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: 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
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.
You can now switch easily between R-Cli and RStudio since RStudio is using the R-Cli installed for SSH purpose.
[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/
User can ask for specific tool/package installation or update using the following link: http://abims.sb-roscoff.fr/contact
module avail