search

apcamargo / RNAsamba

A tool for computing the coding potential of RNA transcript sequences using deep learning classification model
https://rnasamba.lge.ibi.unicamp.br/
GNU General Public License v3.0
52 stars 3 forks source link

Incompatibility with tensorflow version in rnasamba (1,5-2) and keras (2.2<) #11

Closed lucianofrancoo closed 3 years ago

lucianofrancoo commented 3 years ago

Hello, im trying to use RNAsamba but i have a few issues. Im ussing ubuntu 20.10 (groovy) where the default version of python is 3.8 and tensorflow is 2.3. So i proced to install RNAsamba but it throws me the following error : Screenshot from 2021-03-13 14-16-31 So i tried to downgrade the version of my tensorflow but: Screenshot from 2021-03-13 14-17-14 Screenshot from 2021-03-13 14-17-36 So i created a environment with python 3.5 and: Screenshot from 2021-03-13 14-21-41 then i found out that biopython version 1.76 supports python 3.5 and installed it and finally was able to install RNAsamba. I tried to execute and: Screenshot from 2021-03-13 14-26-48 So i forced the upgrade of tensorflow to v 2.2 with pip install tensorflow==2.2 and in the end gives me this error and when i tried to execute RNAsamba it cant execute because it need tensorflow v 1.5-2: Screenshot from 2021-03-13 14-36-09 After this is a chain of errors in a circle given the incompatibility between the version of tensorflow that keras occupies and RNAsamba . Any help on this error is welcome :(

apcamargo commented 3 years ago

Hi @lucianofrancoo

So, the problem is that RNAsamba does not support TensorFlow 2.0 yet, so forcing 2.2 won't solve. Are you using conda to create the environments? If so, create a Python 3.6 environment and install RNAsamba using this command:

conda install -c conda-forge -c bioconda rnasamba

Let me know if that solves your problem.

lucianofrancoo commented 3 years ago

Brrrpp thats work. With an environment in python 3.6. Thx for the help! have a nice day

apcamargo commented 3 years ago

You're welcome!