The document describes the IFB cloud, a French national bioinformatics infrastructure that provides computing resources and appliances. It summarizes the current and planned capacity of the IFB cloud. It then describes a ChIP-seq analysis appliance available on the IFB cloud, which contains tools like snakemake, NGS tools, and example ChIP-seq workflows. It provides instructions for requesting an account, launching a virtual disk and instance, connecting via SSH, loading data, and executing workflows on the appliance using the snakemake framework.

1. IFB cloud:
Integration of snakemake workflows in
an appliance designed for ChIP-seq analysis
Claire Rioualen
2015/10/28

2. French Institute of Bioinformatics (IFB)
● National service infrastructure in
bioinformatics
● 32 platforms grouped into regional
centers
● French node of the European
research infrastructure ELIXIR

3. French Institute of Bioinformatics (IFB)
● National service infrastructure in
bioinformatics
● 32 platforms grouped into regional
centers
● French node of the European
research infrastructure ELIXIR
● Provides services and infrastructures in bioinformatics for
scientists and engineers working in the field of life sciences
http://www.france-bioinformatique.fr

4. IFB cloud
● 200 computing cores
● 2 To of RAM
● 50 To of storage
By 2016
● 3,000 cores
● 500 To of storage
By 2017
● 10,000 cores
● 2 Po of storage

5. IFB cloud appliances

7. ChIP-seq appliance
● Base Ubuntu 14.04
Including ssh, rsync, git, python 2, python 3...

8. ChIP-seq appliance
● Base Ubuntu 14.04
Including ssh, rsync, git, python 2, python 3...
● Programming tools
snakemake, graphviz, pandas library...

9. ChIP-seq appliance
● Base Ubuntu 14.04
Including ssh, rsync, git, python 2, python 3...
● Programming tools
snakemake, graphviz, pandas library...
● NGS tools

10. ChIP-seq appliance
● Base Ubuntu 14.04
Including ssh, rsync, git, python 2, python 3...
● Programming tools
snakemake, graphviz, pandas library...
● NGS tools
● fg-chip-seq git repository
Including workflow examples (py + json)

11. Using the IFB cloud: request account
cloud.france-bioinformatique.fr
Request account

12. Using the IFB cloud: dashboard
cloud.france-bioinformatique.fr
Add ssh key
Create a virtual disk

13. Using the IFB cloud: vDisk
cloud.france-bioinformatique.fr
Size (Go)
Name

14. Using the IFB cloud: create instance
cloud.france-bioinformatique.fr
Choose appliance
Plug vDisk
Up to 8 CPU,
32GB RAM
Name

15. Using the IFB cloud: ssh connection
cloud.france-bioinformatique.fr
ssh connection

16. Using the IFB cloud: data

17. Using the IFB cloud: execute workflow
● Several example workflows already available &
adaptable in the git repository
● 1 config file (json) + 1 workflow file (py)
● Paths to data, genome & results directories
● Parameters

18. Using the IFB cloud: execute workflow
● Several example workflows already available &
adaptable in the git repository
● 1 config file (json) + 1 workflow file (py)
● Paths to data, genome & results directories
● Parameters
● Results are saved in the vDisk

19. Thank you!