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bobeobibo / phigaro

Phigaro is a scalable command-line tool for predicting phages and prophages
MIT License
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phigaro-setup - non-interactive setup possible? #29

Closed rpetit3 closed 3 years ago

rpetit3 commented 3 years ago

Hello!

Is there a built-in method to skip the "please select appropriate "x" location" prompts during setup?

...
Please select appropriate Prodigal location
[1] /local/home/rpetit/miniconda3/envs/bt-phigaro/bin/prodigal
[2] Add another path manually
Choose your option (Enter for /local/home/rpetit/miniconda3/envs/bt-phigaro/bin/prodigal):
Please select appropriate HMMER location
[1] /local/home/rpetit/miniconda3/envs/bt-phigaro/bin/hmmsearch
[2] Add another path manually
Choose your option (Enter for /local/home/rpetit/miniconda3/envs/bt-phigaro/bin/hmmsearch):
Found Prodigal in: /local/home/rpetit/miniconda3/envs/bt-phigaro/bin/prodigal
Found HMMER in: /local/home/rpetit/miniconda3/envs/bt-phigaro/bin/hmmsearch
...

Thank you!

PollyTikhonova commented 3 years ago

Not for now. Is it neccessary?

rpetit3 commented 3 years ago

Probably not necessary, but would be useful.

I'm building a Nextflow workflow for Phigaro using the conda build. It would be useful to just run phigaro-setup without interacting since Prodigal and HMMER will always be available.

As an alternative, if a config file is provided does it use the provided paths or also ask to verify? (I can check shortly)

PollyTikhonova commented 3 years ago

As far as I remember it does not ask to verify

rpetit3 commented 3 years ago

Ok, so here's what I'm doing to allow "non-interactive" setup of databases.

rm -rf .phigaro/* && printf '\n\nN\n' | phigaro-setup --no-updatedb

This would allow the database to at least be setup in a programmatic way (e.g. in a workflow).

Going to close this issue.

iferres commented 2 years ago

+1 for non-interactive setup