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xuxif / DeepMEI

A CNN model to identify MEIs in WGS
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Don't find environment.yaml #5

Closed knakamura6222053 closed 4 months ago

knakamura6222053 commented 4 months ago

The error occurs because environment.yaml is missing. How can I solve this? The same thing happened with docker.

xuxif commented 4 months ago

Could you please send me the error message? The current version of DeepMEI doesn't seem to require an environment.yaml file. The Conda version can install all dependencies with conda install deepmei, and the Docker version has resolved all dependencies. I'm wondering if you need a separate environment.yaml file or a configuration file for docker build.

Additionally, a new version of DeepMEI is coming soon. I recommend pulling the code again later.

knakamura6222053 commented 4 months ago

Thanks developers!

I get error message

############################################################################################ conda install deepmei

Channels:

PackagesNotFoundError: The following packages are not available from current channels:

Current channels:

To search for alternate channels that may provide the conda package you're looking for, navigate to

https://anaconda.org

and use the search bar at the top of the page.

############################################################################################

I look forward to the updated version because I would like to use DeepMEI to analyze the genome of mitochondrial diseases.

xuxif commented 4 months ago

I recommend resolving the dependencies for DeepMEI using the deepmei.yml file, which can be downloaded from the DeepMEI GitHub page. You can create the environment with the command conda env create -f deepmei.yml. After that, clone the DeepMEI code from GitHub. The code has been updated, so you can try the latest version.

Based on my experience with analyzing the 1000 Genomes Project data, mobile element insertions (MEI) in mitochondrial DNA seem to be very rare. You might need to use multiple tools to analyze your sample effectively.