bioinfomaticsCSU / deepsignal

Detecting methylation using signal-level features from Nanopore sequencing reads
GNU General Public License v3.0
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Don't import tensorflow when extracting features #29

Closed snajder-r closed 4 years ago

snajder-r commented 4 years ago

Hi!

This would just be a small quality-of-life improvement. Currently, deepsignal.py imports train_model and call_mods even when I am actually calling extract. train_model and call_mods then want to import tensorflow, and tensorflow depends on libcuda, none of which is required by the feature extraction command.

This can be a bit problematic in a compute cluster environment where you have dedicated GPU nodes (which have libcuda) and non-GPU nodes (which don't have libcuda). It forces me to run the feature extraction on a GPU node, despite it not using a GPU, thus reserving a valuable resource I'm not actually using.

Thanks a lot!

PengNi commented 4 years ago

Hi @snajder-r , this is truly a problem. please checkout the latest version of deepsignal after commit 0973161, see if it works.

Best, Peng