Demultiplexing (Automatic)

This page describes the steps to be taken in order to activate the automatic demultiplexing script, which is already running on the phoenix server.

NOTE: The details here will change as the automated system is developed further

For details about what the demultiplexing process entails, see the Manual Demultiplexing section.

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A cron job has been set up to run the automatic demultiplexing script:

scripts$ cat cron/automatic-demultiplex.job
*/15 * * * 4,5,6,7 . /ifs/home/kellys04/.profile; . /ifs/home/kellys04/.bash_profile; /ifs/data/molecpathlab/scripts/automatic-demultiplex.sh >> /ifs/data/molecpathlab/scripts/cron/log/cron.log 2>&1
# run every 15 minutes, 0,15,30,45
# run only on Thurs, Fri, Sat, Sun

This will automatically run the script on the days and times described.

To run the script outside of those timeframes, you should run the command shown there, but point it to your own home directory profile files instead;

. $HOME/.profile; . $HOME/.bash_profile; /ifs/data/molecpathlab/scripts/automatic-demultiplex.sh >> /ifs/data/molecpathlab/scripts/cron/log/cron.log 2>&1

The current implementation of this script depends on the presence of a samplesheet in the following location:

/ifs/data/molecpathlab/quicksilver/to_be_demultiplexed

Sample sheets with the correct naming scheme (*-SampleSheet.csv) will be used to try and start demultiplexing for the run matching the ID given in the name (e.g. 170717_NB501073_0017_AH52FLBGX3-SampleSheet.csv for run 170717_NB501073_0017_AH52FLBGX3).