Problems with $HOME/.nextflow/scm file and accessing private GitHub repo

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1

Hi,

I’m encountering an issue with using test data in my Nextflow pipeline. I created a private GitHub repository to store the test data in my GitHub Enterprise team, generated a fine-grained token with repo and admin permissions and configured the $HOME/.nextflow/scm file accordingly to access the files stored in this repo. However, although the scm file has been configured accordingly, the pipeline instead of downloading the files (gzip files), generates an HTML page, specifically a GitHub login page, or a page requiring authentication (as if the authentication wasn’t done properly. Do you know why I’m still not able to access this repository? Am I missing something in the scm file ?

Below my scm file (I masked the actual password and token):

providers {
    mygit {
        server = 'https://github.ugent.be'
        platform = 'github'
        user = egiuili
        password = 'my_password'
        token = 'my_token'
    }
}

Thanks for your help!

2

Hi @egiuili

Can you confirm you’re setting -hub mygit in the command line when running your pipeline? (Or nextflow run http://github.ugent.br/foo/bar.git)

Also, bear in mind you must also specify the server API endpoint URL if it differs from the server base URL. For example, for GitHub Enterprise V3, add endpoint = 'https://git.your-domain.com/api/v3'.

EDIT: Checking with colleagues from UGent, you can only access github.ugent.be from within the UGent network. Is this error occuring when you try to run the pipeline within the UGent network?

3

Hi @egiuili,

If the comments from Marcel don’t work, you can always enquire within the DICT helpdesk.
From experience I know not all github features are supported on the UGent internal github.

4

Hi @mribeirodantas,

Yes, I confirm I am setting it in the command line. I also double checked to run it within UGent network and adding the endpoint, but it still doesn’t work. I guess, as pointed out by @matthdsm, that this issue comes from some UGent github internal features. If I have some updates, I’ll post them here!

For the moment, thanks for the help!

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