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mrmckain / annoBTD

Annotation software for Verdant.
GNU Affero General Public License v3.0
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Standalone run of annoBTD #2

Open greatfireball opened 7 years ago

greatfireball commented 7 years ago

Good morning @mrmckain,

Due to our interest in using annoBTD for automatic plastid annotation, we would like to run it in a standalone mode. As I understand the source, we need to run the run_annotation_pipeline.sh with three parameters. Can you provide information, what is the meaning of those parameters? Additionally, it seems that run_annotation_pipeline.sh uses a couple of files obviously exported from verdant, eg. *_annotated_regions_fromverdant_genes.fsa or *_annotated_regions_fromverdant_trnas.fsa. Is it possible to download those files from a location? Do I miss other important thinks to run annoBTD in standalone mode?

Thanks in advance!

Best, Frank

mrmckain commented 7 years ago

Hi Frank,

Yes, there is a lot missing from the code I threw up on Github. I have latest versions and can create a standalone version that is downloadable for your use. If you don't see it within a week, please message me again.

On Wed, Aug 30, 2017 at 12:43 AM, Frank Förster notifications@github.com wrote:

Good morning @mrmckain https://github.com/mrmckain,

Due to our interest in using annoBTD for automatic plastid annotation, we would like to run it in a standalone mode. As I understand the source, we need to run the run_annotation_pipeline.sh with three parameters. Can you provide information, what is the meaning of those parameters? Additionally, it seems that run_annotation_pipeline.sh uses a couple of files obviously exported from verdant, eg. _annotated_regions_fromverdant_genes.fsa or _annotated_regions_fromverdant_trnas.fsa. Is it possible to download those files from a location? Do I miss other important thinks to run annoBTD in standalone mode?

Thanks in advance!

Best, Frank

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/mrmckain/annoBTD/issues/2, or mute the thread https://github.com/notifications/unsubscribe-auth/AB6GUy2UY4aCoanvxLmyl6UnDTm5-DMRks5sdPaNgaJpZM4PG5Ju .

-- Michael R. McKain Assistant Professor, Department of Biological Science University of Alabama