Comments (10)
Interesting! Are you able to pip install other packages? Also, are you by chance running a Python 3 version of pip? (pip --version will tell you.)
Right now, the installed version of Nucleus is Python 3 compatible, but the pip package is Python 2 only. We hope to fix that soon.
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Closing for now. Please re-open with version info if problem persists.
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I would like to be a beta tester of a python/pip 3 install of Nucleus.
The Nucleus pip install instructions should include the condition of python 2 only.
I found this page after doing a search, and others may just stop at the pip 3 error.
I was able to install a python 2.7 environment inside of Anaconda 3 (Anaconda 3 is an anaconda version and does not imply python 3 environments only).
Installing the nucleus with pip worked.
Got the notebook to work locally with CPU.
The GPU version runs but repeats/recreates the following about 200 times:
Created TensorFlow device
full message:
2019-02-06 17:29:30.017084: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1115] Created TensorFlow device (/job:localhost/replica:0/task:0/device:GPU:0 with 6999 MB memory) -> physical GPU (device: 0, name: GeForce GTX 1080, pci bus id: 0000:0a:00.0, compute capability: 6.1)
This may just be related to the number of batches.
The result is that the GPU time is about the same as the CPU time.
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@ThomasColthurst is there any new information on when we can expect Nucleus to be available via pip for Python3 as well?
Thanks!
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A Python 3 pip for Nucleus is probably a few weeks away.
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@ThomasColthurst Perfect! Thanks for quick response. Also one more question - will Nucleus be compatible with Tensorflow 2.0 in the near future?
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Thomas, Thank you very much
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@TimSmole -- yes. We have an upcoming Nucleus release that removes our dependencies on TensorFlow's Python code, and this will make it easy to use Nucleus with whatever version of Tensorflow you want.
(Nucleus's C++ code will still depend on a specific version of TensorFlow, and that specific version will get upgraded to TensorFlow 2.0 once 2.0 is out of alpha. But that shouldn't effect most Nucleus users.)
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Great news! Thanks again @ThomasColthurst! I'm looking forward to this release.
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The long awaited Python 3-compatible pip package for Nucleus is now available.
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Related Issues (20)
- Install process is completely broken in presence of existing tensorflow install, and breaks that also HOT 5
- User Menu for Nucleus HOT 2
- hdf5 file format not supported HOT 3
- Is there any limitation for calling rare mutation? HOT 2
- MD tag HOT 2
- ImportError for `nucleus.io.gfile` HOT 2
- RuntimeError: PythonNext() argument variant is not valid: Dynamic cast failed. HOT 1
- RuntimeError: PythonNext() argument read is not valid: Dynamic cast failed HOT 4
- Nucleus Proto is colliding with Tensorflow protos? HOT 8
- Failed to install google-nucleus HOT 2
- Nucleus Proto is colliding with Tensorflow protos HOT 7
- Error runing codelab : dna_sequencing_error_correction HOT 4
- Read strand HOT 1
- ImportError: libbz2.so.1.0: cannot open shared object file: No such file or directory HOT 3
- Nucleus not building for Python3.7-3.9 via pip. HOT 5
- Compatibility with Tensorflow 2.11.0 HOT 2
- install google-nucleus error HOT 14
- PythonNext() argument read is not valid HOT 2
- PythonNext() argument read is not valid: Dynamic cast failed
- Complex version of error correction example?
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