Maaslin2 1.16.0 fails with more then 1 cpu

Downstream analysis and statistics MaAsLin
1

We are currently trying to integrate the newest bioconda version of maaslin2 into Galaxy: maaslin2 version update to 1.16.0 by renu-pal · Pull Request #5999 · galaxyproject/tools-iuc · GitHub

But we discovered, that using --cores 1 works and using more than 1 core fails with:

Error in checkForRemoteErrors(val) : 
  8 nodes produced errors; first error: object 'current_args' not found
Calls: Maaslin2 ... clusterApply -> staticClusterApply -> checkForRemoteErrors
Execution halted

I think this is a bug with version 1.16.0 (multiple cpus worked with 0.99.12).
Do you have a fix for this ? If so, if you could update the bioconda recipe, that would be great.

2

Hi @Paul_Zierep,

I wasn’t able to recreate this bug when installing the current version through Github. Would you be able to provide me with your session information so I can look into this deeper.

Thanks,
Jacob Nearing

3

Hi @nearinj,
as said, the error is only there for version 1.16.0 which is the current release via BioConductor and Bioconda (which is what we need to write a wrapper to be used in Galaxy).
If you could release the latest version from GitHub via Bioconda, we could provide a wrapper for this version and then the issue with the cores for 1.16.0 is probably not relevant anymore.

4

Hi @Paul_Zierep Thanks for the ping! I created a PR to update the MaAsLin2 version released in Bioconda: Update Maaslin2 version to use latest release from BioC v3.19 by ljmciver · Pull Request #49266 · bioconda/bioconda-recipes · GitHub . I will work on addressing the current build issues so we can get it pushed.

Thanks!
Lauren

5

Hi @Paul_Zierep The new MaAsLin2 bioconda package should be all set! Please ping me if you run into any other issues.

Thanks!
Lauren