How to set PATH to OrthoFinder2 correctly?

[janstrauss1]

Hi @drostlab,

I'm trying to set up orthologr for detection of orthologs in multiple species.

I've installed orthofinder into my PATH using conda install orthofinder. Calling orthofinder -h from terminal shows OrthoFinder version 2.4.0 Copyright (C) 2014 David Emms suggesting that orthofinder is installed correctly.

Yet, I still run into the following issue when running the example code:

# specify species names
orgs <- c("Arabidopsis lyrata", 
          "Capsella rubella", "Solanum lycopersicum")
# download proteome files for all species          
biomartr::getProteomeSet(db = "refseq", organisms = orgs, path = "of_proteomes")
# download annotation files for all species          
biomartr::getGFFSet(db = "refseq", organisms = orgs, path = "of_gff")
# select longest splice variant per gene locus
retrieve_longest_isoforms_all(proteome_folder = "of_proteomes", 
                              annotation_folder = "of_gff",
                              annotation_format = "gff", 
                              output_folder = "of_proteomes_longest_sv")

> orthofinder2(proteome_folder = "of_proteomes_longest_sv", comp_cores = 4)
sh: orthofinder: command not found
Error: It seems like you don't have OrthoFinder2 installed locally on your machine or the PATH variable to the OrthoFinder2 program is not set correctly.

How should I setup orthofinder correctly?

Many thanks in advance for your help!

[HajkD]

Hi Jan,

Many thanks for your feedback.

So far, orthologr didn't support the conda path version of Orthofinder2, but assumed that it is installed as system tool accessed via usr/local/bin. I realise that most people will install OF2 via conda, so I now changed the default path to the miniconda path /opt/miniconda3/bin/orthofinder. I just pushed the new version of orthologr and this new feature should be accessible to you now.

Please also make sure you have DIAMOND installed as executable tool (/usr/local/bin).

Does this work for you?

Best wishes, Hajk

[janstrauss1]

Hi Hajk,

Many thanks for your quick response!

Unfortunately, this still doesn't seem to work for me and I get the error:

...
> # run orthofinder2 to infer ortho groups for the specified species
> orthofinder2(proteome_folder = "of_proteomes_longest_sv", comp_cores = 4)
sh: /opt/miniconda3/bin/orthofinder: No such file or directory
Error: It seems like you don't have OrthoFinder2 installed locally on your machine or the PATH variable to the OrthoFinder2 program is not set correctly.

I'm in a macOS environment and my path to OF2 appears to be /Users/janstrauss/miniconda3/bin/orthofinder and /Users/janstrauss/miniconda3/bin/diamond for DIAMOND.

Is there maybe a way to set a custom path in orthologr as for the orthologs() function?

Many thanks in advance for your help!

Jan

[HajkD]

Hi Jan,

Thank you very much for coming back to me and for this great feature request.

I now added a new path argument to orthofinder2() that allows you to specify your own path.

The only problem that I still see is that you cannot pass the diamond path to the orthofinder command line call. So far, orthofinder assumes that DIAMOND is installed in the classic usr/local/bin environment and not in the conda/miniconda path. See also details here: https://github.com/davidemms/OrthoFinder/issues/406 .

I will see if I can find a way around this so that users can also set the diamond path in orthofinder2(), but would be grateful if you could also share some ideas on how to approach this. I would then implement whatever is required.

I hope this helps?

Many thanks, Hajk

[mcatto]

Hi, when I try to set the dNdS functions param ortho_detection to "Orthofinder2" I get the error "Error: Please choose a orthology detection method that is supported by this function." Is there something else I should be doing? Or is this not included in the dNdS function?

[HajkD]

Hi @mcatto

Thank you for your question. Unfortunately, dNdS with orthogroups is not supported yet. It is on my long ToDo list, but it may require a while until this feature is available.

I hope you find pairwise dNdS useful anyway.

Cheers, Hajk