Question: using distinct versions of SEURAT on a SLURM cluster
gravatar for Bogdan
26 days ago by
Palo Alto, CA, USA
Bogdan950 wrote:

Dear all, 'd appreciate having your suggestions on the following please :

I am running scRNA-seq analyses (in R 3.6.1) on a SLURM CLUSTER , and I do have 2 scripts :

a) a script that requires the package Seurat 2.3.4 (historically, for "compatibility" with older data), and

b) another script that requires (a newer version) Seurat 3.1.

When I submit the jobs to the SLURM cluster, how could specify in the R script the use of the library Seurat 2.3.4 versus Seurat 3.1 ?

(as we know, when we load the Seurat library , we just write : library("Seurat"), without specifying the version).

do I need to use a docker/singularity container for R.3.6.1 with Seurat 2.3.4, and another docker/singularity container with Seurat 3.1 ? thanks !

scrnaseq seurat • 105 views
ADD COMMENTlink modified 26 days ago • written 26 days ago by Bogdan950

I would probably make two separate environments, e.g. via conda and then install in each of them the version you need. You can then simply set RSCRIPT="/path/to/anaconda/environment(1/2)/bin/Rscript for the respective jobs. If possible I would try tough to convert the "older" data to a Seurat3 compatible format (just thinking aloud, you probably thought about that already).

ADD REPLYlink written 26 days ago by ATpoint29k

thanks a lot for your suggestion on making 2 separate virtual environments ... very helpful !

ADD REPLYlink written 26 days ago by Bogdan950

Sounds like your cluster does not use modules. Otherwise you could do this at that level when you submit SLURM jobs.

ADD REPLYlink written 26 days ago by genomax78k

It does use modules ; typically, we do write "module load r/3.6"

ADD REPLYlink written 26 days ago by Bogdan950

Ah I see. You are referring to using distinct versions of seurat with same R. I suppose you could build two modules for R with two separate versions of seurat. Analogous to conda solution suggested below. I suppose you can use the conda solution on your own where as for the modules you will need to get your sys admins to do that.

ADD REPLYlink written 25 days ago by genomax78k

thank you very much for your suggestion ;)

ADD REPLYlink written 25 days ago by Bogdan950
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