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YttriLab / B-SOID

Behavioral segmentation of open field in DeepLabCut, or B-SOID ("B-side"), is a pipeline that pairs unsupervised pattern recognition with supervised classification to achieve fast predictions of behaviors that are not predefined by users.
GNU General Public License v3.0
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v2 on linux #19

Open shinhs0506 opened 3 years ago

shinhs0506 commented 3 years ago

Is version 2 compatible with Ubuntu 18.04? I have failed to create the environment with given requirements.yaml file

runninghsus commented 3 years ago

hi @shinhs0506

I'll create one for linux. Haven't had the chance to yet. Will keep you posted, just wanted to let you know I saw this.

shinhs0506 commented 3 years ago

@runninghsus fantastic! Thanks a lot!

christinalim commented 3 years ago

@runninghsus Hi, was just wondering if there is an updated requirements.yaml for linux? Or some way to work around one of the other requirements.yaml files?

s-ewbank commented 3 years ago

Hi, I was also wondering if there is a Linux requirements file available. Thanks!

rlabuguen commented 3 years ago

Hello, wonderful, putting up this issue. I am also having difficulty resolving the packages for ubuntu. Thanks!

runninghsus commented 3 years ago

hi all,

Linux UMAP function clusters differently, I will have to run some benchmarking to make sure that it still pulls out similar time-series groups.

Keeping this open until I release the requirements for linux.

laurelrr commented 2 years ago

Our lab is also very interested in running this on Linux. Please let us know when you have something! Thanks!

jglanzberg commented 2 years ago

Any update regarding the Linux requirements?

emdbell17 commented 2 years ago

Our lab would also love to use this on Linux!

Kim-EunKyeoung commented 1 year ago

Our lab also really want to run this on Linux! :) I'm waiting... And it was able to be installed using requirement_m2.yaml (modify libgfortan == 5.0.0 to libgfortran)

samarth-wustl commented 1 year ago

Hi! I can create the environment using the requirements file. However I can't seem to run it since I don't know the linux terminal instructions. Does anyone have the commands or is there a doc I could reference?

Kim-EunKyeoung commented 1 year ago

Hi! I can create the environment using the requirements file. However I can't seem to run it since I don't know the linux terminal instructions. Does anyone have the commands or is there a doc I could reference?

I wanna share an environment.ymal file that i using in linux with you. but github comment not support .ymal file upload.

If you give me a mail (kek3731@gmail.com), i'll send you environment file. And i recommend to install using anaconda.

conda install command example : conda env create --file environment.yaml

samarth-wustl commented 1 year ago

Hi Kim! Thanks for the response! I was able to run the environment file, but as you said I need terminal instructions to run BSOiD on a Ubuntu machine!

Kim-EunKyeoung commented 1 year ago

Hi Kim! Thanks for the response! I was able to run the environment file, but as you said I need terminal instructions to run BSOiD on a Ubuntu machine!

You already installed the virtual environment, but you don't know how to run the app, right? I hope this capture helps. streamlit run bsoid_app.py

b-soid run

samarth-wustl commented 1 year ago

This is awesome! Thanks a lot

kamdh commented 1 year ago

FYI I was able to get it working on linux by making sure my conda was up to date and using a slightly tweaked version of requirements_m2.yaml where I commented out the version of the libgfortran package. I haven't tested all functionality yet, but the main interface loads.