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My singularity cache very quickly grew to > 11GB during development of QC steps. The limit on biowulf in /home/$USER is 15GB. Is there another location we can put it with a better capacity?
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Problem
- Current repo is linked to dnousome account
Solution
- after change of ownership; update FRCE biowulf pull to reflect correct repo path
- /mnt/projects/CCBR-Pipelines/pipelines/Exo…
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- [x] Complete all steps in MVP on Biowulf
- [x] test the pipeline with E2E on Biowulf
- [ ] test the pipeline E2E on ec2 instance
- [x] Add case name hierarchy
- [ ] Run the pipeline on AWS with 10…
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Hi,
Happy to finally see this tool released, thanks.
I initiated the test run on local configuration but encountered the error below with the protein conversion step
python3 Tools/software/eg…
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Change kraken2 db on biowulf to include Mouse
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Add feature here:
https://github.com/daler/dotfiles/blob/095fc12649d4434cbcb71d3219cfd05eb42a58f6/setup.sh#L449
that asks if the user is in BSPC and if so appends the NICDH-core1 tools to us…
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A number of rules in `workflow/rules/somatic_snps.common.smk` use a custom temporary directory based on the slurm job id set in `config/config.json`. This assumes users only run these jobs on slurm, n…
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# Problem
FRCE is loading singularity and snakemake default values without setting a version. This is causing failures in snakemake calls which have been updated on Biowulf and Biowulf8
# Solution…
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Working with XAVIER `frce_test` branch (that was previously merged with `hotfix`) and running `xavier` on frce with hg38 data.
```
srun -N 1 -n 2 --time=12:00:00 --mem=16gb --pty bash
module p…
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- Using [RENEE](https://github.com/CCBR/RENEE/tree/dev/bin)'s template, create a bin folder for XAVIER
- `redirect` script loads required modules and conda environments
- `redirect` works on both BI…