Tools

Software / Tools

ABiMS cluster hosts more than 665 bioinfomatic tools and 1074 versions dedicated to sequence similarity search, genome/transcriptome assemblies, phylogeny, population genetics, metabarcoding, etc. (update: 09/2024)

Module/Conda/Singularity

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: https://gitlab.com/ifb-elixirfr/cluster/tools
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 : https://rstudio.sb-roscoff.fr

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