The monitor scripts are designed to track and analyze Stanford Sequencing Center operations on DNAnexus.
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monthly_seq_stats.py: Collect metrics on monthly sequencing output based on DNAnexus records and lane.html files generated by bcl2fastq2. On completion it will call "monthly_seq_stats.R" to generate summary plots. Designed to be called monthly by a Cron job.
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monthly_seq_stats.R: Create R plots describing monthly sequencing output. Plots are generated from files created by monthly_seq_stats.py.
To run the python script to gather data and then automatically generate plots:
$ python monthly_seq_stats.py -y 2016 -m 12 -o seq_stats.txt
Or to run the Rscript indepedently:
$ Rscript monthly_seq_stats.R -f stats_files/seq_stats.txt -o seq_stats
0 12 1 * * bash -l -c "python /usr/local/autocopy/cron_scripts/monthly_seq_stats.py -c

