As a transition, Brian will hand off such duty onto me and Matt, in an attempt that Matt and I can cover each other in case one is on vacation.

1. Background:

Currently, two pars of run composes the seqware automation pipeline

a. a cron job is run to convert runfolder to srf format (module Illumina2SRF)
b. a manually submitted run, afterward basically, from srf to the end of RNAseqAlignment. this job is run by firing up a script “decider.pl” where? In the long run, this needs to change:
i) Does not need to run off any single user’s home directory, but rather a seqware user
ii) It needs a cron job too to periodically initiate the pipeline run.

2. Error checking

Need to learn “how to detect errors”

a. Go to LIMS at and look for processes with “error”s

b. All run (log) are stored at “/home/brianoc/scratch/pegasus/RNASeqAlignmentBWA/run####”

c. Use the MetaDB to query for the cause of errors
Log in to an instance of swmaster, and log in seqware metadb as following. Detail see

psql -h swmaster.bioinf.unc.edu -U seqware -W seqware_meta_db
u: seqware
p: seqware