JAMg complains cannot find the transposons database file when running repeatmasker #2
Description
This error happened due to the default transposons database path specified ($transposon_db = $ENV{'HOME'} . "/src/jamg/databases/hhblits/transposons") in the "prepare_domain_exon_annotation.pl" script doesn't match well with the database path established with current JAMg installation. I worked around by specifiy "-transposon_db $JAMG_PATH/databases/hhblits/transposons " to override the default value when running the "prepare_domain_exon_annotation.pl" script.