Software / Tools

ABiMS cluster hosts more than 500 bioinfomatic tools dedicated to sequence similarity search, genome/transcriptome assemblies, phylogeny, population genetics, metabarcoding, etc. 


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: IFB Core Cluster, ABiMS, the IGBMC and on the Strasbourg University Datacenter.

What's new is that all Conda env and Singularity images can be loaded via module:

Common documentations:

$ module load trinity/2.8.5
$ module load trinity # loads the latest version 

To know all the available

$ module avail
$ module avail trinity/ 

Self-completion works

$ module load tri [TAB]

/!\ The tools that used to be in the PATH are no longer in the PATH. You can load a specific module to grab them:

$ module load _genome2-legacy

But be aware that a lot of tool won't work because they need some library on the system, we didn't and don't want to install. Conda <3 <3 <3



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 .

R <-> RStudio

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


From the Slurm cluster

[login@slurm0 ~]$ module avail r/
---------------------------------------- /shared/software/modulefiles ----------------------------------------
r/3.5.1  r/3.6.3  r/4.0.2

[login@slurm0 ~]$ module load r/4.0.2

A documentation is available to help you to jump from RStudio to R if more resources are needed:

Request a tool

User can ask for specific tool/package installation or update using the following link:

Available tools

module avail