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SionBayliss / PIRATE

A toolbox for pangenome analysis and threshold evaluation.
GNU General Public License v3.0
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PIRATE_to_roary.pl: command not found #36

Closed mabouelk closed 4 years ago

mabouelk commented 4 years ago

I am trying to convert the output files but not working. Any help?

SionBayliss commented 4 years ago

The script can be found in the /tools/convert_format/ directory of your PIRATE installation folder e.g. path_to_PIRATE/tools/convert_format/PIRATE_to_roary.pl

mabouelk commented 4 years ago

Thank you

iferres commented 3 years ago

Hi, I have a related problem. I can't find the PIRATE_to_roary.pl script when installed through conda. Would be nice to have it that way too. Thanks for the software btw!

SionBayliss commented 3 years ago

Hi Ignacio,

They are downloaded but not in PATH. They can be found in ~/path_to_miniconda/envs/name_of_pirate_environment/tools/ I believe. I agree that they should probably be in PATH 🙂

All the best, Sion

From: Ignacio Ferrés @.> Sent: 17 June 2021 13:36 To: SionBayliss/PIRATE @.> Cc: Sion Bayliss @.>; State change @.> Subject: Re: [SionBayliss/PIRATE] PIRATE_to_roary.pl: command not found (#36)

Hi, I have a related problem. I can't find the PIRATE_to_roary.pl script when installed through conda. Would be nice to have it that way too. Thanks for the software btw!

— You are receiving this because you modified the open/close state. Reply to this email directly, view it on GitHubhttps://github.com/SionBayliss/PIRATE/issues/36#issuecomment-863245852, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ACXFVLAXQP4NS5TFZOAT4H3TTH27DANCNFSM4LOE6O7Q.

iferres commented 3 years ago

I found it! My bad. Yes, it will avoid people like me asking for the scripts in the github issue tracker :sweat_smile: Thanks!