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AfshinLab / BLR

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Load R before submitting SLURM batch job (and other necessary modules) #83

Open ajdesalvio opened 2 months ago

ajdesalvio commented 2 months ago

I apologize in advance if this is common knowledge, but I did not realize an R module was required to be able to run picard CollectMultipleMetrics until burning through several days of computing time. I also struggled a bit to find the modules/compilers necessary to run BLR on my university's high performance research computing cluster, and the following worked in my case, hopefully this can save someone else unnecessary trial-and-error. I also had to set the locale to UTF-8:

module load Anaconda3/2023.07-2 WebProxy GCC/7.3.0-2.30 OpenMPI/3.1.1 git/2.21.0-nodocs Mamba/23.1.0-4 R/3.5.1-bare
export LC_ALL=en_US.UTF-8
export LANG=en_US.UTF-8
pontushojer commented 1 month ago

This seems to be an oversight on our end, I can feel your struggles. We are using the picard-slim bioconda package for our conda environment which lacks the R dependency.

https://github.com/AfshinLab/BLR/blob/c0d699601252263ceac8e2eb2839841c1700289a/environment.yml#L37

This should be replaced with no-so-slim picard (https://bioconda.github.io/recipes/picard/README.html) which does depend on r-base. The *.lock files would also need to be updated.