5. Data Management Topics
: 5.2 post-analysis script
5.2
post-analysis script
Each processing pipeline chosen for a sequencing Run on the GS Junior or the GS FLX+ Instrument can call a user-provided script, postAnalysisScript.sh, to copy the partially processed data (
e.g.
“imageProcessingOnly”) from the instrument to the DataRig when the processing is complete. The script can optionally trigger an automated analysis or send notifications.
The following environmental variables are available to the post analysis script:
Environmental Variable
Description
$SOURCE_DIR
The directory from which the source data was read
$PIPELINE_NAME
The data analysis pipeline name
$SW_REVISION
The revision number of the data analysis pipeline
$GSREPORTER_BIN
The full path of the gsReporter executable
The full path of the directory containing the output files (the -o parameter to gsRunProcessor) is passed on the command line, then the name of each generated file relative to the output path is passed in the following order: CWF files, SFF files, then log/error files.
The order in which the postAnalysisScript.sh and the backupScript.sh are called is indeterminate. postAnalysisScript.sh is called when the analysis is complete, and backupScript.sh is called when the fluidics part of the Run is complete. If both the partially processed data and the raw data are sent to the same destination, in creating directories, scripts should not assume one script was called before the other.
