Importing ChemStation data

ChemStation or MS ChemStation data found in the GC directory (under GCDIR/chemstation) are imported with gcimport. Chromatograms which have already been imported will be skipped.

ChemStation data (XXXXX.D directories) may be grouped in sub-directories, or may be placed directly in the chemstation directory.

GCDIR/
    chemstation/
        11/
            XXXXX.D
            XXXXX.D
        12/
            XXXXX.D
            XXXXX.D

The example batch script below imports from subdirectory chemstation/12 (gcimport), then batch integrates (gcupdate) and calculates the results (gccalc). This could be done from automatically from a cron job.

/data/gcwerks-3/bin/gcimport  GCDIR   -import_dir  chemstation/12
/data/gcwerks-3/bin/gcupdate  GCDIR
/data/gcwerks-3/bin/gccalc    GCDIR

The -import_dir specifies the directory containing the XXXXX.D data. To import from all sub-directories (11/ and 12/ in the example above):

/data/gcwerks-3/bin/gcimport  GCDIR   -import_dir  chemstation/\*

Importing the sample identification

The sample identification maybe imported from the ChemStation file. This may be only the inlet port number or the run type and inlet port number (type.port). This is is appended to the GCWerks run name (yymmdd.hhmm.port or yymmdd.hhmm.type.port). The default is to use the ChemStation data_name field for the sample identification. Options to use ‘method name’ or ‘none’ may be specified in the gcwerks.conf file:

import-runtype: data_name
import-runtype: method
import-runtype: none

Specifying which files to import

The example configuration below (in the gcwerks.conf file) tells GCWerks to import ECD1A.ch data into channel0 and FID2B.ch data into channel1.

import-channels: ECD1A.ch FID2B.ch