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Can't download file behind authenticated proxy #5571

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braffes opened this issue Dec 4, 2024 · 0 comments
Open

Can't download file behind authenticated proxy #5571

braffes opened this issue Dec 4, 2024 · 0 comments

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@braffes
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braffes commented Dec 4, 2024

Bug report

Expected behavior and actual behavior

I want to download a remote file behind a proxy with authentication, but the authentication part in http(s)_proxy variables seem to not be interpreted.

Steps to reproduce the problem

main.nf:

process test {
    input:
    path cute_file

    script:
    """
    ls $cute_file >result_ls
    """
}

workflow {
    cute_file = file("https://files.rcsb.org/header/5FID.pdb")
       test(
        cute_file
    )
}

nextflow main.nf

Program output

WARN: Unable to stage foreign file: https://files.rcsb.org/header/5FID.pdb (try 1 of 3) -- Cause: Unable to access path: https://files.rcsb.org/header/5FID.pdb
WARN: Unable to stage foreign file: https://files.rcsb.org/header/5FID.pdb (try 2 of 3) -- Cause: Unable to access path: https://files.rcsb.org/header/5FID.pdb
WARN: Unable to stage foreign file: https://files.rcsb.org/header/5FID.pdb (try 3 of 3) -- Cause: Unable to access path: https://files.rcsb.org/header/5FID.pdb
ERROR ~ Error executing process > 'test'

Caused by:
  Can't stage file https://files.rcsb.org/header/5FID.pdb -- reason: Unable to access path: https://files.rcsb.org/header/5FID.pdb

nextflow.log

Environment

  • Nextflow version 24.10.2
  • Java version: openjdk 11.0.1
  • Operating system: RHEL 8.8
  • Bash version: GNU bash, version 4.4.20

Additional context

On the proxy side, it always returns http code : 407 Proxy Authentication Required

The variable NO_PROXY also seems to not be interpreted by nextflow.

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