Tools

Tools

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

Tools are mainly available through the $PATH, you just have to write the name of the command to use it. But some are installed via Conda and can't be use without the activation of a Conda environment (for more information see the Howto)

For regular tools, we provide a "sort of" list below. But you can also list them:

  • The tools are installed here:
ls /usr/local/genome2

For tools installed through Conda:

  • To get all the Conda environments:
$CONDA2/conda env list
$CONDA3/conda env list
  • To list tools within a specific Conda environment:
source $CONDA3/activate eba2017_rnaseq_denovo
conda list

R

RStudio

ABiMS proposes also an instance of RStudio (http://r.sb-roscoff.fr) for formation purpose and prototyping/tools development, but not for heavy computation.

R

But heavy and consuming process, please use R (qlogin) and RScript (qsub) directly on the Cluter. This R installation share its libraries with RStudio.

Request a tool

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