Sequencing billing is unavoidably complicated. As well as the info provided by the submitters (Submissions and Samples) we need run info and samplesheet info pre-loaded by running scripts. Christian will mark each Submission as BILLABLE as appropriate and then we can go to the InvoiceGenerator.
Pre-Billing script 1 - the RunInfo files
Each run deposits a file with info about the name, the flowcell and other details. Each of these needs to be uploaded. As scanning the filesystem takes a while I generally just run it on directories in the current month. The command looks like
for i in /n/seqcfs/sequencing/analysis_finished/1501*; do php plugins/Illumina/scripts/load_RunInfoFile.php -d $i -s ; done
where 1501 is yymm and replace as necessary. For testing purposes just remove the -s from the php line to check all is well.
Pre-Billing script 2 - the SampleSheet files
These are very important as they contain which samples from which submissions were in each run. These entries are then used to calculate how many lanes each submission occupied.
for i in /n/seqcfs/sequencing/analysis_finished/1501*; do php plugins/Illumina/NewSampleSheet.php -f $i/SampleSheet.csv -s done
As before 1501 is yymm and replace as necessary. For testing purposes just remove the -s from the php line to check all is well. This script can take a while to complete.