Eventalign: multi-threading does not function for the conda version

[mmiladi]

Hi,

The conda binary ignores the thread option for eventalign mode (at least). I could verify that the git-make-based installation runs with the palatalization on the same system. So there must be a problem with the conda recipe, and very likely with the hdf5 dependency. Is this a known issue?

Best, Milad

[jts]

Are you on OSX or Linux?

Jared

[mmiladi]

Linux Ubuntu 18.04

[jts]

I confirm I see the same thing if I install the latest version from conda. I don't know why this happens

[mmiladi]

Our first guess was the pinning to the fixed and old version of hdf5: https://github.com/bioconda/bioconda-recipes/pull/21399

Since the newer versions of hdf5 have separate conda builds for mpi:

Old:

New:

So if that be correct then an older version should not have this problem using this command conda install nanopolish=0.12.4. But even that version doesn't seem to work with multithread for me.

[jts]

Could you try 0.11.3? The build script changed for 0.12.x

[mmiladi]

I can confirm that it works for 0.11.3! Also the patch has changed in that PR.

[jts]

Yeah I need to fix the patch, no time right now though