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NGI specific scripts

scilifelab_denovo, automated convenience for NGI users.

Requirements

  • Fastq sequence data in the folder structure as delivered by NGI Stockholm
  • Needs to be run on UPPMAX.

The commandline tool scilifelab_denovo supports customizable parameter defaults for all it's sub-commands. It attempts to read a configuration file found in the file $HOME/.nougat/scilifelab.conf.

mkdir $HOME/.nougat
cp ../config_files/scilifelab.conf $HOME/.nougat/

# Now edit the template
vim $HOME/.nougat/scilifelab.conf