Tools

Software / Tools

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

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: 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: https://ifb-elixirfr.gitlab.io/cluster/doc/module/

$ 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

 

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 .

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:
https://ifb-elixirfr.gitlab.io/cluster/doc/r/

Request a tool

User can ask for specific tool/package installation or update using the following link: http://abims.sb-roscoff.fr/contact

Available tools

module avail