Biocontainers 2019: Presentation for the ELIXIR All Hands

www.elixir-europe.org
BioContainers: From tools to services
Challenges and opportunities
BioContainers Community
github: github.com/Biocontainers
twitter: @BioContainers

http://biocontainers.pro | @biocontainers | github.com/biocontainers
ELIXIR All Hands June, 2019
BioContainers Community

http://biocontainers.pro | @biocontainers | github.com/biocontainershttp://biocontainers.pro | @biocontainers | github.com/biocontainers
Outline
I. Introduction to BioContainers
II. Results of the ELIXIR Implementation Study (2018-2019)
III. Bioinformatics Services to Cloud
Question : https://www.sli.do Code: Y726

Software
Publication
Research
What is BioContainers
Implementation of Guidelines:
• Versioning
• Testing
• Dependency management
• Documentation
My Data
Container Publication
Results
Results
mulled
dockerfile

BioContainers / BioConda Architecture
Leprevost, F., Grüning, ... & Perez-Riverol Y. (2017). Bioinformatics, 33(16), 2580-2582.
Grüning B, Dale R, ... BioConda Team. Nat Methods. 2018 Jul;15(7):475-476.

Findability
# Base Image FROM biocontainers/biocontainers:latest
# Metadata
LABEL base.image="biocontainers:latest”
LABEL version="3"
LABEL software="Comet”
LABEL software.version="2016012”
LABEL description="an open source tandem mass spectrometry
sequence database search tool"
LABEL website="http://comet-ms.sourceforge.net/"
LABEL
documentation="http://comet-ms.sourceforge.net/parameters/param
eters_2016010/"
LABEL license="http://comet-ms.sourceforge.net/"
LABEL tags="Proteomics"
# Maintainer
MAINTAINER Felipe da Veiga Leprevost
<felipe@leprevost.com.br>
USER biodocker
…..
Metadata should be able to connect
to other relevant software registries
such as: bio.tools , pubmed or
omicstools
Versions should be defined in an
standard format for the container and
the software inside.
Software duplications should be
removed between mulled and
dockerfile containers.
Metadata of bioconda packages and
Dockerfile recipes should be the
same.

Implementation Study (2018-2019)
Development of Architecture for Software Containers at ELIXIR and its use by
EXCELERATE use-cases communities.
1. Develop the Bioinformatics Containers Central Service (BCCS) to support the use of
software containers in ELIXIR.
2. BioContainers integration with bio.tools and OpenEBench.
3. BioContainers Registry 2.0 and Command Line tool.
4. BioContainers for Training and Support
5. Demonstration of the use of software containers in selected ELIXIR’s Use Cases
a. Rare Diseases use-case. Proof-of-concept implementation of a human genomics
variant calling pipeline using BioContainers and Galaxy.
b. EGA Integration.

Architecture BioContainers 2.0
1. Continuous integration for Dockerfile containers:
https://jenkins.biocontainers.pro/jenkins/
2. Binary and recipes ELIXIR Compute backup:
https://containers.biocontainers.pro/s3/
3. Internal ELIXIR registry:
http://containers.biocontainers.pro/containers
4. Biocontainers TRS API:
https://api.biocontainers.pro/api/ga4gh/v2/ui/
5. BioContainers Web: https://biocontainers.pro

Planemo - A Scientific Workflow SDK
> planemo run --docker …
> planemo test --docker … workflow[xml.yml]
> planemo mull build-and-test …
> mulled-build-channel --channel bioconda
--namespace biocontainers

Training containers based on Galaxy VRE with:
● tools (versioned)
● workflows (versioned)
● Interactive tours
● example data
● linked to and from hands-on material
● reference data

BioContainers TRS API
Code (Flask, MongoDB, Python): https://github.com/BioContainers/biocontainers-backend
https://api.biocontainers.pro/api/ga4gh/v2/ui/

Biocontainers Statistics and Usage
Pipeline and tools using
BioContainers:
● Galaxy: ~1500
● CWL: ~300
● Shell: ~200
● WDL: 60
● Python: 50
● Nextflow: 50

Selected Publications (2018-2019)
https://scholar.google.co.uk/citations?user=O6xG2-EAAAAJ&hl=en
1. da Veiga Leprevost, F., Grüning, B. et. al. Bioinformatics. 2017 Aug 15;33(16):2580-2582. doi:
10.1093/bioinformatics/btx192.
2. Grüning B, Dale R et. al. Nat Methods. 2018 Jul;15(7):475-476. doi: 10.1038/s41592-018-0046-7.
3. Gruening B., Sallou O., Moreno, P.,et. al. 2019. F1000Research, 7. doi:
10.12688/f1000research.15140.2
4. Moreno P. et. al. 2019. biorxiv. doi: 10.1101/488643v2
5. Perez-Riverol Y, et. al. 2019 biorxiv. doi: . 10.1101/604413v1

Moving services to Cloud
1. Services are not tools
• Services needs to be re-define/re-implemented to be cloud compatible.
• Services needs high-level of orchestration. Most of these services contains DB,
APIs, Web, etc.
2. Data should be open, transferable from the source into the deployed cloud instances.
3. A public list of important/interesting services for the community and industry should be
collected.
4. Funding from industry / public to help service teams to move into Cloud.
https://elixir-europe.org/services/tag/data-resources

First efforts
1. BioContainers Architecture is fully deployable into Cloud using Kubenetes helm
charts. (https://github.com/BioContainers/biocontainers-backend)
2. Some other projects moving within this efforts:
- Omics Discovery Index (www.omicsdi.org)
- Identifiers.org
- Reactome (https://reactome.org/)

Thanks!!!
and 700+ contributors

Biocontainers 2019: Presentation for the ELIXIR All Hands

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