Comments (5)
Pull request is done, but it seems that Bloocoo has been compiled properly.
This project lacks tests.
gatb-minia-pipeline/bloocoo/Bloocoo -h
minia-pipeline/bloocoo/Bloocoo: /home/rayan/.linuxbrew/lib/ld.so: bad ELF interpreter: Aucun fichier ou dossier de ce type
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Hi John,
I don't understand why your test failed, but your are right, gatb try to use all the core available.
nb_cores_system = int(check_output(["nproc"]))
I think it's no big deal to add a parameter. I'll check with the project manager.
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Thanks, an argument for setting the cores would really help.
If you are setting a default value for this, i generally think it is a good idea to set it low (not as the maximum number of available cores). I am always anxious to allow tools on shared computation servers, that have default values grabbing all the cores (or memory).
The problem is that sometime some user is going to forget setting the approriate parameter and then all other users are screwed as well.
If you set the default at a low value, the worst that can happen is that this users job runs slowly (reminding him to set the appropriate argument next time).
from gatb-minia-pipeline.
Apologies for the rough edges, this project is not battle-tested hence you'll likely to run into issues of this type.
Thanks Sebastien for handling this issue and Charles for the commit.
John, it looks like in the latest master version you can specify the number of cores. Regarding the error you're getting with Bloocoo, I suggest you bypass it for now using the --no-error-correction flag.
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Bloocoo has been disabled by default in current version
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