Placeholder of length limit

shandley / hecatomb

hecatomb is a virome analysis pipeline for analysis of Illumina sequence data

MIT License

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Placeholder of length limit #106

Open KailunZM opened 7 months ago

KailunZM commented 7 months ago

Hello! Thanks a lot for sharing this powerful tool.

I got the error below when testing the program installation with hecatomb test

PaddingError: Placeholder of length '255' too short in package /ref/gdlab/software/spack-0.18.0/opt/spack/linux-rocky8-x86_64/gcc-8.5.0/miniconda3-4.10.3-buvzc6uug3orkopkzbq3muf4f2o7c32y/envs/hecatomb/lib/python3.12/site-packages/heca
tomb/snakemake/conda/984a2c62df4691818afcb8b7a0ec4cc3_/lib/python3.12/site-packages/trimnami/workflow/conda/1e503641665bf5d3c4de834fc9a4c013_/lib/libtinfo.so.6.4.
The package must be rebuilt with conda-build > 2.0.

Is there a way to change the length limit or fix the error within the conda evnn?

beardymcjohnface commented 6 months ago

Hi, what version of conda are you running? EDIT: I think the issue is that the prefix filepath is just too long. Can you please try and run the following?

hecatomb test build_envs --conda-prefix hecatomb.out/conda/

If that works, for your production run just add --conda-prefix hecatomb.out/conda/ to the command. It might fail though; I can patch in a fix but you could also try and install miniconda on a shorter path e.g. /home/users/USERNAME/miniconda/

KailunZM commented 6 months ago

Hi Michael,

It's conda 4.12.0

Best, Kailun

From: Michael Roach @.> Sent: Tuesday, March 5, 2024 16:39 To: shandley/hecatomb @.> Cc: KailunZM @.>; Author @.> Subject: Re: [shandley/hecatomb] Placeholder of length limit (Issue #106)

Hi, what version of conda are you running?

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beardymcjohnface commented 6 months ago

Thanks Kailun, can you please try with the custom conda prefix? hecatomb test build_envs --conda-prefix hecatomb.out/conda/ or if you haven't installed the databases yet: hecatomb install --conda-prefix hecatomb.out/conda/