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When Jing ran renee with `--sif-cache /data/CCBR_Pipeliner/SIFS`, the snakemake log shows that the containers are pulled from the internet. They're supposed to be copied from the shared sif cache dir …
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I've had trouble getting CDA and Oncoexporter to work on my new MacBook. I had to set up a new Conda env because my old mb was intel and the new one is M2. I kept having trouble either getting cdapy…
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# Steps
- [x] Run test data through main branch on biowulf
- [x] Run test data through main branch on FRCE
- [x] Most recent commit passes **Tests / Dryrun_Lint** github actions workflow.
# Te…
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## `gnlrem()`: that is, `gnlrim()` that allows for two random effects, possibly correlated
### the `i` changes to an `e`, but the `i` wasn't necessarily just an intercept since you had the freedom t…
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move resources for `/data/Ziegelbauer_lab` to `/data/CCBR_Pipeliner` ... and make them "open-to-all-Biowulf" users.
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### Description of the bug
Hi again,
I'm having trouble running the test profile of the pgsc calc in a new environment. When I run the test command, I get the error line "Module path must start wi…
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### Description of feature
Run real project data from ccbr1187
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Hi,
when I test diff_length script using mouse transcript length (this is similar to example file but the transcript name length), it comes out with error:
File "./scripts/diff_length.R", line 31…
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Currently, the default `--tmp-dir` is `/lscratch/$SLURM_JOBID`, which only works on biowulf. FRCE users are expected to set this to `/scratch/cluster_scratch/$USER/`. We could instead have the default…
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RENEE requires a shared resource dir which is outside the git repo.
It's set here:
https://github.com/CCBR/RENEE/blob/22a558115a7edd0893023cbb9e3bc612e978947b/renee#L46-L48
This makes RENEE onl…