https://github.com/ctubbs750/cbs-db3-annotate
Component in the cbs-db multi-repo designed to produce all CTCF Binding Site annotations included in the database.
https://github.com/ctubbs750/cbs-db3-annotate
annotation-tool cbs-db3 ctcf-binding-sites encode-ccres python shell-scripting snakemake-pipeline
Last synced: about 1 month ago
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Component in the cbs-db multi-repo designed to produce all CTCF Binding Site annotations included in the database.
- Host: GitHub
- URL: https://github.com/ctubbs750/cbs-db3-annotate
- Owner: ctubbs750
- Created: 2025-04-06T20:56:49.000Z (about 1 year ago)
- Default Branch: main
- Last Pushed: 2025-04-06T21:14:04.000Z (about 1 year ago)
- Last Synced: 2025-04-09T22:02:37.192Z (about 1 year ago)
- Topics: annotation-tool, cbs-db3, ctcf-binding-sites, encode-ccres, python, shell-scripting, snakemake-pipeline
- Language: Jupyter Notebook
- Homepage:
- Size: 298 KB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
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README
# cbs-db3-annotate
### Executing the pipeline
To execute the pipeline without HPC resources, execute the command:
```snakemake --rerun-triggers mtime --use-conda --conda-prefix ~/snakemake_condas/ --use-conda --conda-prefix ~/snakemake_condas/ -c12 --rerun-incomplete -np```
To execute the pipeline with HPC resources, execute the command:
```snakemake --rerun-triggers mtime --use-conda --conda-prefix ~/snakemake_condas/ --jobs 25 --cluster-config "config/cluster.yaml" --cluster "sbatch --mem={resources.mem_mb} --time={resources.runtime} --cpus-per-task {threads} --output={cluster.output} --error={cluster.error} --account={cluster.account}" -np```