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Dfam-consortium / RepeatModeler

De-Novo Repeat Discovery Tool
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RepModelConfig.pm need to account for more binaries #177

Closed EricDeveaud closed 11 months ago

EricDeveaud commented 1 year ago

hello, some programs are not dicumented in RepModelConfig.pm eg imagespread, edgeredef, and famdef are not documented in RECON_DIR section of config file hile they are used in RepeatModeler currently only eledef and eleredef are "checked"

same applies to filter-stage-1.prl for RSCOUT_DIR that only contains build_lmer_table and RepeatScout same for blastx missing the RMBLAST_DIR while used in RepeatClassifier

regards

Eric

rmhubley commented 11 months ago

Software dependencies are configured by project. The RECON package includes all of the binaries you listed and are expected to be in the folder pointed to by the RepeatModeler configuration file. The same is true for RepeatScout. If you are referring to the 'expected_binaries' section of the config file, those list contain only a minimal set for sanity checking and haven't been expanded to include all possible files contained in a dependencies distribution.