Issue calling make_examples.py

[helizabeth1103]

Hello! I'm experiencing an issue when trying to run make_examples. Instead of Docker we're using Singularity, and deepvariant has run before with just calling the run_deepvariant.py.

For example, this is what has worked for us in the past in our environment:

module load singularity source activate $condapath/DeepVariant

singularity exec $softwarepath/Singularity_files/deepvariant_1.5.0.sif python3 $softwarepath/deepvariant/run_deepvariant.py [...]

When trying to run make_examples, this code:

singularity exec $softwarepath/Singularity_files/deepvariant_1.5.0.sif python3 $softwarepath/deepvariant/deepvariant/make_examples.py [...]

is now throwing this error code:

Traceback (most recent call last): File "/$softwarepath/deepvariant/deepvariant/make_examples.py", line 35, in from deepvariant import dv_constants ModuleNotFoundError: No module named 'deepvariant'

Does this mean there is a problem with our install? Any ideas or suggestions?

Thank you very much for any light you can shed on this issue!

Best, Haley

[akolesnikov]

Hello @helizabeth1103,

dv_constants.py is the part of DeepVariant installation. You may take a look at https://github.com/google/deepvariant/blob/r1.6/docs/deepvariant-quick-start.md#notes-on-singularity for more details on DeepVariant with Singularity. You may also check https://github.com/google/deepvariant/blob/r1.6/docs/deepvariant-training-case-study.md that shows how to run make_examples from docker.

[pichuan]

Hi @helizabeth1103 , Due to inactivity on this issue, I'll close it. Please feel free to follow up if you have more questions.