lower overhead for launching a new process than existing container systems. LPMX can import Docker and Singularity images.Availability and Implementation The source code of LPMX is available at https://github.com/jasonyangshadow/lpmx under Apache 2.0 License.Contact mkasa{at}k.u-tokyo.ac.jpSupplementary information Supplementary data are available at Bioinformaticsonline.Competing Interest StatementThe authors have declared no competing interest.