0.6.0-alpha.1 version ModuleNotFoundError about medaka

[cjw85]

Hi @damientully

Thanks for trying our alpha release, and sorry that it has not installed smoothly.

We have noticed this. Something in the python build chain is becoming confused; on failing to build whatshap the build of the libmedaka module is also being neglected.

We have asked the whatshap developers to create a new release, which will make this simpler.

Here's what I did this morning to get things working:

# grab medaka and whatshap sources
git clone [email protected]:nanoporetech/medaka.git
git clone https://bitbucket.org/whatshap/whatshap
cd medaka
# remove whatshap as a requirement
sed -i 's/git\+/#git\+/' requirements.txt
make install
source venv/bin/activate
cd ../whatshap
pip install pyvcf
python setup.py install

I hope this gets you a working install, and look forward to seeing any variant calling results that you produce.

[damientully]

Hi @cjw85

Thanks for your reply and those instructions. Seems to be working now!
Damien

[cjw85]

The v0.6.0-alpha.2 now depends on whatshap==0.18 and builds correctly.

It is available with pip, needing the --pre option to opt-in to prereleases:

pip install --pre medaka