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trajectoread monitor

Overview

The monitor scripts are designed to track and analyze Stanford Sequencing Center operations on DNAnexus.

  • 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.

  • monthly_seq_stats.R: Create R plots describing monthly sequencing output. Plots are generated from files created by monthly_seq_stats.py.

Output

Sequencing Center Output 2013-2016

2016 Production by Platform

Usage

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

Crontab

0       12      1       *       *       bash -l -c "python /usr/local/autocopy/cron_scripts/monthly_seq_stats.py -c

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