Command "hostname" is not portable

[pditommaso]

The hostname command may not exist in all environments and cause the pipeline execution to fail

tools/nf_core/pipeline-template/lib/NfcoreTemplate.groovy

Line 27 in b989701

def hostname = "hostname".execute().text.trim()

Consider replacing it with

def hostname = ['sh', '-c', 'echo $HOSTNAME'].execute().text.trim()

x-ref nextflow-io/nextflow#2199

[pontus]

What cases are fixed by this, I'd rather think it's the other way around (hostname being available on all target platforms, although handling options differently, whereas $HOSTNAME is not set without a fancy shell).

Also, if one go for the environment variable, is there some "this runs on the target machine" magic that would explain the execution rather than picking it up from the environment variables directly?

[drpatelh]

An alternative is to use the hostname command but wrap it in a try/catch statement like here nf-core/rnaseq@fd5c9eb

Would that be a better solution @pontus @pditommaso ?

[pontus]

I'm mostly confused, so I'm not sure.

In my view hostname should work. uname -n might be slightly better but is mostly the same.

An optimisation (if there is no magic involved) could be to look at the environment first (in groovy) and run the command if there is no hostname, don't think it's worth the complexity though.

[drpatelh]

Ok. This should be fixed in #1213 Can change if there is another, better solution :)

[pditommaso]

@Zethson likely can provide more details about the env in which hostname was not found. In any case wrapping into a try catch is super suggested

[Zethson]

@Zethson likely can provide more details about the env in which hostname was not found. In any case wrapping into a try catch is super suggested

A fresh Arch installation without inetutils being installed. I did not notice this and just expected the hostname command to always be available :)

[pditommaso]

May you check if the var HOSTNAME is present ?

[Zethson]

May you check if the var HOSTNAME is present ?

It's empty.

[pditommaso]

Then try { .. } catch(Exception e) { .. } is the way to go

[drpatelh]

Changed here #1214