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EichlerLab / pav

Phased assembly variant caller
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'intervaltree' installed using pip install, but pav still complained as "No module named 'intervaltree' " #56

Open chunlinxiao opened 1 month ago

chunlinxiao commented 1 month ago

I was tesitng pav following the instruction for Native install. I surely installed 'intervaltree' using pip install, but pav still complained as "No module named 'intervaltree' " as below:

./runlocal 8 --nt pav_HG00733.vcf.gz ModuleNotFoundError in file /net/intdev/varpipe/pav/dep/svpop/Snakefile, line 29: No module named 'intervaltree' File "/net/intdev/varpipe/pav/dep/svpop/Snakefile", line 29, in

Any suggestion? thanks

paudano commented 1 month ago

If Snakemake is installed in a conda environment, then PAV will run with the Python environment within that Conda environment. Was intervaltree installed in the same Conda environment?

Docker or Singularity is the easiest way run it. PAV and all dependencies are in the PAV container images.

chunlinxiao commented 1 month ago

thanks Peter - indeed Singularity is much easier.