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centre-for-microbiome-research / GroopM

Metagenomic binning suite
GNU General Public License v3.0
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explicit versions pytables=3.1.1 & numexpr=2.3.1 required as dependencies #28

Open jvollme opened 7 years ago

jvollme commented 7 years ago

When trying to run GroopM, I kept running into this error:

    with tables.openFile(dbFileName, mode = "w", title = "GroopM") as h5file:
AttributeError: 'module' object has no attribute 'openFile'
groopm core -c 1500 -p groopmdb.gm

Some googling suggested This may be a problem with the pytables version, so I downgraded to version 3.1.1. However, this also required downgrading numexpr to version 2.3.1.

Now it seems to work.

Maybe these version-requirements could be listed in the dependencies?