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smarco / gem3-mapper

GEM-Mapper v3
GNU General Public License v3.0
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how do GEM accept input from pipe #16

Closed sleepvet closed 4 years ago

sleepvet commented 4 years ago

I donot want to output a temporary file. Here is what I did: cat /mnt/*.fa|gem-indexer -i -o newsuper cat /mnt/*.fa|gem-indexer -o newsuper cat /mnt/*.fa|gem-indexer -i - -o newsuper But none of them worked. Could please help me with it?

smarco commented 4 years ago

I'm afraid you will have to create this temporal file. The gem-indexer executes a rewind of the input file, so it needs it to be stored (so it can be read twice).

Sorry for the inconvenience,