Python3 and nextflow - Githubissues

NationalGenomicsInfrastructure / irma-provision

Ansible playbooks for provisioning NGI pipeline and related sw

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Python3 and nextflow #436

Closed ssjunnebo closed 2 years ago

ssjunnebo commented 2 years ago

Nextflow 21.04.3-all
ampliseq 2.0.0
viralrecon 2.2
nf-core tools 2.1
rnaseq 3.3
python2 -> python3

ssjunnebo commented 2 years ago

The click version is still fixed to 7.0, so I'll try removing that. Maybe that will solve your issue @slohse 🤞

slohse commented 2 years ago

Hm, #439 didn't actually fix my issue (I cherry-picked it into my local copy of this branch to verify). But I think it's a result of the unusual locale (LANG and LC_CTYPE are en_DE.UTF-8) I have on my desktop machine, that SSH apparently carries over to irma. If I do export LANG=en_US.UTF-8; unset LC_CTYPE; in my shell before I run ansible, it works fine. It's just weird that the click branch worked without changing my Locale, whereas this branch doesn't.