haotianteng / Chiron

A basecaller for Oxford Nanopore Technologies' sequencers
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Tensorflow version #14

Closed marchoeppner closed 6 years ago

marchoeppner commented 6 years ago

Hi, been trying to install Chiron, unsuccessfully. I tried both the git and the pip installation routine, both failed on the tensorflow requirement. We have a cluster-wide installation for python 2.7.10 as well as 2.7.14 - in both cases, tensorflow=1.0.1 could not be found via pip.

pip search tensorflow: tensorflow (1.6.0rc0)

And that breaks the installation.



Collecting chiron

  Using cached chiron-0.3.tar.gz

Collecting tensorflow==1.0.1 (from chiron)

  Could not find a version that satisfies the requirement tensorflow==1.0.1 (from chiron) (from versions: )

No matching distribution found for tensorflow==1.0.1 (from chiron)```
haotianteng commented 6 years ago

If pip install tensorflow==1.0.1 does not work, you can muanually install tensorflow 1.0.1 here https://pypi.python.org/pypi/tensorflow/1.0.1

昊天滕 havens.teng@gmail.com于2018年2月7日 周三23:45写道:

marchoeppner notifications@github.com于2018年2月7日 周三21:47写道:

Hi, been trying to install Chiron, unsuccessfully. I tried both the git and the pip installation routine, both failed on the tensorflow requirement. We have a cluster-wide installation for python 2.7.10 as well as 2.7.14 - in both cases, tensorflow=1.0.1 could not be find via pip.

pip search tensorflow: tensorflow (1.6.0rc0)

And that breaks the installation.

pip install chiron Collecting chiron Using cached chiron-0.3.tar.gz Collecting tensorflow==1.0.1 (from chiron) Could not find a version that satisfies the requirement tensorflow==1.0.1 (from chiron) (from versions: ) No matching distribution found for tensorflow==1.0.1 (from chiron)

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mbhall88 commented 6 years ago

Hi @marchoeppner . I don't seem to be able to reproduce the error. That version of tensorflow does not have Python3 support so could you check which version of pip your cluster is using? Is it maybe pointing at pip3 or something like that hence why it can't see it. Or potentially upgrade pip?

haotianteng commented 6 years ago

One way is to train a new model under Version 1.4. As the graphdef and checkpoint are not compatible between Ten sorflow 1.4.0 and 1.0.1. https://www.tensorflow.org/programmers_guide/version_compat

haotianteng commented 6 years ago

Tensorflow r1.4 - r1.6 is supported.