Software / Tools

ABiMS cluster hosts more than 522 bioinfomatic tools and 890 versions dedicated to sequence similarity search, genome/transcriptome assemblies, phylogeny, population genetics, metabarcoding, etc. (update: 07/2022)


ABiMS is part of the IFB NNCR Cluster. With the IFB, we share more and more components. We are now installing the tool through a central GitLab repository:
The tools deploied at the same time on the 8 IFB cluster whole IFB Core Cluster, ABiMS.

All the tools installed come from either Conda or Singularity.

Please check our documentation: Conda / Singularity / Module

R / RStudio

A new Rstudio instance

Since April 2020, ABiMS is providing a new RStudio instance :

Note that this instance is the result of a strong collaboration with the IFB Core Cluster Task Force. It is a clone of the IFB rstudio server.

  • The server that now hosts this instance is newer and more powerful than the previous one.
  • The application was installed using Ansible and will be updated more regularly.
  • The packages are installed simultaneously on the ABiMS and IFB servers via a centralized GitLab repository.
  • You will be able to access the same R deployment, with the same packages via RStudio and via SSH usage. This will make it easier to switch from one interface to the other.
  • As the mechanisms and packages are shared between the IFB and ABiMS, we'll now share to a group of experts in case of problems .

Please check our documentation: R / RStudio

R <-> RStudio

You can now switch easily between R-Cli and RStudio since RStudio is using the R-Cli installed for SSH purpose.

Please check our documentation: Migrate from RStudio 2 R/Rscript

Request a tool

User can ask for specific tool/package installation or update by contacting our support

Available tools

module avail