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James Fellows Yates 2022-04-25 11:46:32 +02:00
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# Cedars-Sinai Medical Center HPC # Cedars-Sinai Medical Center HPC
- You will need HPC access from EIS, which can be requested in the Service Center. - You will need HPC access from EIS, which can be requested in the Service Center.
- You will need to load the nextflow module on the HPC before running any pipelines (`module load nextflow`). This should automatically load Java as well. - You will need to load the nextflow module on the HPC before running any pipelines (`module load nextflow`). This should automatically load Java as well.
- Run this with `-profile cedars` - Run this with `-profile cedars`
- By default this config file does not specify a queue for submission, and things will thus go to `all.q`. Because of that, the memory and cpu limits have been set accordingly. - By default this config file does not specify a queue for submission, and things will thus go to `all.q`. Because of that, the memory and cpu limits have been set accordingly.
- We highly recommend specifying a location of a cache directory to store singularity images (so you re-use them across runs, and not pull each time), by specifying the location with the `$NXF_SINGULARITY_CACHE_DIR` bash environment variable in your `.bash_profile` or `.bashrc` - We highly recommend specifying a location of a cache directory to store singularity images (so you re-use them across runs, and not pull each time), by specifying the location with the `$NXF_SINGULARITY_CACHE_DIR` bash environment variable in your `.bash_profile` or `.bashrc`