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PacificBiosciences / kineticsTools

Tools for detecting DNA modifications from single molecule, real-time sequencing data
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build failure: pbcommand no longer offers pbparser_runner #72

Closed smoe closed 4 years ago

smoe commented 4 years ago

Hello, The pbparser_runner is imported in three different files (see https://github.com/PacificBiosciences/kineticsTools/search?q=pbparser&unscoped_q=pbparser) but no longer offered by https://github.com/PacificBiosciences/pbcommand. That changed API together with the pb* packages not offering releases makes it all a bit difficult to install the right thing and affects the Debian package that I was about to update. Are there suggestions on what to do? I added a comment on a somewhat related issue https://github.com/PacificBiosciences/pbcommand/issues/190, you may have better ideas how to word that or whom to address. Many thanks! Steffen

natechols commented 4 years ago

Looks like the GitHub versions of our repos are out of sync - the tool contract/pbsmrtpipe support has been removed from pbcommand and everything has been ported to Python 3. I'll see if I can get this repo updated to the current code.

natechols commented 4 years ago

The current version has been pushed to the repo, hopefully this resolves the problem.