Get a List of Strings, each one holding
Run Name Application Investigator CIM BIC Primary Delivered Secondary Complete Secondary Delivered
delimited with either a tab or a comma
Queries the portal database and returns a list of SGEScriptSummary
containing the average of cpuseconds consumed by the scripts defined by
the provided SGEFilter
Queries the portal database and returns a list of SGEScriptSummary
containing the sum of cpuseconds consumed by the scripts defined by the
provided SGEFilter
Get a default Secondary Project Reanalysis name from the server given the run, PI, and appType,
then ask the user for the reanalysis name, given the default name
Get a default Secondary Project Reanalysis name from the server given the run, PI, and appType,
then ask the user for the reanalysis name, given the default name
A1-Input_hMeDIP.FCC3PBEACXX_L7_IACAGTG.flagstat
fastqc/A1-Input_hMeDIP.FCC3PBEACXX_L7_R1_IACAGTG_fastqc/fastqc_data.txt*
Get the read from the split up components of the FastQ File name
Get all the secondary projects that don't have an analysis group pointing to them, and that share a
set of samples with secondary projects that also don't have an analysis group pointing to them
Get all the samples for a run from the database and print the results in the following order:
Run Name Flow Cell Instrument RLIMS BatchID Start Date Primary Analysis Status
Instrument Complete Date Primary Complete Date Primary QC Complete Date Primary Delivery Date
Sample Name Sample RLIMS ID Sequencing RLIMS Project ID Lane App Type Read Type
Num Cycles Is Control Is Vendor Index Index Sequence
Get all the samples from the specified runs and print the information out in this order:
Run Name Flow Cell Instrument RLIMS BatchID Start Date Primary Analysis Status
Instrument Complete Date Primary Complete Date Primary QC Complete Date Primary Delivery Date
Sample Name Sample RLIMS ID Sequencing RLIMS Project ID Lane App Type Read Type
Num Cycles Is Control Is Vendor Index Index Sequence
Get a count of all the samples for a run from the database and print the results in the following order:
Run Name Num Sequences
If the run does not exist in the DB, return it with 0 sequences
Queries the portal database and returns a list of SGEScriptSummary
containing the total script invocations in the runs defined by the
provided SGEFilter
Get all the samples (possibly of a given application type) for all the runs from the database that
had primary analysis finish within a specified time, and print the results in the following order:
Run Name Application Investigator CIM BIC Primary Delivered Secondary Complete Secondary Delivered
Queries the portal database and returns a list of SGEScriptSummary
containing the sum of cpuseconds consumed by the scripts defined by the
provided SGEFilter