Renaming runs

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The run type, port number and sample_id in the run name may be changed with the rename-runs program. This is typically done after importing data when the imported sample information is not in a format understood by GCWerks. It can also be done after acquiring data with GCWerks. The general form of the run name is below (see identifying samples for more).

yymmdd.hhmm.type.port.sample_id

The rename-runs program may be run for the entire database or for a specified time period in a number or ways.

Specify an individual mapping

Specify the from and to mapping for a time period (for example to change the run type and port number).

/data/gcwerks-3/bin/rename-runs  GCDIR  start_time  end_time  from  to

/data/gcwerks-3/bin/rename-runs  GCDIR  110412.1400   110414.2100   tank.3   cal.3

The run-index is automatically rebuilt after renaming runs, except when renaming an individual run using the method above. In this case, the run index must be run manually after all the individual runs are renamed:

/data/gcwerks-3/bin/run-index  GCDIR

From a sample.map file

A sample.map file may contain several mappings at once.

/data/gcwerks-3/bin/rename-runs  GCDIR  start_time  end_time  -map sample.map

/data/gcwerks-3/bin/rename-runs  GCDIR  110412.1400   110414.2100   -map sample.map
Sample120   air.3
Sample200   air.4
#
Target3     target.5
Target4     target.6

From values in the sample.log

Runs may be renamed based on run type, port number or sample ID values found in the sample.log.

/data/gcwerks-3/bin/rename-runs  GCDIR  -samplelog

Renaming individual runs from a list

When there are many individual runs to rename, a list of each run to rename can be specified in a “sample.list” file as below. The first column of the sample.list contains the old name, including the run date and time, and the second column contains the new information which is added after yymmdd.hhmm.

/data/gcwerks-3/bin/rename-runs  GCDIR  -list sample.list

An example sample.map file is below:

120101.1400.sample120    air.1
120101.1410.sample120    air.1
120101.1420.target3      target.3
120101.1420.target3      target.4

To find a list of current run names, copy the “.run-index” file (hidden file GCDIR/.run-index).

Checking the rename before doing it

For any of the rename modes described above, use the -check option to check what rename-runs would do.

/data/gcwerks-3/bin/rename-runs  GCDIR  -list sample.list  -check