1. Reproducible Bioinformatics
Bioconda and BioContainers
enabling sustainable bioinformatic infrastructure
Yasset Perez-Riverol PhD.
github: github.com/ypriverol
Bioconda/BioContainers community

3. Outline
Reproducibility in Science.
What is a containers? & Why they are so popular?
BioContainers Architecture
Future Directions

4. Bioinformatics Software: Reproducibility/Usability Challenge
Publication
Software
Research
Dependency Issues
Versioning
Testing/Integration ?
My Data ?
Publication
Software

5. Learning from some communities: Bioconductor
Publication
Software: R Package
Research
Implementation of Guidelines:
Versioning
Testing
Dependency management
Documentation
My Data ?
Publication
Software

6. Matrix of Hell

7. Containers Solution.

8. Docker Architecture

9. Why is so popular
Build once, run anywhere
A clean, safe & portable runtime environment for your app.
No worries about missing dependencies, packages & other pain points during subsequent deployments.
Run each app in its own isolated container
Automate testing, integration, packaging…anything you can script
A VM without the overhead of a VM

10. Current BioContainers Architecture

11. Dockerfile Container # Base Image
FROM biocontainers/biocontainers:latest
# Metadata
LABEL base.image="biocontainers:latest"
LABEL version="3"
LABEL software="Comet"
LABEL software.version=" "
LABEL description="an open source tandem mass spectrometry sequence database search tool"
LABEL website="
LABEL documentation="
LABEL license="
LABEL tags="Proteomics"
# Maintainer MAINTAINER Felipe da Veiga Leprevost
USER biodocker
RUN ZIP=comet_binaries_ zip && \ wget -O /tmp/$ZIP && \ unzip /tmp/$ZIP -d /home/biodocker/bin/Comet/ && \ chmod -R 755 /home/biodocker/bin/Comet/* && \ rm /tmp/$ZIP
RUN mv /home/biodocker/bin/Comet/comet_binaries_ /comet linux.exe /home/biodocker/bin/Comet/comet ENV PATH /home/biodocker/bin/Comet:$PATH WORKDIR /data/ CMD ["comet"]

12. Dockerfile Container # Base Image
FROM biocontainers/biocontainers:latest
# Metadata
LABEL base.image="biocontainers:latest"
LABEL version="3"
LABEL software="Comet"
LABEL software.version=" "
LABEL description="an open source tandem mass spectrometry sequence database search tool"
LABEL website="
LABEL documentation="
LABEL license="
LABEL tags="Proteomics"
# Maintainer MAINTAINER Felipe da Veiga Leprevost
USER biodocker
RUN ZIP=comet_binaries_ zip && \ wget -O /tmp/$ZIP && \ unzip /tmp/$ZIP -d /home/biodocker/bin/Comet/ && \ chmod -R 755 /home/biodocker/bin/Comet/* && \ rm /tmp/$ZIP
RUN mv /home/biodocker/bin/Comet/comet_binaries_ /comet linux.exe /home/biodocker/bin/Comet/comet ENV PATH /home/biodocker/bin/Comet:$PATH WORKDIR /data/ CMD ["comet"]

13. Tool deployment & sustainability in science
Programming language agnostic
OS independent
No root privileges needed
Management of multiple version
HPC and Cloud compatible
easy to maintain
What is needed?

14. Tool deployment & sustainability in science
Conda is an open source package management system and environment management system for installing multiple versions of software packages and their dependencies and switching easily between them.

15. BioContainers: Mulled based Containers
Meeting, August 2017

16. But the new cool kid is called Containers
Get all the other nice technologies for free
rkt
singularity
modules
Meeting, August 2017

17. How to find a container http://biocontainers.pro/registry/#/ 17
Meeting, August 2017 17

18. Name spaces Namespace for Dockerfile based containers:
docker pull biocontainers/blast
Namespace for Dockerfile free based containers:
docker pull quay.io/biocontainers/bedtools

19. Who is using it?

20. What is next: MultiContainers

22. Some Numbers Relevant Links More than 2000 Containers.
Use in production by: Galaxy, Phenomenal2020, Cyverse, OSG.
210 issues discussed.
More than 30 Contributors.
Relevant Links