RE: Issue with running skipper in mamba/conda environment

[TimothyTse001]

Hello,

Is it necessary to run this in a conda/mamba environment or would it possible to also to run skipper with packages installed on guix profile? Our institute has blocked anaconda/bioconda access & there is a lot of workaround that is required to installed the software and all the dependencies.

In addition, even with manual installation, skipper is only able to partially run but cannot complete its output because it seems that r-matrix & matrix.so requires libm.so.6 from glibc2.35 but conda only offers glibc2.19 & for whatever reason it can't seem to detect that I have glibc2.35 in my guix profile or in usr/bin/

Any help would be greatly helpful! Thanks!

[augustboyle]

Hello,

I am not familiar with GUIX but it should be possible to run everything with manual installation. Even without Snakemake you can piece together all the scripts as needed (no example as of yet). Can you manually install R without using Conda or anything else? If you use the released version of the code you can specify the path to the R executable you want to use in the config file (R_EXE). R is not the easiest thing to install in general but you just have to figure it out once.

https://github.com/YeoLab/skipper/tree/v1.1.0