problem with infernal when running ./paprica-run.sh test bacteria

bowmanjeffs / paprica

paprica - PAthway PRediction by phylogenetIC plAcement

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problem with infernal when running ./paprica-run.sh test bacteria #72

Closed lottedemaeyer closed 4 years ago

lottedemaeyer commented 4 years ago

Dear Jeff,

When I try to run: ./paprica-run.sh test bacteria I get the following error: ./paprica-run.sh: line 26: paprica-pick_domain.py: command not found ./paprica-run.sh: line 30: paprica-place_it.py: command not found

When I check these lines in the scripts it says: infernal

However, when I installed infernal (easel instelled seperately) I don't get any error messages. Do you have any idea what could be wrong?

Thanks in advance!

Cheers, Lotte

jdwiyanto commented 4 years ago

Hi Lotte,

you have to include paprica in your PATH. For example, run the following in your terminal:

export PATH=$PATH:/your paprica directory

bowmanjeffs commented 4 years ago

You can follow the install instructions here for osx: https://www.polarmicrobes.org/installing-paprica-on-mac-osx/. In particular note the section on adding appropriate files to PATH. If you're installing on Linux installation is a bit simpler, but you still need to add files to PATH.