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README
fix_instance.py
make_instance_from_pmids.py
make_trec_instance.py

README

1) run make_trec_instance.py instance_folder

2) then run fix_instance.py instance_folder

3) rename .fixed files

4) run flamenco start instance_folder

If you wish to make an instance for any given set of pmids replace step 1) by:

1) run make_instance_from_pmids.py pmid_file instance_folder

where pmid_file has one line per pmid.