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epigen / dea_limma

A Snakemake workflow and MrBiomics module for performing and visualizing differential (expression) analyses (DEA) on NGS data powered by the R package limma.
https://epigen.github.io/dea_limma/
MIT License
23 stars 1 forks source link

R environment not being set-up #22

Closed burtonjake closed 2 months ago

burtonjake commented 2 months ago

If you run the pipeline without having already installed R then Rscript cannot be invoked and the rule [all] fails. The expected behaviour (from my perspective) is that the conda environment created for the rule should create an R environment (so r-base or r-essentials should be in the environment specification I guess?) as well as include all the required libraries (limma, edgeR). Alternatively it should be documented that R should be installed.

Tested that is is currently 'fixed' by installing R with conda install r-base first.

Related (or possibly another issue) is that the R libraries from the environment specification aren't being found. If I add them manually to the environment in which I have both R and snakemake installed then the module runs. Which suggests the environment isn't being picked up for some reason.

snakemake --version : 7.32.4 dea_limma version : v1.0.3

sreichl commented 2 months ago

Thanks for reporting. This looks very fishy to me. what's the exact error message? @fwzhao has recently installed and used it without issues? R should NOT be in the Snakemake environment but in the environments for the respective rules that need R. limma for sure has it as dependency. Try the latest version of dea_limme i.e., v2.0.0. please.

burtonjake commented 2 months ago

Never mind :D. It was missing the --use-conda in this particular snakemake setup!

sreichl commented 2 months ago

Okay that makes sense. Sounds like Snakemake 7 (--use-conda is deprecated in v8). Maybe makes sense to upgrade everything to also benefit from the latest module versions.