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IFB cloud: Integration of snakemake workflows in an appliance designed for ChIP-seq analysis

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Informal bioinformatics meeting. TAGC, Inserm, Aix-Marseille University.

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IFB cloud: Integration of snakemake workflows in an appliance designed for ChIP-seq analysis

  1. 1. IFB cloud: Integration of snakemake workflows in an appliance designed for ChIP-seq analysis Claire Rioualen 2015/10/28
  2. 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. 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. 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. 5. IFB cloud appliances
  6. 6. ChIP-seq appliance ● Base Ubuntu 14.04 Including ssh, rsync, git, python 2, python 3...
  7. 7. ChIP-seq appliance ● Base Ubuntu 14.04 Including ssh, rsync, git, python 2, python 3... ● Programming tools snakemake, graphviz, pandas library...
  8. 8. ChIP-seq appliance ● Base Ubuntu 14.04 Including ssh, rsync, git, python 2, python 3... ● Programming tools snakemake, graphviz, pandas library... ● NGS tools
  9. 9. 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)
  10. 10. Using the IFB cloud: request account cloud.france-bioinformatique.fr Request account
  11. 11. Using the IFB cloud: dashboard cloud.france-bioinformatique.fr Add ssh key Create a virtual disk
  12. 12. Using the IFB cloud: vDisk cloud.france-bioinformatique.fr Size (Go) Name
  13. 13. Using the IFB cloud: create instance cloud.france-bioinformatique.fr Choose appliance Plug vDisk Up to 8 CPU, 32GB RAM Name
  14. 14. Using the IFB cloud: ssh connection cloud.france-bioinformatique.fr ssh connection
  15. 15. Using the IFB cloud: data
  16. 16. 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
  17. 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 ● Results are saved in the vDisk
  18. 18. Thank you!

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