About
The IT department is responsible for deploying software and computing tools on the IGBMC's computing infrastructure.
Software deployment is based on 2 main technologies; Conda and Singularity, depending on the specificities of the software and its license.
Most bioinformatics tools are available through Conda packages, thanks to the work of the Bioconda community. If a tool is not available under Bioconda and its license allows it, the IT department will create a conda package before deploying it. If it proves impossible to create a conda package, the tool will be deployed as a Singularity image.
To provide a unified user interface for tool access, each software package is made accessible through the Environment Module system.
All deployed software is available to all users of the computing infrastructure.
Scientific computing tools are deployed via the national deployment repository proposed by the Institut Français de Bioinformatique, to which the IGBMC is a major contributor: https://gitlab.com/ifb-elixirfr/cluster/tools
To request the deployment of a scientific computing tool, please submit a request for assistance, specifying :
- The tool name
- Required version(s)
- The tool website or Git repository
- License if necessary
Key facts
- On-demand deployment of computing tools on the IGBMC computing infrastructure via Conda or Singularity
- Conda package creation for a tool not available on Anaconda cloud
Available for
IGBMC scientific staff
Documentation
Machine learning with PythonTerm of use
Charte des bons usages numérique
Service Level Agreement
We receive your requests for computing tools from Monday to Friday, 9am to 12pm and 1pm to 5pm.
The usual lead times for processing a request are as follows:
- Software available as a Conda package: 4h
- Software not available as a Conda package: minimum 48h (excluding time needed to obtain licenses, if required).
Associated services
High performance computing (SLURM)
Service manager
Infrastructure division