"nextflow pull nf-core/sarek --help" returned "connection failed" ?
2
0
Entering edit mode
13 months ago
Glt • 0

Hi, I am trying to use nextflow and an nf-core pipeline for the first time. I have installed nextflow and nf-core and tried to run this simple command but got the "connection failed" error. I got the same error for a different pipeline such as nf-core/sarek too.

Any suggestion for this?

I am accessing RedHat Linux system of my company remotely and tried to run the below command.

Here is the exact run and error:

$ nextflow run nf-core/sarek --help

N E X T F L O W  ~  version 23.04.2

Pulling nf-core/sarek ...

https://github.com/nf-core/sarek.git: **connection failed**


$ nf-core --version

                                          ,--./,-.
          ___     __   __   __   ___     /,-._.--~\
    |\ | |__  __ /  ` /  \ |__) |__         }  {
    | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                          `._,._,'

    nf-core/tools version 2.8 - https://nf-co.re


nf-core, version 2.8
nextflow sarek nf-core • 1.5k views
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5
Entering edit mode
13 months ago

Most likely, your companies firewall rules do not allow to directly access GitHub? You can download the pipeline first from your laptop and then scp/rsync it on your remote system.

Use nf-core download --container "singularity" -r "3.2.1" sarek to download the pipeline in advance. Include the configs.

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0
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I have installed nextflow and nf-core

Looks like the software is already installed.

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2
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That's good :) The command suggested downloads the pipeline code from GitHub, along with the singularity images. It doesn't install any software.

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0
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Thanks. It looks like you are right. Company has firewall and do not allow to directly access GitHub. If I use the command you shared, how will I be able to catch all the updates? Should I run the same download command each time and upload to the server. Does it have any disadvantage wrt to the default pull command run?

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3
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You'll need to run it again every time you want to use an updated version of the pipeline. So it depends on how often you want to run I guess! :)

It should be equivalent to the nextflow pull command, but with extra stuff (shared nf-core configs and singularity images). Also pulling to a directory instead of NXF_HOME.

Note that if it's _only_ GitHub that doesn't work and the images can be fetched on the fly, you could also just download a zip of the pipeline code from GitHub, transfer expand and run on that.

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1
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13 months ago
GenoMax 143k

You may need to run off-line (LINK) if you don't have direct internet access (which you probably don't on company server).

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