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Untar needs --no-same-owner on DNAnexus #725
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Hi @GHAStVHenry ! Thanks for reporting! This appears to be the same issue as reported by @drejom in #712 We noticed another issue with Salmon recently that we haven't quite been able to get to the bottom of. I am trying to reproduce on AWS Batch via Tower at the moment but maybe it's worth creating an issue here for it too @drejom ? |
Oh I actually just got added to the source of @drejom's source issue, but hadn't looked through yet to see this was one of the issues |
Hi @GHAStVHenry! Do you happen to know why we need this option when running |
Howdy @drpatelh!
Why it is necessary in DNAnexus, but has never been seen before in other environments? I have no idea... actually, I have a half baked idea that's not ready for a public forum until I talk to product engineering and Paolo. |
Yep, you are absolutely right.
Maybe you folks aren't ordinary users - superpower ones instead?! 😆 |
hahaha, I like the sound of that... let's go with that hahaha |
But likely the container runs as root, and therefore the it should be given explicitly |
Check Documentation
I have checked the following places for your error:
Description of the bug
untar Cannot change ownership error
see bottom for suggested fix
@pditommaso @drpatelh
Steps to reproduce
Steps to reproduce the behaviour:
Run workflow on DNAnexus (with xpack)
profile test,docker
NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:UNTAR_SALMON_INDEX (SALMON.TAR.GZ)
fails
Expected behaviour
Log files
Have you provided the following extra information/files:
.nextflow.log
fileSystem
Nextflow Installation
Container engine
Additional context
can be fixed by adding
--no-same-owner
to untar command at:rnaseq/modules/nf-core/modules/untar/main.nf
Line 31 in 964425e
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