From 766eb450be7775798f33dca4be1ef59f8dbcb84d Mon Sep 17 00:00:00 2001 From: Alex Rajewski Date: Fri, 22 Apr 2022 10:23:19 -0700 Subject: [PATCH] usage notes --- docs/cedars.md | 7 +++++++ 1 file changed, 7 insertions(+) create mode 100644 docs/cedars.md diff --git a/docs/cedars.md b/docs/cedars.md new file mode 100644 index 0000000..ba09eb1 --- /dev/null +++ b/docs/cedars.md @@ -0,0 +1,7 @@ +# Cedars-Sinai Medical Center HPC + + - 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. + - 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. + - 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`