The purpose of this pipeline is simply to run MAKER. MAKER can be run to make evidence annotation, abinitio evidence-driven annotation or only as chooser/combiner like evidence modeller (if all annotations computed outside MAKER.)
Prerequisite: MAKER3.02 is not in bioconda we need to update the recipe. GAAS, AGAT
It would be 3 steps:
1) If gff3 files provided as evidence input, check the gff files are match match_part otherwise run the AGAT script to convert them
2) run MAKER
3) run light check the run is complete (GAAS script)
3) run gaas_maker_merge_output_from_datastore.pl (GAAS script, this script needs AGAT to make statistics too)
The parameters needed for MAKER is very verbose and complex. We should find a way to provide a copy of the maker_opt.ctl file. If we chain this pipeline with other pipelines (to feed input files) we need to find a way to modify this file properly/accordingly.
See #17 for the general picture.
The purpose of this pipeline is simply to run MAKER. MAKER can be run to make evidence annotation, abinitio evidence-driven annotation or only as chooser/combiner like evidence modeller (if all annotations computed outside MAKER.)
Prerequisite: MAKER3.02 is not in bioconda we need to update the recipe. GAAS, AGAT
It would be 3 steps: 1) If gff3 files provided as evidence input, check the gff files are match match_part otherwise run the AGAT script to convert them 2) run MAKER 3) run light check the run is complete (GAAS script) 3) run gaas_maker_merge_output_from_datastore.pl (GAAS script, this script needs AGAT to make statistics too)
The parameters needed for MAKER is very verbose and complex. We should find a way to provide a copy of the maker_opt.ctl file. If we chain this pipeline with other pipelines (to feed input files) we need to find a way to modify this file properly/accordingly.