Compatibilities for module load

Dear HPC team,

I would like to run a pipeline which will use cutadapt/Bowtie2/Samtools/picard/bedtools/macs2/bedGraphToBigwig (the last one is part of Kent_tools but is provided as binary on the internet so not really need a module load)

I am looking for a combination of module load that would work for all (for the moment I am doing a lot of module purge/module load/run then module purge/module load/run…).

Is there an automatic way to find a combination that work (I am about to write a bash script which would do module spider for each version but maybe something already exists)?


Lucille Delisle

HI @lucille.delisle ,

having to unload a module to load another one is indeed not very user friendly. In fact we can compile the same software and version for multiple toolchain to help with this issue. You need to determine what is the most common toolchain needed by all the software you use. According to the list of software you want to use, this is a working solution:

ml foss/2021a cutadapt/3.4 Bowtie2/2.4.4 SAMtools/1.13 picard/2.21.1-Java-11 BEDTools/2.30.0 MACS2/

We had to recompile some software for the foss/2021 toolchain, feel free to require other versions or other software you would like to use at the same time.

If you want to do something programmatically, there is an API to module.

module spider lmodule/0.2.0-Python-3.8.2