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seqeralabs / nf-tower

Nextflow Tower system

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remote hung up unexpectedly (git modules)

replikation opened this issue · comments

commented

Hi,

when running a workflow via tower's launchpad I get a remote hung up unexpectedly exit 9 error, when tower tries to pull a private git submodule. Both the workflow git and the attached git submodule are private gits. The github access token works fine if i run it locally (nextflow run username/gitrepo ...) - so the access rights are there.

The full exit via tower:

 Workflow execution completed unsuccessfully

The workflow execution failed to start. Exit status: 9

Execution failed: generic::failed_precondition: while running "nf-workflow-2GvbbCnw8sVSRn": unexpected exit status 1 was not ignored

N E X T F L O W  ~  version 21.09.1-edge
Pulling replikation/workflow ...
git@github.com:replikation/repo_module.git: remote hung up unexpectedly

when searching on how to resolve the issue I only get git configuration suggestions like these:

export GIT_HTTP_MAX_REQUEST_BUFFER=100M
git config --global http.postBuffer 100000000

I tried adding this to the Pre-run script but then I get to exit 127 and it's not even pulling the repo. So I don't really know what might cause the hung-up error (e.g. tower or something else).

commented 
org.eclipse.jgit.errors.UnsupportedCredentialItem: ssh://git@github.com:22: org.eclipse.jgit.transport.CredentialItem$YesNoType:The authenticity of host 'github.com' can't be established.
commented

Hi @replikation ,

Apologies for the inconvenience, however the use of sub-modules is not supported on Tower at the moment.

commented

@abhi18av
Hi, thanks for the response. The error is related to using ssh protocol in the .gitmodules file. So changing from e.g. url = git@github.com: to url = https://github.com/.... resolved this issue and tower works with git modules.

On my end, the issue can be closed. Might be useful if your tower either reports that or automatically changes the ssh to HTTPS :)

best and thanks

commented

Thanks for letting us know @replikation !

I'll take this up internally and would circle back if we have updates. Closing the issue for the time being.