# location of data (on sabazius)
/data/local/PGN/submission/<org>.final/<org>/library info>.archive.pased

# where data NEEDS to end up (after it has been converted to the proper format
/data/shared/pgn_data_processing/incoming_files/

# copy that to a relevant place and unpack it
mkdir /data/local/PGN/submission/<org>.final/<org>/work
cp /data/local/PGN/submission/<org>.final/<org>/library info>.archive.pased /data/local/PGN/submission/<org>.final/<org>/work
cd /data/local/PGN/submission/<org>.final/<org>/work
unzip <org/library info>.archive.pased

# rename/repackage into a format useful for our pipeline
#	there should be many separate zip files for each library, each with the
#	following naming convention:
#		<library>-<plate>.zip
#			<library>-<plate>-<well>.e
#	e.g.:
#		Aam01-10MS1.zip
#			Aam01-10MS1-H11.e
# this format may need to be added to the below file (as a regular expression)
#	(1) <library><plate_number>-<well>(-|_)<plate_desc>.<abi||e>
#	(2) <library>(-|_)<plate>(-|_)<well>.<abi|e>
#	(3) <library><plate><well><reaction>.scf
cd ~/pgn_processing/scripts/processing_components
./00_import_submitted_seq.pl -i /data/local/PGN/submission/<org>.final/work -f <format_type>

# proceed as normal in the processing components pipeline