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The Greenstone Developer's Guide has detailed step by step instructions on building collections from the command line. Here we just give a quick overview.
cd "C:\Program Files\greenstone"
setup.bat
perl -S mkcol.pl mycoll
cd collect\mycoll
perl -S import.pl mycoll
perl -S buildcol.pl mycoll
cd ".../greenstone"
source setup.bash
mkcol.pl mycoll
cd collect/mycoll
import.pl mycoll
buildcol.pl mycoll
rm -r index; mv building index
In some circumstances you may want to use the Librarian Interface to design your collection, then actually build it using command line building. When you click "Create Collection" in the GLI, its carrying out the last three steps: import, buildcol, and renaming building to index. So you can do the earlier steps using the Librarian Interface, and then import and build on the command line. If you are generating archive files by hand, then you will need to do this as you will not be able to use the Librarian Interface to "build" the collection.