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petrov-lab / tuba-seq

Analysis pipeline and utilities for TUmor BArcoded DNA Sequencing
https://github.com/petrov-lab/tuba-seq
MIT License
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ModuleNotFoundError: No module named 'striped_smith_waterman' #1

Closed mcolic closed 2 years ago

mcolic commented 2 years ago

Hi,

I am trying to run the preprocess.py file, however, I keep getting the error that there is no module name 'striped_smith_waterman'? I have successfully installed the Complete-Striped-Smith-Waterman-Library, but not sure what the problem is. I would greatly appreciate it if you could assist with this.

Thank you. Medina

cd-mcfarland commented 2 years ago

Hi Medina,

This library is a submodule within the repo, which requires the --recursive keyword argument when cloning, e.g.
git clone --recursive https://github.com/petrov-lab/tuba-seq.git Be sure to 'build' this C library using the 'make' command, as described in the Install Instructions.

Also, please note that this library is intended for Single-End Illumina reads. We recommend using Paired-End (PE) sequencing now. I can host software intended for PE reads, if you would like, although I would recommend accessing our tumor calls directly on GEO if you are using published data from the Petrov/Winslow labs.

Bests, Chris

mcolic commented 2 years ago

Hi Chris,

Thanks for getting back my question. Yes, I have done it that way - however, I keep getting errors with it; either no module names striped_smith_waterman or libssw.so does not exist in PATH (even after I copy it to the tuba_seq folder).

Yes, we have used the paired-end sequencing, and are using the merged reads for downstream analysis. Thanks, Medina

cd-mcfarland commented 2 years ago

Hi Medina,

Your system's PATH is an Environment Variable, which is a parameter specific to your programming setup or 'environment' and hard for me to troubleshoot without knowing more about your setup (you can learn more here: https://superuser.com/questions/284342/what-are-path-and-other-environment-variables-and-how-can-i-set-or-use-them).

cd-mcfarland commented 2 years ago

Also, you shouldn't need to copy over any files. I'd go into the sub-module and see if it installs fine, as suggested by their Install README. My guess is that there is something unique about your compiler setup. Also, we say it should work with gcc or clang, but 90% of the unit testing is in gcc.

mcolic commented 2 years ago

Yep, resolved it. Thank you!