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lvrcek / NeuralLayout

A GNN model that executes simplification algorithms used in the layout phase of de novo genome assembly process.
MIT License
10 stars 3 forks source link

Raven needs to be installed #2

Closed Tina9 closed 2 years ago

Tina9 commented 2 years ago

Hello,

I am trying to test this model on some other reads in FASTQ format. However, when I run the command, there is an error.

Screenshot 2022-04-18 at 4 58 21 PM

Then I went to ./vendor/raven/build, and found

Screenshot 2022-04-18 at 5 07 24 PM

Hence, we need to install Raven first, right?

Thanks for your help at first.

lvrcek commented 2 years ago

Hi,

Yes, if you want to use Raven, you should also download and install Raven. You can find the instructions below.

First download the code:

git clone --recursive https://github.com/lvrcek/NeuralLayout.git
cd NeuralLayout

Create the virtual environment:

python -m venv env
source env/bin/activate

Install the requirements:

pip install -r requirements.txt

If you want to use Raven for creating the graphs from raw genomic reads in FASTQ format, run the following script. If not, you can skip this part.

source setup.sh

If you did all this, did you maybe forget to put --recursive for git clone while downloading the repo? This might be the reason that the Raven is not installed.

Tina9 commented 2 years ago

Got it. Thanks for your reply.

lvrcek commented 2 years ago

Let me know if you encounter some further issues.