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farm-notes

Getting Started - accounts & installing conda/bioconda, etc.

Integrate your github username & password

Partitions/queues we have access to

Example scripts

More advanced usage- includes:

  • using local temp directory on nodes
  • nodes, tasks, and cpus-per-task

Using Snakemake

Magic commands and informative links

The appropriate help mailing list is [email protected] - the list [email protected] is for things that you don't want followed up on.

Other references

New farm docs: www.hpc.ucdavis.edu/posts/about_farm/

CSE wiki: wiki.cse.ucdavis.edu/support/systems/farm

Whitehead lab wiki: wiki/Using-the-farm-cluster

Convenient SLURM commands (Harvard): https://www.rc.fas.harvard.edu/resources/documentation/convenient-slurm-commands/

Quick tips

Copy files onto farm using port 2022:

scp -P 2022 here_file [email protected]:there_file

You can also use GLOBUS - see globus docs

Getting an account

If you have a UC Davis account, you can apply to get a farm account here:

wiki.cse.ucdavis.edu/cgi-bin/index2.pl

Select "Farm/CAES", and "Brown."

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