Enabling rootless Linux Containers in multi-user environments: The udocker tool

Gomes, Jorge; Bagnaschi, Emanuele; Campos, Isabel; David, M.; Alves, Luís M.; Martins, J.P.; Pina, J.; García, Álvaro López; Orviz, Pablo

doi:10.1016/j.cpc.2018.05.021

Cited by 55 publications

(48 citation statements)

References 29 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Docker is a tool that allows for PharmacoGx to be uniformly deployed with all software dependencies, in a containerized runtime environment where all of our computations are performed and PSets are produced 20 . The Docker container is invoked upon CWL workflow execution, where all the input files for a given pipeline become mounted into the container and all output files produced in the isolated environment are recovered into a local environment 22,23 . Another advantage of Docker is the ability of containers to utilize and share the hardware resources of the environment it is being run in 24 .…”

Section: Harnessing Docker To Create a Reproducible Runtimementioning

confidence: 99%

Creating reproducible pharmacogenomic analysis pipelines

Mammoliti

Смирнов

Safikhani

et al. 2019

Preprint

View full text Add to dashboard Cite

The field of Pharmacogenomics presents great challenges for researchers that are willing to make their studies reproducible and shareable. This is attributed to the generation of large volumes of high-throughput multimodal data, and the lack of standardized workflows that are robust, scalable, and flexible to perform large-scale analyses. To address this issue, we developed pharmacogenomic workflows in the Common Workflow Language to process two breast cancer datasets in a reproducible and transparent manner. Our pipelines combine both pharmacological and molecular profiles into a portable data object that can be used for future analyses in cancer research. Our data objects and workflows are shared on Harvard Dataverse and Code Ocean where they have been assigned a unique Digital Object Identifier, providing a level of data provenance and a persistent location to access and share our data with the community.

show abstract

Section: Harnessing Docker To Create a Reproducible Runtimementioning

confidence: 99%

Creating reproducible pharmacogenomic analysis pipelines

Mammoliti

Смирнов

Safikhani

et al. 2019

Preprint

View full text Add to dashboard Cite

show abstract

“…As a result we have provided a flexible user-level solution to give autonomy to users in shared computing facilities [12]. Section 3.1 contains a thorough discussion on the strategy and outcomes.…”

Section: Context and State Of The Artmentioning

confidence: 99%

“…For OpenNebula [46] sites the solution consists in a Network Orchestrator Wrapper (NOW) 12 and a corresponding backend in the rOCCI-server. 13 NOW enforces site-wide policy and network configuration by making sure that only LANs designated by site administrators are made available to users, and that users cannot reuse LANs assigned to others while they remain reserved.…”

Section: Virtual Networkmentioning

confidence: 99%

See 1 more Smart Citation

INDIGO-DataCloud: a Platform to Facilitate Seamless Access to E-Infrastructures

et al. 2018

View full text Add to dashboard Cite

This paper describes the achievements of the H2020 project INDIGO-DataCloud. The project has provided e-infrastructures with tools, applications and cloud framework enhancements to manage the demanding requirements of scientific communities, either locally or through enhanced interfaces. The middleware developed allows to federate hybrid resources, to easily write, port and run scientific applications to the cloud. In particular, we have extended existing PaaS (Platform as a Service) solutions, allowing public and private e-infrastructures, including those provided by EGI, EUDAT, and Helix Nebula, to integrate their existing services and make them available through AAI services compliant with GEANT interfederation policies, thus guaranteeing transparency and trust in the provisioning of such services. Our middleware facilitates the execution of applications using containers on Cloud and Grid based infrastructures, as well as on HPC clusters. Our developments are freely downloadable as open source components, and are already being integrated into many scientific applications.

show abstract

“…Containers encompass all dependencies of the provisioned tools and greatly simplifies software installations for end users. The most widely used containerization solution is Docker ( www.docker.com ), but Singularity [8] , uDocker [9] , and Shifter [10] are recent alternatives that prevent users to run containers with root privileges, addressing most commons security issues when deploying contains in a multi-tenant computing clusters such as on on high-performance computing (HPC) clusters. Docker containers are commonly shared via Docker Hub ( https://hub.docker.com ).…”

Section: Containersmentioning

confidence: 99%

Approaches for containerized scientific workflows in cloud environments with applications in life science

Spjuth

Capuccini

Carone

et al. 2018

Preprint

View full text Add to dashboard Cite

Containers are gaining popularity in life science research as they encompass all dependencies of provisioned tools and simplifies software installations for end users, as well as offering a form of isolation between processes. Scientific workflows are ideal to chain containers into data analysis pipelines to sustain reproducible science. In this manuscript we review the different approaches to use containers inside the workflow tools Nextflow, Galaxy, Pachyderm, Luigi, and SciPipe when deployed in cloud environments. A particular focus is placed on the workflow tool's interaction with the Kubernetes container orchestration framework.

show abstract

Enabling rootless Linux Containers in multi-user environments: The udocker tool

Cited by 55 publications

References 29 publications

Creating reproducible pharmacogenomic analysis pipelines

Creating reproducible pharmacogenomic analysis pipelines

INDIGO-DataCloud: a Platform to Facilitate Seamless Access to E-Infrastructures

Approaches for containerized scientific workflows in cloud environments with applications in life science

Contact Info

Product

Resources

About