This code is designed to upload integration sites, PCR breakpoints, and multihits identified by intSiteCaller and upload them to the intsitesdev database. The database is currently located at microb98.med.upenn.edu:3309 and is described by the included schema, insitesdev.sql.
intSiteUploader expects to be passed the primaryAnalysisDirectory as defined when intSiteCaller was run. This directory must have the following minimal file structure:
primaryAnalysisDirectory
├── sample1
│ ├── sites.final.RData
│ ├── multihitData.RData
│ └── allSites.RData
├── processingParams.csv
└── sampleInfo.csv
There can be as few or as many samples as the user desires in the primaryAnalysisDirectory, so long as each sample is represented in both processingParams.csv and sampleInfo.csv. See intSiteCaller's Documentation for a description of the values contained in these two metadata files.
Uploading is started by running Rscript intSiteUploader.R <primaryAnalysisDir>.
At this time, it is highly recommmended to only run one instance of intSiteUploader at a time in order to avoid primary key collisions. Uploading an entire MiSeq run should take less than 2 minutes, so this restriction should be functionally inconsequential.
DO NOT run intSiteUploader after intSiteCaller by using the && command line operator. intSiteCaller.R is only a 'kickoff' script and will exit with a status of 1 before the full analysis has completed. It is highly recommended that the user manually confirm that the analysis succeeded and that vaguely reasonable results have been returned before running intSiteUploader. There is currently no way to automatically purge a run from the database (not to mention this is poor practice in a production environment), so make sure you're happy with it before uploading!
intSiteUploader.R does not directly output any commands or data, as all MySQL commands are generated and executed internally.
This code is dependent on the RMySQL and stats R packages as well as the mysql executable.
Additionally, the database connection information is expected to be stored in ~/.my.cnf in the following format:
[intSitesDev]
user=foo
password=bar
host=microb98.med.upenn.edu
port=3309
database=intsitesdev
user and password coorespond to the account you wish to use to log into the MySQL database.