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Singularity container execution of pangolin crashes with recent nextflow versions #272
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ah "OSError: [Errno 30] Read-only file system: '/home/'" is a singularity error @hoelzer can you tune in you had this OS errors before |
maybe the answer with the --writable helps for singularity: https://stackoverflow.com/questions/65599721/unable-to-build-writable-singularity-container |
I'm wondering why this error occurs (only?) with the pangolin container. Apparently, it needs to have access to home? @Krannich479, did you also try setting |
based on the error pangolin wants to write something in its own container home directory. and singularitys home is not writable. as far as i understand (?) but this is something that the user controls with its own singularity system. it could be that however, we need to add as a flag to the config or so |
Uff... yes that is annoying and someone else here had this problem recently - for me it still worked bc my nf version is 22.x.x or so. I am not sure what is happening inside the pangolin container but yeah, the problem is that pangolin wants to write something in /home which is fine with a encapsulated Docker container but fails with Singularity. Because here the process actually tries to write in the HPC system path. |
Tried this, didn't work for me :/ |
Hi,
I noticed that poreCov crashes when running pangolin via singularity and a reasonably modern nextflow version. It seems that recent updates in the path mounting defaults of nextflow broke the default behavior of poreCov test profiles when using Singularity. More precise, when using the command
with
nextflow 23.10.1
andporeCov 1.9.4
I end up withAdditional Info:
The same command works fine and tests finish if I use
nextflow 21.04.0
. @MarieLataretu found these update notes that seem on point for this issue:https://github.com/nextflow-io/nextflow/blob/d8f8bf56cfe79dc05db7c149dafa0174717ae7f4/docs/container.md?plain=1#L580
https://github.com/nextflow-io/nextflow/blob/d8f8bf56cfe79dc05db7c149dafa0174717ae7f4/docs/container.md?plain=1#L584
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