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45 lines
1.6 KiB
Markdown
45 lines
1.6 KiB
Markdown
# nf-core/configs Mana (at University of Hawaii at Manoa) Configuration
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To use, run the pipeline with `-profile mana`. It will use the following parameters for Mana (UHM HPCC):
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- Load singularity and use it as default container technology
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- Setup a container cache directory in your home (~/.singularity_images_cache)
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- Select appropriate queues (currently: `shared,exclusive,kill-shared,kill-exclusive`)
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- Set the maximum available resources (available in 09/02/2022):
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- CPUs: 96
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- Memory: 400.GB
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- Time: 72.h
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## Pre-requisites
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In order to run a nf-core pipeline on Mana, you will need to setup nextflow in your environment.
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At the moment, nextflow is not available as a module (but might be in the future).
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### Install nextflow in a conda environment
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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):
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```bash
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# Request an interactive sandbox node for 30 min
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srun --pty -t 30 -p sandbox /bin/bash
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```
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To setup nextflow on your account, follow these steps.
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```bash
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# Load the latest anaconda3 module
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module load lang/Anaconda3/2022.05
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# Initialize environment
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. $(conda info --base)/etc/profile.d/conda.sh
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# Install nextflow (here in base environment, but you can create a new one if you'd like)
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conda install -c bioconda nextflow
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```
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If you want these settings to be persistent, you can add the first 2 commands in your .bash_profile file like this:
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```bash
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echo "module load lang/Anaconda3/2022.05" >> ~/.bash_profile
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echo "$(conda info --base)/etc/profile.d/conda.sh" >> ~/.bash_profile
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```
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