From 32cdea4b59788dedee89fd88e0e4f799fb91cc20 Mon Sep 17 00:00:00 2001 From: Cedric Arisdakessian Date: Mon, 3 Oct 2022 03:38:48 +0000 Subject: [PATCH] documentation for mana config --- docs/mana.md | 46 ++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 46 insertions(+) create mode 100644 docs/mana.md diff --git a/docs/mana.md b/docs/mana.md new file mode 100644 index 0000000..030749c --- /dev/null +++ b/docs/mana.md @@ -0,0 +1,46 @@ +# nf-core/configs Mana (at University of Hawaii at Manoa) Configuration + +To use, run the pipeline with `-profile mana`. It will use the following parameters for Mana (UHM HPCC): + +- Load singularity and use it as default container technology +- Setup a container cache directory in your home (~/.singularity_images_cache) +- Select appropriate queues (currently: `shared,exclusive,kill-shared,kill-exclusive`) +- Set the maximum available resources (available in 09/02/2022): + - CPUs: 96 + - Memory: 400.GB + - Time: 72.h + + +## Pre-requisites + +In order to run a nf-core pipeline on Mana, you will need to setup nextflow in your environment. +At the moment, nextflow is not available as a module (but might be in the future). + +### Install nextflow in a conda environment + +Before we start, we will need to work on an interactive node (currently, mana doesn't let you execute any program in the login node): + +```bash +# Request an interactive sandbox node for 30 min +srun --pty -t 30 -p sandbox /bin/bash +``` + +To setup nextflow on your account, follow these steps. + +```bash +# Load the latest anaconda3 module +module load lang/Anaconda3 + +# Initialize environment +. /opt/apps/software/lang/Anaconda3/5.1.0/etc/profile.d/conda.sh + +# Install nextflow (here in base environment, but you can create a new one if you'd like) +conda install -c bioconda nextflow +``` + +If you want these settings to be persistent, you can add the first 2 commands in your .bash_profile file like this: + +```bash +echo "module load lang/Anaconda3" >> ~/.bash_profile +echo ". /opt/apps/software/lang/Anaconda3/5.1.0/etc/profile.d/conda.sh >> ~/.bash_profile" +``` \ No newline at end of file