R version on CEG Server

[alexandriai168]

If we want the pipeline to run on CEG, we need to iron out how to get a version of R on there that can run the Dada2QAQC script. if I remember correctly, it can't install the seqinr package bc the version is too old.

Idk how we'd go about doing this, but maybe we could have a local version of R that we use (not really sure how to execute that)? Thoughts?

[invertdna]

Yep. We have to ask Chris B, the sysadmin for CEG. He didn't want to update R because doing so would break things for other people. But we can ask again. R on the server is v 4.0.4 (from 2021), and maybe it's time. In the meantime, an earlier version of seqinr might be worth a shot. Here is the archive for those versions: https://cran.r-project.org/src/contrib/Archive/seqinr/

[eandrusz]

I think you can create an "environment" where you can have a different version of R. See: https://conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html

On Thu, Mar 30, 2023 at 2:28 PM Ryan Kelly @.***> wrote:

Yep. We have to ask Chris B, the sysadmin for CEG. He didn't want to update R because doing so would break things for other people. But we can ask again. R on the server is v 4.0.4 (from 2021), and maybe it's time. In the meantime, an earlier version of seqinr might be worth a shot. Here is the archive for those versions: https://cran.r-project.org/src/contrib/Archive/seqinr/

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[avancise]

Anaconda has to be loaded on the HPC before you can set up conda environments, but once it's set up then conda environments are a pretty easy best practice, even if R is updated. They do take a lot of extra storage space, since every conda environment has every software program loaded as a separate instance, but so far I haven't encountered an HPC manager who is against it (but might be good to ask 1) if it exists on the CEG computer, and 2) can we reload cutadapt, R and all of its associated packages in our own conda environment).

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On Thu, Mar 30, 2023 at 3:11 PM Elizabeth Andruszkiewicz Allan < @.***> wrote:

I think you can create an "environment" where you can have a different version of R. See:

https://conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html

On Thu, Mar 30, 2023 at 2:28 PM Ryan Kelly @.***> wrote:

Yep. We have to ask Chris B, the sysadmin for CEG. He didn't want to update R because doing so would break things for other people. But we can ask again. R on the server is v 4.0.4 (from 2021), and maybe it's time. In the meantime, an earlier version of seqinr might be worth a shot. Here is the archive for those versions: https://cran.r-project.org/src/contrib/Archive/seqinr/

— Reply to this email directly, view it on GitHub < https://github.com/MMARINeDNA/metabarcoding_QAQC_pipeline/issues/8#issuecomment-1490988365 , or unsubscribe < https://github.com/notifications/unsubscribe-auth/ADG46SYC2YMQ73VPDS5TV2DW6X3IFANCNFSM6AAAAAAWNYJPW4

. You are receiving this because you are subscribed to this thread.Message ID: @.*** com>

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[alexandriai168]

this has been fixed by developing a docker/singularity image that people can run on either their local machine or HPC.