This is a repository of my tools used for Torrent Server administration and data migration / analysis work.

The current programs that are in this repository with a brief description. See the individual program's help text for more details.

• batch_loader.pl: From a SQL Run Plan dump file, batch run change of plans on experiments to be batched. Still working on this. Want to add ability to actually launch the analysis too

• batch_planner.pl: Create a CSV file to upload into the Torrent Browser run planner in order to batch process several samples. Currently only have 32 barcodes set up, and this will not add in the rest of the information required to run (e.g. plan template, plugins, reference, etc.). Can easily copy and paste this into a fully formatted template that's been downloaded from the TS. Run before batch_loader.pl.

• change_of_plans.pl: Simple program to create a new explog.txt file from the original (making a backup copy of the original first) that can be used to when reanalyzing an Ion Torrent Run. This will allow the run plan in the DB to associate with the data in order to link plugins, sample names, etc.

• dataCollector.pl: A program to extract Ion Torrent Runs for importation to another TS, or to archive for permanent storage on a secure server for historic purposes.

• from_archive_analyze.pl: A program to extract the data exported from dataCollector and launch a reanalysis of the experiment using the current software version.

• mocha_mirror.pl: Script to mirror processed Ion Torrent report data to an external harddrive. The program will store as many runs as can fit on the drive by assessing the du of the drive and pushing the newest runs onto the stack. This will, of course, remove older runs that won't fit.

• sample_renamer.pl: Using a tab delimited samplekey file with the barcode and sample name, rename any ion file (e.g. IonXpress_xxx_rawlib.bam) with the sample name. The barcode will be replaced by the sample name that's indicated in the key file.