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DROP_1.3.3.yaml package update required? #489
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Hi @chrisodhams , |
Thanks @ischeller , |
Hi @ischeller , |
Hi @chrisodhams , sorry, we were on holidays. We've now resumed to check this, but it's not straightforward as it seems some packages have conflicts. We'll keep you updated |
Hi @chrisodhams , we uploaded an updated DROP_1.3.3.yaml to our public server. Could you kindly give it a try and let us know, if it fixes the issue? Thanks again for pointing this out |
Hi @neverov-am @vyepez88 - it seems that the drop bioconda package is not in the yaml. |
Hi @chrisodhams , I apologise for this bug, there was an issue with exporting the environment. I have updated the |
Hi @chrisodhams , we have updated now DROP including its dependencies. Can you please try with 1.4.0? |
Hi @chrisodhams, any updates on this? As mentioned above using DROP 1.4.0 will fix your issue. Let us know if it still persists. |
Hi,
I've installed DROP v1.3.3 as per:
mamba env create -f DROP_1.3.3.yaml
taken from: https://www.cmm.in.tum.de/public/paper/drop_analysis/DROP_1.3.3.yaml
When running the demo, OUTRIDER throws an error in the
pvalsOutrider.R
script at the lineods <- computePvalues(ods, subsets=subsets_final)
.I believe this is because the OUTRIDER version specified in DROP_1.3.3.yaml uses v1.16.0 (bioconductor-outrider=1.16.0=r42hc247a5b_0) and at this version I don't believe the
subsets
argument has been implemented yet (thus the errorunused argument subsets
get's thrown).> ods <- computePvalues(ods, subsets=subsets_final) Error in .local(object, ...) : unused argument (subsets = NULL)
Note - no error thrown when removing subsets:
ods <- computePvalues(ods)
Was this change was implemented in 1.16.1?
Unfortunately, if I point to the latest version of OUTRIDER (bioconductor-outrider-1.18.1-r43hf17093f_0.tar.bz2) - it causes many package conflicts with the existing packages in the YAML. Note that 1.18.1 is the only later version of OUTRIDER available on bioconda.
Is there anyway this can be circumvented or the YAML updated? The FRASER version may also need to be looked into if new features in drop are implemented but not reflected in the package version.
Cheers,
Chris
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